Skip to main content
NCBI home page
Data in Brief logoLink to Data in Brief
. 2020 Jan 7;28:105076. doi: 10.1016/j.dib.2019.105076

The oxygen-oxygen distance of water in crystallographic data sets

Luigi Leonardo Palese 1
PMCID: PMC6965711  PMID: 31970272

Abstract

Water is a key component of cellular biochemistry and numerous water molecules are visible in crystallographic structures. Here we report a series of data sets of crystallographic water: a high resolution data set, a cytochrome c oxidase (subunit I) data set and a carbonic anhydrase data set. These data support the evidence that short distance water molecule pairs are present both at the surface and inside the cavities of proteins. These data are related to article entitled “Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters” (Palese, 2020) [1].

Keywords: Water, Proton, X-ray crystallography, Water cluster, Confined water, Protein surface

Specifications Table

Subject Biochemistry
Specific subject area Biochemistry, biophysics, structural biology, bioenergetics.
Type of data Table
Figure
Graph
Text files
How data were acquired Survey of the protein crystal structures obtained by X-ray diffraction deposited in the Protein Data Bank (PDB). Input data for analysis were obtained as pdb, cif or ccp4 files from public databases.
Data format Raw: pdb files, ccp4 files, cif files and text files.
Analyzed: table, csv files, text file, graph, figure.
Parameters for data collection Raw pdb files were checked for quality (resolution). Atoms in cif files were compared with the electron density maps in ccp4 files.
Description of data collection Raw data were analyzed by different computational protocols.
Data source location Department of Basic Medical Sciences, Neurosciences and Sense Organs (SMBNOS), Bari 70124, Italy.
Data accessibility All the data produced in this work are available within the article.
Related research article Luigi Leonardo Palese, Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters, Biochemical et Biophysical Acta - General Subjects, https://doi.org/10.1016/j.bbagen.2019.129480.
Open in a new tab
Value of the Data
  • •

    X-ray crystallography has shown that proteins contain numerous water molecules

  • •

    The role of these protein-bound water molecules is still not fully understood

  • •

    Water molecules in large data sets of high resolution structures are reported

  • •

    Positions of candidate protonated water clusters in some model proteins are reported

Open in a new tab

1. Data

Fig. 1 reports the atomic radial pair distribution function (RDF) in the region between 2.15 and 2.85 Å of the high resolution (HR) data set and of the HR subset not refined by SHELX (see Ref. [1]).

Fig. 1.

Fig. 1

Open in a new tab

The RDF of the protein-bound water oxygen atoms. Left panel reports the HR data set (see Table 1); right panel reports the HR data set not refined by SHELX (see Table 2). See Ref. [1] for details. Red crosses refer to the experimental RDF; colored curves indicated with dashed lines are the Gaussian curves used for the fitting, and their sum is reported as a thin red line.

Fig. 2 reports the RDF for the water oxygen atoms in the sodium free HR data set [1].

Fig. 2.

Fig. 2

Open in a new tab

The RDF of the water oxygen atoms in the sodium free HR data set (see Table 3) described in Ref. [1].

Fig. 3 shows the RDF of the water oxygen atoms in the sodium free and not refined by SHELX subset described in Ref. [1] (see also Table 4 below).

Fig. 3.

Fig. 3

Open in a new tab

The RDF of the water oxygen atoms in the sodium free, not refined by SHELX subset (see Table 4) described in Ref. [1].

Table 4.

The sodium free, no-SHELX HR data set.

1R2M 1SY2 1SY3 1UG6 1V0L 1W0N 2AT3 2AT8 2AYW 2CNQ 2GG2 2GGC 2H3L
2OFR 2XFR 2XU3 2Z6W 3A02 3A4R 3AKQ 3C78 3E4G 3FSA 3I2Y 3I30 3I34
3I37 3JUD 3NED 3NIR 3O5Q 3PUC 3QL9 3QPA 3QPC 3UI4 3UI6 3V1A 3VIF
3VIG 3VII 3WCQ 3WGE 3WGX 3WVM 3X2G 3X2M 3ZR8 3ZUC 4ACJ 4AQO 4BCT
4BJ0 4DRQ 4E3Y 4F18 4G9S 4GA2 4GCA 4GNR 4IGS 4J5E 4LAU 4LAZ 4LB3
4LB4 4LBR 4LBS 4M7G 4O6U 4PRT 4Q9W 4QB3 4QBX 4QXI 4RTZ 4TJZ 4TKB
4TKH 4TKJ 4XZH 4Y9W 4YXI 4Z8J 4ZC9 4ZM7 5A8C 5B28 5B5H 5DGJ 5DJ7
5DK1 5DP2 5E9N 5EMB 5F82 5FLK 5HB7 5IVN 5JDK 5JIG 5KWM 5MAE 5MAJ
5MEH 5MN1 5MNC 5MNG 5MNK 5MNN 5NFK 5NFM 5O2X 5O99 5OTN 5OU0 5OUJ
5OUK 5TDA 5TIF 5XBU 5XP6 5YCE 5ZGE 5ZGY 5ZGZ 5ZIO 5ZJ1 5ZJ7 5ZJ8
5ZJC 6B00 6FMC 6G1I 6MU9 6NFR 6Q2Y
Open in a new tab

Fig. 4 shows the scatter plot of the RDFs relative to the no SHELX subset and the sodium free, no SHELX subset [1]. The Figure reports also the line of best fit, whose equation is y = 1.0191x - 0.0001 (R2 = 0.9966).

Fig. 4.

Fig. 4

Open in a new tab

Scatter plot of the RDFs relative to the no SHELX subset (horizontal axis) and the sodium free, no SHELX subset (vertical axis) described in Ref. [1]. Solid black line is the best fit.

Fig. 5 reports the number of water molecules in cytochrome c oxidase (CcO) subunit I vs the structure resolution. Data have been obtained from the PDB entries 5B1A, 5B1B, 5B3S, 5XDQ, 5ZCP and 5ZCQ (diffraction temperature 50 K; resolution 1.5 Å, 1.6 Å, 1.68 Å, 1.77 Å, 1.65 Å, 1.65 Å, respectively) and 1V54, 2DYR, 3AG2 and 3AG3 (diffraction temperature 100 K; all these structures have a resolution of 1.8 Å). Both subunits of the same type have been considered, labeled as A and N in the original pdb file.

Fig. 5.

Fig. 5

Open in a new tab

Number of crystallographic water molecules in CcO subunit I structures as a function of the resolution of the relative PDB entry. Structures diffracted at 100 K and 50 K have been considered for this analysis.

Fig. 6, Fig. 7 report the Euclidean distance distribution of oxygen-oxygen (O–O) pairs for the data set of CcO structures obtained at 50 K and 100 K, respectively. Two major peaks are present in both distributions, centered at 2.73 and 2.88 Å.

Fig. 6.

Fig. 6

Open in a new tab

Distribution of the Euclidean oxygen-oxygen (O–O) distances of water molecules in the CcO subunit I data set. Data are obtained from the 50 K structures. Only water pairs with O–O distances <5 Å are reported.

Fig. 7.

Fig. 7

Open in a new tab

Distribution of the Euclidean oxygen-oxygen (O–O) distances of water molecules in the CcO subunit I data set. Data are obtained from the 100 K structures. Only water pairs with O–O distances <5 Å are reported.

Table 1 reports the pdb codes for the entries of the HR data set [1], containing 469 elements.

Table 1.

The HR data set.

1A6M 1B0Y 1BXO 1C75 1DY5 1EA7 1EB6 1EXR 1F94 1FN8 1FY4 1FY5 1G4I
1G6X 1GA6 1GCI 1GDN 1GDQ 1GQV 1GVK 1HJ8 1I1W 1IQZ 1IR0 1IUA 1J0P
1JFB 1K2A 1K6U 1KWF 1L9L 1LNI 1LUG 1M1Q 1M40 1 MC2 1MJ5 1MN8 1MUW
1MXT 1N1P 1N4U 1N4V 1N4W 1N9B 1NQJ 1OAI 1OD3 1OEW 1OK0 1PQ5 1PQ7
1PQ8 1PWM 1R2M 1R6J 1RTQ 1SSX 1SY2 1SY3 1T2H 1TG0 1TQG 1TT8 1UG6
1UNQ 1US0 1V0L 1VB0 1VBW 1VL9 1VYR 1W0N 1X8P 1XMK 1XVO 1YK4 1YLJ
1YWA 1YWB 1YWC 1Z8A 1ZLB 1ZUU 1ZZK 2A6Z 2ABB 2AGT 2AT3 2AT8 2AYW
2B97 2BF6 2CE2 2CNQ 2CWS 2DDX 2E4T 2EWI 2EWK 2FDN 2FLA 2FMA 2FOU
2FVY 2GBA 2GEW 2GG2 2GGC 2GKG 2H3L 2H5C 2H5D 2I4A 2IDQ 2IDS 2IDT
2IDU 2IXT 2JFR 2JJJ 2NLS 2NRL 2NX0 2O7A 2O9S 2OFR 2OV0 2P5K 2P74
2PEV 2PF8 2PFH 2PND 2PNE 2PVB 2PVE 2PYA 2PZN 2QCP 2QDV 2QDW 2QSK
2RBK 2V1M 2V8B 2VB1 2VHK 2VHR 2VI3 2VK5 2VU6 2WFI 2WFJ 2WUR 2X46
2XFR 2XJP 2XOD 2XU3 2Z6W 2ZPM 2ZQ7 2ZQA 3A02 3A4R 3AJ4 3AKQ 3AKS
3AKT 3B3R 3BOI 3C78 3CNJ 3D1P 3D43 3DHA 3E4G 3E6Z 3EA6 3FSA 3FYM
3G9X 3GHR 3GHS 3GOE 3GYI 3GYJ 3H31 3HGP 3I2Y 3I30 3I34 3I37 3IP0
3JUD 3K34 3KFF 3KLR 3KS3 3LEP 3LL1 3LL2 3LZ5 3M4H 3MFJ 3 MI4 3NE0
3NED 3NIR 3O5P 3O5Q 3ODV 3P8J 3PUC 3QL9 3QM5 3QM6 3QM8 3QM9 3QMA
3QPA 3QPC 3S6E 3SOJ 3TEU 3TRV 3U2C 3U7C 3UI4 3UI6 3V1A 3VHG 3VIF
3VIG 3VII 3VJQ 3VN3 3VOR 3WCQ 3WGE 3WGX 3WL2 3WOU 3WVM 3X2G 3X2M
3X32 3X33 3X34 3X35 3ZR8 3ZSJ 3ZSK 3ZUC 3ZZP 4A02 4ACJ 4AQO 4AWS
4AWT 4BCT 4BJ0 4BM8 4BVM 4DP9 4DPB 4DRQ 4E3Y 4EIC 4EKF 4F18 4FPT
4FRC 4FU5 4G78 4G9S 4GA2 4GCA 4GNR 4HGU 4HVU 4HVW 4I8G 4I8H 4I8J
4I8K 4I8L 4IAU 4IGS 4J5E 4JP6 4K8Y 4KQP 4LAU 4LAZ 4LB3 4LB4 4LBR
4LBS 4LFS 4M7G 4MTY 4MZC 4N1I 4NPD 4O6Q 4O6U 4O8H 4OO4 4PRT 4PSS
4PSY 4PTH 4Q4G 4Q78 4Q9W 4QB3 4QBX 4QXI 4R5R 4REK 4RTZ 4TJZ 4TKB
4TKH 4TKJ 4UA6 4UA7 4UA9 4UAA 4UYR 4WJX 4WKA 4WPK 4X5P 4X6H 4XDX
4XOJ 4XZH 4Y5L 4Y9W 4YXI 4Z8J 4ZC9 4ZGF 4ZM7 5A8C 5AVD 5AVG 5B28
5B5H 5CMT 5CTM 5D66 5DGJ 5DJ7 5DK1 5DKM 5DP2 5DZE 5E1K 5E1N 5E9N
5EMB 5F82 5FLK 5HB7 5I5B 5IG6 5II8 5IQN 5IVN 5JDK 5JDT 5JIG 5JUG
5KWM 5KXV 5LJT 5LP9 5LXW 5MAE 5MAJ 5MB5 5MEH 5MK9 5MN1 5MNC 5MNG
5MNK 5MNN 5MTU 5NFK 5NFM 5NW3 5O2X 5O99 5OAV 5OBK 5OGO 5OME 5OTN
5OU0 5OUJ 5OUK 5SV5 5TDA 5TIF 5U3A 5VLE 5WS7 5X9L 5X9M 5XBU 5XP6
5XQU 5XQV 5XR0 5Y2R 5Y2S 5YCE 5ZGE 5ZGI 5ZGW 5ZGX 5ZGY 5ZGZ 5ZIO
5ZJ1 5ZJ7 5ZJ8 5ZJC 6B00 6CNW 6EQE 6ETK 6ETM 6EUW 6F1O 6F7R 6F81
6FMC 6FO5 6FVI 6G1I 6HMD 6HMQ 6I74 6J93 6JJ1 6JJQ 6MU9 6NFR 6Q2Y
6Q49 6Q4G 6Q4H 6Q6T 6RGP 6RHH 6RHU 6RHX 6RI0 6RI6 6RI8 6RII 7A3H
8A3H
Open in a new tab

Table 2 reports the pdb codes of the subset of the HR data set containing structures not refined by SHELX (the no-SHELX HR data set discussed in Ref. [1]).

Table 2.

The no-SHELX HR data set.

1EB6 1OAI 1OD3 1R2M 1SY2 1SY3 1T2H 1UG6 1V0L 1W0N 1ZUU 2ABB 2AT3
2AT8 2AYW 2CE2 2CNQ 2DDX 2GG2 2GGC 2H3L 2I4A 2IXT 2NLS 2NRL 2NX0
2OFR 2P5K 2PND 2PNE 2QCP 2V1M 2VHK 2VHR 2VI3 2VU6 2XFR 2XU3 2Z6W
2ZQ7 2ZQA 3A02 3A4R 3AJ4 3AKQ 3AKS 3AKT 3BOI 3C78 3E4G 3E6Z 3FSA
3I2Y 3I30 3I34 3I37 3IP0 3JUD 3LL1 3LL2 3NED 3NIR 3O5Q 3P8J 3PUC
3QL9 3QM5 3QM6 3QM8 3QM9 3QMA 3QPA 3QPC 3TEU 3UI4 3UI6 3V1A 3VIF
3VIG 3VII 3VN3 3WCQ 3WGE 3WGX 3WL2 3WVM 3X2G 3X2M 3ZR8 3ZUC 4ACJ
4AQO 4BCT 4BJ0 4BVM 4DP9 4DPB 4DRQ 4E3Y 4F18 4G9S 4GA2 4GCA 4GNR
4HVU 4HVW 4IGS 4J5E 4K8Y 4KQP 4LAU 4LAZ 4LB3 4LB4 4LBR 4LBS 4M7G
4MTY 4MZC 4O6Q 4O6U 4O8H 4OO4 4PRT 4Q4G 4Q78 4Q9W 4QB3 4QBX 4QXI
4R5R 4REK 4RTZ 4TJZ 4TKB 4TKH 4TKJ 4WJX 4WKA 4WPK 4X5P 4X6H 4XDX
4XOJ 4XZH 4Y5L 4Y9W 4YXI 4Z8J 4ZC9 4ZM7 5A8C 5AVD 5AVG 5B28 5B5H
5CMT 5CTM 5DGJ 5DJ7 5DK1 5DKM 5DP2 5DZE 5E1N 5E9N 5EMB 5F82 5FLK
5HB7 5I5B 5IG6 5II8 5IQN 5IVN 5JDK 5JDT 5JIG 5JUG 5KWM 5KXV 5LJT
5LP9 5LXW 5MAE 5MAJ 5MB5 5MEH 5MN1 5MNC 5MNG 5MNK 5MNN 5NFK 5NFM
5NW3 5O2X 5O99 5OAV 5OBK 5OGO 5OME 5OTN 5OU0 5OUJ 5OUK 5SV5 5TDA
5TIF 5U3A 5WS7 5XBU 5XP6 5XQU 5XQV 5XR0 5Y2R 5Y2S 5YCE 5ZGE 5ZGI
5ZGW 5ZGX 5ZGY 5ZGZ 5ZIO 5ZJ1 5ZJ7 5ZJ8 5ZJC 6B00 6CNW 6EQE 6EUW
6F1O 6FMC 6FO5 6FVI 6G1I 6HMD 6HMQ 6I74 6J93 6JJ1 6JJQ 6MU9 6NFR
6Q2Y 6Q49 6Q4G 6Q4H 6Q6T 6RGP 6RHH 6RHU 6RHX 6RI0 6RI6 6RI8 6RII
7A3H 8A3H
Open in a new tab

Table 3 reports the pdb codes of the subset of the HR data set containing structures in which no sodium is declared in the crystallization methods (the sodium free HR data set discussed in Ref. [1]).

Table 3.

The sodium free HR data set.

1B0Y 1DY5 1EA7 1F94 1G4I 1I1W 1IQZ 1IR0 1J0P 1JFB 1K6U 1LNI 1LUG
1M1Q 1 MC2 1MJ5 1MUW 1N1P 1N4W 1N9B 1PWM 1R2M 1R6J 1SSX 1SY2 1SY3
1TG0 1TT8 1UG6 1V0L 1VB0 1VL9 1W0N 1X8P 1XMK 1YWA 1YWB 1YWC 1Z8A
1ZZK 2A6Z 2AGT 2AT3 2AT8 2AYW 2BF6 2CNQ 2EWI 2EWK 2FDN 2FMA 2FOU
2FVY 2GEW 2GG2 2GGC 2H3L 2H5C 2H5D 2JFR 2O9S 2OFR 2P74 2PEV 2PF8
2PFH 2PVE 2PZN 2WFI 2WFJ 2WUR 2XFR 2XU3 2Z6W 2ZPM 3A02 3A4R 3AKQ
3C78 3D1P 3D43 3DHA 3E4G 3EA6 3FSA 3FYM 3GHR 3GHS 3GOE 3I2Y 3I30
3I34 3I37 3JUD 3K34 3KFF 3LEP 3LZ5 3M4H 3NED 3NIR 3O5P 3O5Q 3PUC
3QL9 3QPA 3QPC 3SOJ 3TRV 3U2C 3U7C 3UI4 3UI6 3V1A 3VHG 3VIF 3VIG
3VII 3VJQ 3VOR 3WCQ 3WGE 3WGX 3WOU 3WVM 3X2G 3X2M 3ZR8 3ZUC 3ZZP
4ACJ 4AQO 4AWS 4AWT 4BCT 4BJ0 4DRQ 4E3Y 4EIC 4F18 4FU5 4G78 4G9S
4GA2 4GCA 4GNR 4IAU 4IGS 4J5E 4JP6 4LAU 4LAZ 4LB3 4LB4 4LBR 4LBS
4M7G 4O6U 4PRT 4PSS 4PSY 4PTH 4Q9W 4QB3 4QBX 4QXI 4RTZ 4TJZ 4TKB
4TKH 4TKJ 4UA6 4UA7 4UA9 4UAA 4XZH 4Y9W 4YXI 4Z8J 4ZC9 4ZGF 4ZM7
5A8C 5B28 5B5H 5DGJ 5DJ7 5DK1 5DP2 5E9N 5EMB 5F82 5FLK 5HB7 5IVN
5JDK 5JIG 5KWM 5MAE 5MAJ 5MEH 5MN1 5MNC 5MNG 5MNK 5MNN 5NFK 5NFM
5O2X 5O99 5OTN 5OU0 5OUJ 5OUK 5TDA 5TIF 5VLE 5XBU 5XP6 5YCE 5ZGE
5ZGY 5ZGZ 5ZIO 5ZJ1 5ZJ7 5ZJ8 5ZJC 6B00 6F7R 6F81 6FMC 6G1I 6MU9
6NFR 6Q2Y
Open in a new tab

Table 4 reports the subset of the HR data set containing structures not refined by SHELX and in which the use of sodium in the crystallization conditions is not reported.

Table 5 reports the statistics of water pairs analyzed in human carbonic anhydrase II (hCA II), as detailed in Ref. [1].

Table 5.

The number of water molecules in each considered hCA II is reported (#H2O). The table reports also the number of calculated oxygen-oxygen Euclidean distances (# O–O) and the number of oxygen-oxygen pairs considered as putative, charged (protonated or deprotonated), water clusters as defined in Ref. [1] (# OHO).

4MTY 4Q78 4YXI 5LJT 5OGO 5Y2R 5Y2S 6B00
# H2O 398 214 264 439 333 441 429 409
# O–O 79003 22791 34716 96141 55278 97020 91806 83436
# OHO 3 3 1 1 9 12 17 10
Open in a new tab

Table 6 reports the statistics of water pairs analyzed in subunit I of bovine CcO, as detailed in Ref. [1].

Table 6.

The number of water molecules in each considered CcO subunit I is reported (#H2O). The table reports also the number of calculated oxygen-oxygen Euclidean distances (# O–O) and the number of oxygen-oxygen pairs considered as putative, charged (protonated or deprotonated), water clusters as defined in Ref. [1] (# OHO).

5B1A_A 5B1A_N 5B1B_A 5B1B_N 5B3S_A 5B3S_N 5XDQ_A 5XDQ_N 5ZCP_A 5ZCP_N 5ZCQ_A 5ZCQ_N
# H2O 297 290 289 286 273 278 257 267 235 203 228 215
# O–O 43956 41905 41616 40755 37128 38503 32896 35511 27495 20503 25878 23005
# OHO 3 1 3 2 9 5 1 1 3 3 4 2
Open in a new tab

Table 7 contains the pseudo-code for the RDF calculations (see the Experimental Design, Materials, and Methods section).

Table 7.

The RDF pseudo-code.

set num_mol [molinfo num]
for {set i 0} {$i < $num_mol} {incr i} {
set name_prot [molinfo $i get name]
set sel [atomselect $i “water"]
set gr [measure gofr $sel $sel]
set outfile [open gofr_$name_prot.dat w]
set r [lindex $gr 0]
set gr1 [lindex $gr 1]
set igr [lindex $gr 2]
foreach j $r k $gr1 l $igr {
puts $outfile "$j $k $l"
}
close $outfile
}
Open in a new tab

In the water_pairs.csv file in Supplementary data all the short distance water molecules (SDWMs) in the model proteins discussed in Ref. [1] are listed. These are pairs of water molecules whose O–O distance is in the range 2.29 Å - 2.50 Å, confirmed by inspection of the electron density maps at 1.0 and 4.0 sigma as described in Ref. [1]. Columns in this csv file are: the PDB id of the molecule, the residue number in the original pdb file of the two water molecules in the pair (two columns), and the O–O distance in this water pair obtained from the pdb coordinates. Water molecules in Fig. 2, Fig. 4 in Ref. [1] are listed in this file.

In the Supplementary file raw_data.zip there are the raw data used in this work. The files contained in this zipped archive are: raw_data.txt, raw_RDF.csv, raw_RDF_CcO.csv, water_resolution.csv, 50K_distance.txt, 100K_distance.txt, which are described in detail below.

The file raw_data.txt lists the URLs for all the *.pdb, *.cif and *.ccp4 files considered in this work.

The file raw_RDF.csv contains all the raw RDF data used for calculating the plots shown in Fig. 1, Fig. 2, Fig. 3, Fig. 4; these data were also used for the calculation of Fig. 1 in Ref. [1]. Each row corresponds to a crystallographic structure (PDB codes are in the first column).

The file raw_RDF_CcO.csv contains all the raw RDF data used for calculating the plot reported as Fig. 3 in Ref. [1]. Each row corresponds to a subunit I structure (A and N subunits in the PDB entries reported in the first column).

The file water_resolution.csv contains the number of water molecules in the CcO data set; these are the raw data for Fig. 5.

The file 50K_distance.txt reports all the Euclidean O–O distances of crystallografic water molecules in subunits I of CcO structures obtained by X-ray diffraction at 50 K (A and N subunits in the PDB entries 5B1A, 5B1B, 5B3S, 5XDQ, 5ZCP and 5ZCQ). Distances <5 Å, but above the reported experimental resolution in the relative PDB record, were considered. These are the raw data used to calculate the distribution shown in Fig. 6.

The file 100K_distance.txt reports all the Euclidean O–O distances of crystallografic water molecules in subunits I of CcO structures obtained by X-ray diffraction at 100 K (A and N subunits in the PDB entries 1V54, 2DYR, 3AG2 and 3AG3). Distances <5 Å, but above the reported experimental resolution in the relative PDB record, were considered. These are the raw data used to calculate the distribution shown in Fig. 7.

2. Experimental Design, materials, and methods

The X-ray structures were obtained from the Protein Data Bank (PDB) [2] (Table 1, Table 2, Table 3, Table 4; direct URLs to these data are in the raw_data.txt file in the Supplementary data). The HR data set was obtained by searching in the PDB for structures corresponding to the following constraints: resolution ≤1 Å; X-ray only; protein only; monomer only. After this, we considered only structures whose diffraction pattern was obtained at 100 K. Some entries have been discarded at the radial distribution function (RDF) calculation stage (typically small structures with few water molecules that give anomalous RDF). After these steps, the HR data set contained 469 entries. Two subset have been obtained from the HR data set by adding additional constraints: (a) the absence of sodium in all buffer and solution declared in the deposited methods (the sodium free HR data set), or (b) the absence of the SHELX program in the software reported in the deposited refinement methods (the no SHELX HR data set). The entries in this last data set reported as hCA II are those considered as models for this enzyme (see Ref. [1]). From the HR data set, a further subset has been obtained, containing only entries obtained in absence of sodium in the crystallization protocol and not refined by SHELX.

For the bovine CcO data set, only structures with a resolution of at least 1.8 Å were considered for analysis. The high resolution data set of CcO contained the PDB entries (see Ref. [1]): 5B1A (fully oxidized state, pH 6.8), 5B1B (fully reduced state, pH 6.8), 5B3S (carbon monoxide-bound mixed-valence, pH 6.8), 5XDQ (fully oxidized state, pH 7.3), 5ZCP and 5ZCQ (azide-bound states obtained by long time exposure to 20 mM or 10 mM azide solutions, respectively, pH 6.8). All these structures, obtained at 50 K, are characterized by a resolution between 1.65 and 1.50 Å (5XDQ has been considered here, even if its resolution is 1.77 Å, because it is the structure characterized by the higher resolution at alkaline pH). We have also considered a data set of structures obtained at 100 K, with a resolution of 1.8 Å: 1V54, 2DYR, 3AG2 and 3AG3, which are respectively fully oxidized, fully reduced, carbon monoxide-bound fully reduced and nitric oxide-bound fully reduced species, all at pH 6.8 [[3], [4], [5]].

The data sets containing a single type of protein were analyzed in detail as specified below. From the pdb files, the atomic coordinates of all atoms belonging to the subunit of interest were used to make a new pdb file (consider that bovine CcO is in dimeric form in crystals, and the type I subunits are labeled as A and N in the files retrieved from the PDB). Sequence and structural analyses have been performed as described previously [1,[6], [7], [8]]. The mutual Euclidean distance between all the oxygen atoms of the water molecules contained into the protein, at the protein surface or near lipids [9] was calculated by means of a Tcl program in a VMD environment [10]. The RDF for each pdb file has been calculated in VMD using a code similar to that reported in Table 7, and further analyzed in a Jupyter environment (see below). Electron density maps at 1.0 and 4.0 sigma of the model proteins discussed in Ref. [1] were obtained using the *.cif and *.ccp4 files in Jmol (http://www.jmol.org/). The URLs for these files are reported in the raw_data.txt file in the Supplementary data where * is the PDB code of the protein of interest (4mty, 4q78, 4yxi, 5ljt, 5ogo, 5y2r, 5y2s, 6b00, 5b1a, 5b1b, 5b3s, 5xdq, 5zcp, 5zcq).

The mean displacement of atoms U was calculated considering that the B-factor is given by B = 8π2U2.

Numerical calculations were implemented in Python (www.python.org) in an IPython/Jupyter environment, using the NumPy numerical software library, the Scipy and the Matplotlib packages [[11], [12], [13], [14]]. Final editing of images was performed by means of the GNU Image Manipulation Program (The GIMP team, GIMP 2.8.10, www.gimp.org) or the ImageMagik (imagemagick.org) software packages.

Acknowledgments

This work has been supported by the fund for research at the University of Bari.

Footnotes

Appendix A

Supplementary data to this article can be found online at https://doi.org/10.1016/j.dib.2019.105076.

Conflict of Interest

The author declares that he has no known financial interests or competing personal relationships that could have appeared influence the work reported in this document.

Appendix A. Supplementary data

The following are the Supplementary data to this article:

Multimedia component 1
mmc1.zip (352.5KB, zip)
Multimedia component 2
mmc2.csv (1.8KB, csv)

References

  • 1.Palese L.L. Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters. Biochim. Biophys. Acta. 2020;1864:129480. doi: 10.1016/j.bbagen.2019.129480. [DOI] [PubMed] [Google Scholar]
  • 2.Berman H.M., Westbrook J., Feng Z. The protein Data Bank. Nucleic Acids Res. 2000;28:235–242. doi: 10.1093/nar/28.1.235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Tsukihara T., Shimokata K., Katayama Y. The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc. Natl. Acad. Sci. U.S.A. 2003;100:15304–15309. doi: 10.1073/pnas.2635097100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 4.Shinzawa-Itoh K., Aoyama H., Muramoto K. Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. EMBO J. 2007;26:1713–1725. doi: 10.1038/sj.emboj.7601618. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Muramoto K., Ohta K., Shinzawa-Itoh K. Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. Proc. Natl. Acad. Sci. U.S.A. 2010;107:7740–7745. doi: 10.1073/pnas.0910410107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Bossis F., De Grassi A., Palese L.L., Pierri C.L. Prediction of high- and low-affinity quinol-analogue-binding sites in the aa3 and bo3 terminal oxidases from Bacillus subtilis and Escherichia coli. Biochem. J. 2014;461:305–314. doi: 10.1042/BJ20140082. [DOI] [PubMed] [Google Scholar]
  • 7.Palese L.L. Protein states as symmetry transitions in the correlation matrices. J. Phys. Chem. B. 2016;120:11428–11435. doi: 10.1021/acs.jpcb.6b09216. [DOI] [PubMed] [Google Scholar]
  • 8.Palese L.L. Conformations of the HIV-1 protease: a crystal structure data set analysis. Biochim. Biophys. Acta. 2017;1865:1416–1422. doi: 10.1016/j.bbapap.2017.08.009. [DOI] [PubMed] [Google Scholar]
  • 9.Lobasso S., Palese L.L., Angelini R., Corcelli A. Relationship between cardiolipin metabolism and oxygen availability in Bacillus subtilis. FEBS Open Bio. 2013;3:151–155. doi: 10.1016/j.fob.2013.02.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996;14:33–38. doi: 10.1016/0263-7855(96)00018-5. [DOI] [PubMed] [Google Scholar]
  • 11.Pérez F., Granger B.E. IPython: a system for interactive scientific computing. Comput. Sci. Eng. 2007;9:21–29. [Google Scholar]
  • 12.Oliphant T.E. Python for scientific computing. Comput. Sci. Eng. 2007;9:10–20. [Google Scholar]
  • 13.Van Der Walt S., Colbert S.C., Varoquaux G. The NumPy array: a structure for efficient numerical computation. Comput. Sci. Eng. 2011;13:22–30. [Google Scholar]
  • 14.Hunter J.D. Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 2007;9:90–95. [Google Scholar]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Multimedia component 1
mmc1.zip (352.5KB, zip)
Multimedia component 2
mmc2.csv (1.8KB, csv)

Articles from Data in Brief are provided here courtesy of Elsevier

RESOURCES