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. Author manuscript; available in PMC: 2016 Jan 31.
Published in final edited form as: J Mol Recognit. 2015 Jan 20;28(2):59–73. doi: 10.1002/jmr.2412

Table 4.

Accessibility of the water tunnel to solvent and hydrogen bonding of the two heme propionate groups in the crystal structures of CYP51

Heme A-propionate
 Heme B-propionate
Organism PDB ID Liganda Accessibilityb Conformationc H-bondingd Conformationc H-bondingd
T. brucei 3TIK, 3P99, 2WV2, 4G3J + + Distal Y103, R361 Proximal Y116, R124, H420
3G1Q - + Distal Y103, R361 Proximal Y116, R124, H420
2X2N + + Distal Y103, R361 Parallel Y116, H420
3GW9, 4G7G + + Distal R361 Proximal Y116, R124, H420
T. cruzi 4H60, 3KSW + + Distal Y103, R361 Parallel H420
2WX2 + + Distal Y103, R361 Parallel Y116, H420
3KHM + + Distal R361 Proximal R124, H420
3K10 + + Distal Y103, R361 Distal Y116, H420
2WUZ + - Distal Y103, R361 Proximal Y116, R124, H420
L infantum 3L4D + + Distal Y103, R361 Proximal Y116, R124, H420
Human 3JUS, 3LD6 + - Distal Y131, R382 Distal Y145, K156, H447
3JUV - + Proximal R382 Distal Y145
M. tuberculosis H37Rv 2W09e + + Distal R326 Proximal ----
2W0Ae + + Distal Q72, R326 Distal H392
2W0B + + Distal Y76, R326 Proximal K97, H392
2VKU + + Distal Y76, R326 Distal (R)f Ligands
2CI0e + + Distal R326 Distal&Proximalg H392
2CIBe + + Distal R326 Distal H392
M. tuberculosis 2BZ9, 1 H5Ze - + Distal R326 Proximal ----
1U13 - + Distal Y76, R326 Proximal K97, H392
1X8Ve + + Distal Y76, R326 Proximal K97, H392
1EA1, 1E9X + + Distal Y76, R362 Proximal R95, H392

If there is more than one chain, chain A is used.

a

With (+) or without (-) ligand in the active site.

b

The water tunnel (tunnel W) is accessible (+) or inaccessible (-) to the solvent (with a probe radius of 1.4 Å in PyMOL).

c

The propionate is on the distal side (distal) or the proximal side (proximal) of the heme plane, or roughly parallel (parallel) to it.

d

The hydrogen-bonding partners of the heme propionate groups. A hydrogen bond is considered to be formed when the distance between the two non-hydrogen atoms is less than 3.3 Å. The residue number is the residue number in the corresponding PDB structures. “----” indicates that the propionate has no hydrogen bonding with surrounding residues. “Ligands” indicate that the propionate makes hydrogen bonds to the ligands.

e

There are residues missing in the B-C loop and C helix region of the crystal structures. 2W09, 2W0A, 2CI0, and 1X8V have the B′-C loop missing. 2CIB has the B′-C loop and the beginning of the C helix missing, and 1H5Z has the C helix missing.

f

The B-propionate has rotated 120° toward the 1 helix because of the interaction with the two ligands (one in the binding site and the other in the ligand tunnel 1).

g

There are two conformations of the B-propionate group in the crystal structure. One conformation is on the distal and one on the proximal side of the heme plane.