Table 2. NMR structure determination statistics of CCL2 in the free form and in complex with the fucosylated chitobiose (GlcNAcβ1,4[Fucα1,3]GlcNAc-spacer, the spacer [CH2]5COOH was truncated in the structure calculations to a methyl group.).
CCL2–carbohydrate complex | |||
CCL2 free | CCL2 | carbohydrate | |
NMR distance and dihedral constraints | |||
Distance restraints | |||
Total NOE | 2514 | 2054 | 42 |
Intra-residue | 482 | 446 | 23 |
Inter-residue | 2032 | 1608 | 19 |
Sequential (|i−j| = 1) | 593 | 489 | 9 |
Nonsequential (|i−j|>1 ) | 1439 | 1119 | 10 |
Hydrogen bonds | 46 | 49 | – |
Protein–carbohydrate intermolecular | 82 | ||
Total dihedral angle restraints | 186 | 178 | |
Protein | |||
φ | 91* | 85* | |
ψ | 95 | 91 | |
Carbohydrate | |||
HN-CO peptide bonds of acetamido | 2 | ||
Structure statistics | |||
Violations (mean and s.d.) | |||
Number of distance constraint violations >0.2 Å | 0.42±0.64 | 0.45±0.61 | |
Number of dihedral angle violations >5° | 0.05±0.22 | 4.75±1.48 | |
Max. dihedral angle violation (°) | 2.6±3.4 | 17.4±8.5 | |
Max. distance constraint violation (Å) | 0.24±0.07 | 0.20±0.04 | |
Deviations from idealized geometry | |||
Bond lengths (Å) | 0.010 | 0.010 | |
Bond angles (°) | 2.29 | 2.38 | |
Average pairwise r.m.s. deviation** (Å) | |||
Protein (residues G22-V153) | |||
Heavy | 0.98±0.14 | 1.18±0.15 | |
Backbone | 0.45±0.10 | 0.71±0.13 | |
carbohydrate | |||
All glycan heavy | 0.47±0.21 | ||
Complex | |||
Protein and carbohydrate heavy | 1.17±0.15 |
Phi values for prolines were omitted.
Pairwise r.m.s. deviation was calculated among 20 refined structures.