SMTL ID : 2par.2 (1 other biounit)

Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and TMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x CO: COBALT (II) ION(Non-covalent)

CO.1: 5 residues within 4Å: Chain A: H.35, H.70, D.71, D.139 Ligands: TMP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.35, A:H.70, A:D.71, A:D.139, H2O.1 CO.4: 5 residues within 4Å: Chain B: H.35, H.70, D.71, D.139 Ligands: TMP.5 6 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: B:H.35, B:H.70, B:D.71, B:D.139, H2O.2, TMP.5 CO.6: 5 residues within 4Å: Chain C: H.35, H.70, D.71, D.139 Ligands: TMP.7 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.35, C:H.70, C:D.71, C:D.139, H2O.2 CO.9: 5 residues within 4Å: Chain D: H.35, H.70, D.71, D.139 Ligands: TMP.10 6 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:H.35, D:H.70, D:D.71, D:D.139, H2O.3, TMP.10 CO.11: 5 residues within 4Å: Chain E: H.35, H.70, D.71, D.139 Ligands: TMP.12 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.35, E:H.70, E:D.71, E:D.139, H2O.4 CO.14: 5 residues within 4Å: Chain F: H.35, H.70, D.71, D.139 Ligands: TMP.15 6 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: F:H.35, F:H.70, F:D.71, F:D.139, H2O.5, TMP.15

6 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.2: 13 residues within 4Å: Chain A: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, D.139, A.143, L.165 Ligands: CO.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.21, A:A.143, A:L.165 Hydrogen bonds: A:W.21, A:D.79, A:T.82, A:D.139 Water bridges: A:R.20, A:R.20, A:R.20 Salt bridges: A:R.20, A:H.35 pi-Stacking: A:W.21 TMP.5: 14 residues within 4Å: Chain B: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, P.83, D.139, A.143, L.165 Ligands: CO.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.21, B:A.143, B:L.165 Hydrogen bonds: B:W.21, B:D.79, B:T.82, B:D.139, B:D.139 Salt bridges: B:R.20, B:H.35 pi-Stacking: B:W.21 TMP.7: 13 residues within 4Å: Chain C: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, D.139, A.143, L.165 Ligands: CO.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:W.21, C:A.143, C:L.165 Hydrogen bonds: C:W.21, C:D.79, C:T.82, C:D.139 Water bridges: C:R.20, C:R.20, C:R.20 Salt bridges: C:R.20, C:H.35 pi-Stacking: C:W.21 TMP.10: 14 residues within 4Å: Chain D: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, P.83, D.139, A.143, L.165 Ligands: CO.9 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.21, D:A.143, D:L.165 Hydrogen bonds: D:W.21, D:D.79, D:T.82, D:D.139, D:D.139 Salt bridges: D:R.20, D:H.35 pi-Stacking: D:W.21 TMP.12: 13 residues within 4Å: Chain E: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, D.139, A.143, L.165 Ligands: CO.11 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:W.21, E:A.143, E:L.165 Hydrogen bonds: E:W.21, E:D.79, E:T.82, E:D.139 Water bridges: E:R.20, E:R.20, E:R.20 Salt bridges: E:R.20, E:H.35 pi-Stacking: E:W.21 TMP.15: 14 residues within 4Å: Chain F: R.20, W.21, P.22, H.35, D.71, D.79, L.80, P.81, T.82, P.83, D.139, A.143, L.165 Ligands: CO.14 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:W.21, F:A.143, F:L.165 Hydrogen bonds: F:W.21, F:D.79, F:T.82, F:D.139, F:D.139 Salt bridges: F:R.20, F:H.35 pi-Stacking: F:W.21

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 3 residues within 4Å: Chain A: E.124, Y.127, K.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.124, A:E.124, A:K.136 PEG.8: 3 residues within 4Å: Chain C: E.124, Y.127, K.136 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.124, C:E.124, C:K.136 PEG.13: 3 residues within 4Å: Chain E: E.124, Y.127, K.136 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.124, E:E.124, E:K.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zimmerman, M.D. et al., Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli. J.Mol.Biol. (2008)

Release Date

2008-03-04

Peptides

5'-deoxynucleotidase YfbR: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

5'-deoxynucleotidase YfbR

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