SMTL ID : 3bp1.1 (2 other biounits)

Crystal structure of putative 7-cyano-7-deazaguanine reductase QueF from Vibrio cholerae O1 biovar eltor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-tetramer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: T.152, C.157, H.189, H.191 Ligands: PO4.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.152, A:T.152 Water bridges: A:G.155, B:N.143, B:N.143 Salt bridges: A:H.189, A:H.191 PO4.4: 8 residues within 4Å: Chain B: H.213, Q.254, S.255, H.277 Chain C: N.143, T.146 Chain D: T.152 Ligands: PO4.12 7 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: B:S.255 Water bridges: B:H.277, C:N.143, C:T.146, D:T.152 Salt bridges: B:H.213, B:H.277 PO4.5: 4 residues within 4Å: Chain B: T.152, C.157, H.189, H.191 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.152 Water bridges: B:T.152, B:G.155, B:C.157, B:H.191, B:H.191, A:N.143 Salt bridges: B:H.189, B:H.191 PO4.8: 8 residues within 4Å: Chain A: T.152 Chain B: N.143, T.146 Chain C: H.213, Q.254, S.255, H.277 Ligands: PO4.1 8 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:S.255, B:T.146 Water bridges: C:H.277, B:N.143, B:T.146, A:T.152 Salt bridges: C:H.213, C:H.277 PO4.9: 4 residues within 4Å: Chain C: T.152, C.157, H.189, H.191 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.152, C:T.152 Water bridges: C:C.157, D:N.143, D:T.146 Salt bridges: C:H.189, C:H.191 PO4.12: 5 residues within 4Å: Chain D: T.152, C.157, H.189, H.191 Ligands: PO4.4 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Water bridges: D:T.152, D:T.152, C:N.143, C:N.143, C:N.143 Salt bridges: D:H.189, D:H.191

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: T.66, Y.68, R.261, D.269, R.286, Q.290 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.68, A:D.269, H2O.2 MG.13: 6 residues within 4Å: Chain D: T.66, Y.68, R.261, D.269, R.286, Q.290 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:Y.68, D:D.269, H2O.36

4 x GUN: GUANINE(Non-covalent)

GUN.3: 8 residues within 4Å: Chain A: W.65, L.95, I.96, E.97, S.98, F.235, H.236, E.237 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.96, A:E.97, A:S.98, A:H.236 Salt bridges: A:E.237 pi-Stacking: A:F.235, A:F.235 pi-Cation interactions: A:F.235 GUN.6: 9 residues within 4Å: Chain B: W.65, L.95, I.96, E.97, S.98, F.235, H.236, E.237, I.270 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.96, B:E.97, B:E.97, B:S.98, B:H.236 Salt bridges: B:E.237 pi-Stacking: B:F.235, B:F.235 pi-Cation interactions: B:F.235 GUN.10: 9 residues within 4Å: Chain C: W.65, L.95, I.96, E.97, S.98, F.235, H.236, E.237, I.270 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:I.96, C:E.97, C:E.97, C:S.98, C:H.236 Water bridges: C:S.98, C:S.98 Salt bridges: C:E.237 pi-Stacking: C:F.235, C:F.235 pi-Cation interactions: C:F.235 GUN.14: 8 residues within 4Å: Chain D: W.65, L.95, I.96, E.97, S.98, F.235, H.236, E.237 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:I.96, D:E.97, D:S.98, D:S.98, D:H.236 Salt bridges: D:E.237 pi-Stacking: D:F.235, D:F.235

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.7: 7 residues within 4Å: Chain A: R.265, G.266, G.267 Chain B: K.102, R.264, R.265, G.266 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.266, A:G.266, A:G.267 Water bridges: B:K.102, B:K.102, B:R.265, B:R.265, B:R.265, B:G.267, B:G.267 Salt bridges: B:K.102, B:R.265, A:R.265 POP.11: 7 residues within 4Å: Chain C: Q.202, R.264, R.265, G.266 Chain D: Q.202, R.265, G.266 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:Q.202, D:G.266, D:G.267, C:G.266 Water bridges: D:R.265, D:R.265, C:R.265, C:G.267, C:G.267 Salt bridges: D:R.265, C:R.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism. J.Mol.Biol. (2010)

Release Date

2008-01-08

Peptides

NADPH-dependent 7-cyano-7-deazaguanine reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NADPH-dependent 7-cyano-7-deazaguanine reductase

Related Entries With Identical Sequence