SMTL ID : 4csp.1 (1 other biounit)

Structure of the F306C mutant of nitrite reductase from Achromobacter xylosoxidans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

6 x CU: COPPER (II) ION(Non-covalent)

CU.1: 4 residues within 4Å: Chain A: H.88, C.129, H.138, M.143 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.88, A:C.129, A:H.138 CU.2: 5 residues within 4Å: Chain A: D.91, H.93, H.128 Chain C: H.248, H.299 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.93, A:H.128, C:H.299, H2O.11 CU.8: 4 residues within 4Å: Chain B: H.88, C.129, H.138, M.143 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.88, B:C.129, B:H.138 CU.9: 5 residues within 4Å: Chain A: H.248, H.299 Chain B: D.91, H.93, H.128 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.93, B:H.128, A:H.299, H2O.22 CU.15: 4 residues within 4Å: Chain C: H.88, C.129, H.138, M.143 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.88, C:C.129, C:H.138 CU.16: 5 residues within 4Å: Chain B: H.248, H.299 Chain C: D.91, H.93, H.128 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.299, C:H.93, C:H.128, H2O.32

12 x ZN: ZINC ION(Non-covalent)

ZN.3: 1 residues within 4Å: Chain A: H.312 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.312, H2O.11 ZN.4: 2 residues within 4Å: Chain A: D.3, H.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.7, H2O.6, H2O.10 ZN.6: 2 residues within 4Å: Chain A: L.297, C.305 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.305 ZN.7: 2 residues within 4Å: Chain A: H.164, D.166 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.164, A:D.166, A:D.166, H2O.1 ZN.10: 1 residues within 4Å: Chain B: H.312 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.312, H2O.21 ZN.11: 2 residues within 4Å: Chain B: D.3, H.7 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.7, H2O.17, H2O.21 ZN.13: 2 residues within 4Å: Chain B: L.297, C.305 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.305 ZN.14: 2 residues within 4Å: Chain B: H.164, D.166 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.164, B:D.166, B:D.166, H2O.11 ZN.17: 1 residues within 4Å: Chain C: H.312 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.312, H2O.32 ZN.18: 2 residues within 4Å: Chain C: D.3, H.7 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.7, H2O.27, H2O.31 ZN.20: 2 residues within 4Å: Chain C: L.297, C.305 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.305 ZN.21: 2 residues within 4Å: Chain C: H.164, D.166 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.164, C:D.166, C:D.166, H2O.22

3 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 5 residues within 4Å: Chain A: P.162, L.163, H.164, T.233, T.287 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.164 Water bridges: A:T.233 MES.12: 5 residues within 4Å: Chain B: P.162, L.163, H.164, T.233, T.287 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.164 Water bridges: B:T.233 MES.19: 5 residues within 4Å: Chain C: P.162, L.163, H.164, T.233, T.287 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.164 Water bridges: C:T.233

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leferink, N.G.H. et al., Impact of Residues Remote from the Catalytic Centre on Enzyme Catalysis of Copper Nitrite Reductase. Nat.Commun. (2014)

Release Date

2014-07-30

Peptides

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
F

C
F

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

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