SMTL ID : 2xx0.1 (1 other biounit)

STRUCTURE OF THE N90S-H254F MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.89, A:C.130, A:H.139 CU.3: 6 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.249, H.300 Ligands: ZN.2 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.94, A:H.129, C:H.300, H2O.14 CU.8: 4 residues within 4Å: Chain B: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.89, B:C.130, B:H.139 CU.10: 6 residues within 4Å: Chain A: H.249, H.300 Chain B: D.92, H.94, H.129 Ligands: ZN.9 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.94, B:H.129, A:H.300, H2O.28 CU.15: 4 residues within 4Å: Chain C: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.89, C:C.130, C:H.139 CU.17: 6 residues within 4Å: Chain B: H.249, H.300 Chain C: D.92, H.94, H.129 Ligands: ZN.16 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.94, C:H.129, B:H.300, H2O.42

9 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.249, H.300 Ligands: CU.3 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.94, A:H.129, C:H.300, H2O.14 ZN.4: 3 residues within 4Å: Chain A: H.165, D.167, T.234 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.165, A:D.167, A:D.167, H2O.14 ZN.7: 2 residues within 4Å: Chain A: D.4, H.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.8, H2O.14, H2O.15, H2O.15, H2O.15 ZN.9: 6 residues within 4Å: Chain A: H.249, H.300 Chain B: D.92, H.94, H.129 Ligands: CU.10 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.94, B:H.129, A:H.300, H2O.28 ZN.11: 3 residues within 4Å: Chain B: H.165, D.167, T.234 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.165, B:D.167, B:D.167, H2O.28 ZN.14: 2 residues within 4Å: Chain B: D.4, H.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.8, H2O.29, H2O.29, H2O.29, H2O.29 ZN.16: 6 residues within 4Å: Chain B: H.249, H.300 Chain C: D.92, H.94, H.129 Ligands: CU.17 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.94, C:H.129, B:H.300, H2O.42 ZN.18: 3 residues within 4Å: Chain C: H.165, D.167, T.234 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.165, C:D.167, C:D.167, H2O.43 ZN.21: 2 residues within 4Å: Chain C: D.4, H.8 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.8, H2O.43, H2O.43, H2O.43, H2O.43

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

MES.5: 6 residues within 4Å: Chain A: P.163, L.164, H.165, T.234, T.288, K.290 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.165 Salt bridges: A:K.290 MES.12: 6 residues within 4Å: Chain B: P.163, L.164, H.165, T.234, T.288, K.290 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.165 Salt bridges: B:K.290 MES.19: 6 residues within 4Å: Chain C: P.163, L.164, H.165, T.234, T.288, K.290 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.165 Salt bridges: C:K.290

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 6 residues within 4Å: Chain A: V.294, A.296, F.306, A.311, H.313 Chain B: L.100 No protein-ligand interaction detected (PLIP) PG4.13: 6 residues within 4Å: Chain B: V.294, A.296, F.306, A.311, H.313 Chain C: L.100 No protein-ligand interaction detected (PLIP) PG4.20: 6 residues within 4Å: Chain A: L.100 Chain C: V.294, A.296, F.306, A.311, H.313 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leferink, N.G.H. et al., Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry (2011)

Release Date

2011-05-18

Peptides

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

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