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

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

Coordinates

PDB Format Compare

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.2: 6 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.249, H.300 Ligands: ZN.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.13 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.9: 6 residues within 4Å: Chain A: H.249, H.300 Chain B: D.92, H.94, H.129 Ligands: ZN.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.25 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.16: 6 residues within 4Å: Chain B: H.249, H.300 Chain C: D.92, H.94, H.129 Ligands: ZN.17 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.300, C:H.94, C:H.129, H2O.38

9 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.249, H.300 Ligands: CU.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.13 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.13 ZN.7: 1 residues within 4Å: Chain A: H.8 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:H.8, H2O.13, H2O.13, H2O.13, H2O.13, H2O.13 ZN.10: 6 residues within 4Å: Chain A: H.249, H.300 Chain B: D.92, H.94, H.129 Ligands: CU.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.25 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.25 ZN.14: 1 residues within 4Å: Chain B: H.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:H.8, H2O.25, H2O.26, H2O.26, H2O.26, H2O.26 ZN.17: 6 residues within 4Å: Chain B: H.249, H.300 Chain C: D.92, H.94, H.129 Ligands: CU.16 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.300, C:H.94, C:H.129, H2O.38 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.38 ZN.21: 1 residues within 4Å: Chain C: H.8 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:H.8, H2O.38, H2O.38, H2O.38, H2O.38, H2O.38

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.165 Water bridges: A:G.232, A:T.234 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.165 Water bridges: B:G.232, B:T.234 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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.165 Water bridges: C:G.232, C:T.234 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
B

B
B

C
B

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

Related Entries With Identical Sequence