SMTL ID : 2bp8.2 (1 other biounit)

M144Q Structure of nitrite reductase from Alcaligenes xylosoxidans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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, Q.144 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.89, A:C.130, A:H.139 CU.2: 5 residues within 4Å: Chain A: D.92, H.94, H.129 Chain B: H.249, H.300 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.94, A:H.129, B:H.300, H2O.6 CU.10: 4 residues within 4Å: Chain B: H.89, C.130, H.139, Q.144 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.89, B:C.130, B:H.139 CU.11: 5 residues within 4Å: Chain B: D.92, H.94, H.129 Chain C: H.249, H.300 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.94, B:H.129, C:H.300, H2O.20 CU.19: 4 residues within 4Å: Chain C: H.89, C.130, H.139, Q.144 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.89, C:C.130, C:H.139 CU.20: 5 residues within 4Å: Chain A: H.249, H.300 Chain C: D.92, H.94, H.129 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.94, C:H.129, A:H.300, H2O.34

15 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: H.70, D.73 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.70, A:D.73, 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.5: 3 residues within 4Å: Chain A: H.313 Ligands: SO4.8, SO4.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.313, H2O.14 ZN.6: 2 residues within 4Å: Chain A: H.8, E.34 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.34, H2O.14, H2O.14, H2O.14 ZN.7: 4 residues within 4Å: Chain A: A.3, D.4, L.6, H.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.8 ZN.12: 2 residues within 4Å: Chain B: H.70, D.73 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.70, B:D.73, H2O.28 ZN.13: 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: 3 residues within 4Å: Chain B: H.313 Ligands: SO4.17, SO4.18 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.313, H2O.28 ZN.15: 2 residues within 4Å: Chain B: H.8, E.34 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.34, H2O.28, H2O.28, H2O.28 ZN.16: 4 residues within 4Å: Chain B: A.3, D.4, L.6, H.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.8 ZN.21: 2 residues within 4Å: Chain C: H.70, D.73 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.70, C:D.73, H2O.42 ZN.22: 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.42 ZN.23: 3 residues within 4Å: Chain C: H.313 Ligands: SO4.26, SO4.27 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.313, H2O.42 ZN.24: 2 residues within 4Å: Chain C: H.8, E.34 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.34, H2O.42, H2O.42, H2O.42 ZN.25: 4 residues within 4Å: Chain C: A.3, D.4, L.6, H.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.8

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 4 residues within 4Å: Chain A: H.313 Chain C: E.133 Ligands: ZN.5, SO4.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.313 SO4.9: 5 residues within 4Å: Chain A: T.222, F.306, H.313 Ligands: ZN.5, SO4.8 3 PLIP interactions: 3 interactions with chain A Water bridges: A:F.306, A:A.311 Salt bridges: A:H.313 SO4.17: 4 residues within 4Å: Chain A: E.133 Chain B: H.313 Ligands: ZN.14, SO4.18 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:H.313 Water bridges: A:E.133 SO4.18: 5 residues within 4Å: Chain B: T.222, F.306, H.313 Ligands: ZN.14, SO4.17 3 PLIP interactions: 3 interactions with chain B Water bridges: B:F.306, B:A.311 Salt bridges: B:H.313 SO4.26: 4 residues within 4Å: Chain B: E.133 Chain C: H.313 Ligands: ZN.23, SO4.27 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.313 SO4.27: 5 residues within 4Å: Chain C: T.222, F.306, H.313 Ligands: ZN.23, SO4.26 3 PLIP interactions: 3 interactions with chain C Water bridges: C:F.306, C:A.311 Salt bridges: C:H.313

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hough, M.A. et al., High Resolution Structural Studies of Mutants Provide Insights Into Catalysis and Electron Transfer Processes in Copper Nitrite Reductase. J.Mol.Biol. (2005)

Release Date

2006-07-26

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