SMTL ID : 2dwt.1

Cu-containing nitrite reductase at pH 6.0 with bound nitrite

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.83, C.124, H.134, M.139 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:C.124, A:H.134 CU.2: 6 residues within 4Å: Chain A: D.86, H.88, H.123 Chain B: H.244, H.295 Ligands: NO2.7 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Metal complexes: A:H.88, A:H.123, B:H.295 CU.5: 4 residues within 4Å: Chain B: H.83, C.124, H.134, M.139 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.83, B:C.124, B:H.134 CU.6: 6 residues within 4Å: Chain B: D.86, H.88, H.123 Chain C: H.244, H.295 Ligands: NO2.11 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.295, B:H.88, B:H.123 CU.9: 4 residues within 4Å: Chain C: H.83, C.124, H.134, M.139 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.83, C:C.124, C:H.134 CU.10: 6 residues within 4Å: Chain A: H.244, H.295 Chain C: D.86, H.88, H.123 Ligands: NO2.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Metal complexes: A:H.295, C:H.88, C:H.123

6 x NO2: NITRITE ION(Non-covalent)

NO2.3: 8 residues within 4Å: Chain A: H.244, I.246, H.295, L.297 Chain C: D.86, H.88, H.123 Ligands: CU.10 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:D.86, A:H.244 NO2.4: 3 residues within 4Å: Chain A: H.17, Q.19, Y.161 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.164 NO2.7: 8 residues within 4Å: Chain A: D.86, H.88, H.123 Chain B: H.244, I.246, H.295, L.297 Ligands: CU.2 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.244, A:D.86 NO2.8: 3 residues within 4Å: Chain B: H.17, Q.19, Y.161 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.164 NO2.11: 8 residues within 4Å: Chain B: D.86, H.88, H.123 Chain C: H.244, I.246, H.295, L.297 Ligands: CU.6 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:H.244, B:D.86 NO2.12: 3 residues within 4Å: Chain C: H.17, Q.19, Y.161 1 PLIP interactions: 1 interactions with chain C Water bridges: C:V.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jacobson, F. et al., pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase. J.Biol.Chem. (2007)

Release Date

2006-12-05

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase

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