SMTL ID : 3x1n.1

Nitrite-bound thermostable copper nitrite reductase at 320 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: W.92, H.124, A.164, H.172, M.177 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.124, A:H.172 CU.2: 6 residues within 4Å: Chain A: D.127, H.129, H.163 Chain C: H.273, H.323 Ligands: NO2.4 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.129, A:H.163, C:H.323, H2O.7 CU.3: 3 residues within 4Å: Chain A: H.71, H.112 Ligands: NO2.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.71, A:H.112 CU.6: 5 residues within 4Å: Chain B: W.92, H.124, A.164, H.172, M.177 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.124, B:H.172 CU.7: 6 residues within 4Å: Chain A: H.273, H.323 Chain B: D.127, H.129, H.163 Ligands: NO2.9 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.323, B:H.129, B:H.163, H2O.14 CU.8: 3 residues within 4Å: Chain B: H.71, H.112 Ligands: NO2.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.71, B:H.112 CU.11: 5 residues within 4Å: Chain C: W.92, H.124, A.164, H.172, M.177 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.124, C:H.172 CU.12: 6 residues within 4Å: Chain B: H.273, H.323 Chain C: D.127, H.129, H.163 Ligands: NO2.14 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.323, C:H.129, C:H.163, H2O.22 CU.13: 3 residues within 4Å: Chain C: H.71, H.112 Ligands: NO2.15 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.71, C:H.112

6 x NO2: NITRITE ION(Non-covalent)

NO2.4: 8 residues within 4Å: Chain A: D.127, H.129, H.163 Chain C: H.273, V.275, H.323, F.325 Ligands: CU.2 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:H.273 Water bridges: A:D.127 NO2.5: 3 residues within 4Å: Chain A: H.71, H.112 Ligands: CU.3 No protein-ligand interaction detected (PLIP) NO2.9: 8 residues within 4Å: Chain A: H.273, V.275, H.323, F.325 Chain B: D.127, H.129, H.163 Ligands: CU.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.273 Water bridges: B:D.127 NO2.10: 3 residues within 4Å: Chain B: H.71, H.112 Ligands: CU.8 No protein-ligand interaction detected (PLIP) NO2.14: 8 residues within 4Å: Chain B: H.273, V.275, H.323, F.325 Chain C: D.127, H.129, H.163 Ligands: CU.12 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Water bridges: C:D.127 Hydrogen bonds: B:H.273 NO2.15: 3 residues within 4Å: Chain C: H.71, H.112 Ligands: CU.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Chem.Commun.(Camb.) (2015)

Release Date

2015-01-21

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase