SMTL ID : 5b1k.1

Crystal structure of the chloride-bound form of blue copper nitrite reductase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.90, C.131, P.133, H.140, M.145 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:C.131, A:H.140 CU.2: 6 residues within 4Å: Chain A: D.93, H.95, H.130 Chain B: H.250, H.301 Ligands: CL.3 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.301, A:H.95, A:H.130, H2O.1 CU.6: 5 residues within 4Å: Chain B: H.90, C.131, P.133, H.140, M.145 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.90, B:C.131, B:H.140 CU.7: 6 residues within 4Å: Chain B: D.93, H.95, H.130 Chain C: H.250, H.301 Ligands: CL.8 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.301, B:H.95, B:H.130, H2O.12 CU.11: 5 residues within 4Å: Chain C: H.90, C.131, P.133, H.140, M.145 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.90, C:C.131, C:H.140 CU.12: 6 residues within 4Å: Chain A: H.250, H.301 Chain C: D.93, H.95, H.130 Ligands: CL.13 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.95, C:H.130, A:H.301, H2O.24

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: D.93, H.130 Chain B: I.252, H.301, L.303 Ligands: CU.2 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain B: D.93, H.130 Chain C: I.252, H.301, L.303 Ligands: CU.7 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain A: I.252, H.301, L.303 Chain C: D.93, H.130 Ligands: CU.12 Ligand excluded by PLIP

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

PG4.4: 6 residues within 4Å: Chain C: M.88, E.134, G.135, M.136, A.195, Y.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.134 PG4.5: 6 residues within 4Å: Chain A: V.295, A.297, F.307, A.312, H.314 Chain C: L.101 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:K.105, C:E.134, A:T.223, A:T.223 PG4.9: 6 residues within 4Å: Chain A: M.88, E.134, G.135, M.136, A.195, Y.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.134 PG4.10: 6 residues within 4Å: Chain A: L.101 Chain B: V.295, A.297, F.307, A.312, H.314 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:T.223, B:T.223, A:K.105, A:E.134 PG4.14: 6 residues within 4Å: Chain B: M.88, E.134, G.135, M.136, A.195, Y.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.134 PG4.15: 6 residues within 4Å: Chain B: L.101 Chain C: V.295, A.297, F.307, A.312, H.314 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Water bridges: B:K.105, B:E.134, C:T.223, C:T.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nojiri, M., Structure and function of copper nitrite reductase. Metalloenzymes in denitrification: Applications and Environmental impacts (2016)

Release Date

2016-11-23

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase