SMTL ID : 5i6k.1

Crystal Structure of Copper Nitrite Reductase at 100K after 0.69 MGy

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.07 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: 5 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.300 Ligands: NO2.3 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.300, A:H.94, A:H.129, H2O.1 CU.9: 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.10: 5 residues within 4Å: Chain A: H.300 Chain B: D.92, H.94, H.129 Ligands: NO2.11 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.14 CU.17: 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.18: 5 residues within 4Å: Chain B: H.300 Chain C: D.92, H.94, H.129 Ligands: NO2.19 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.28

18 x NO2: NITRITE ION(Non-covalent)

NO2.3: 8 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.249, I.251, H.300, L.302 Ligands: CU.2 No protein-ligand interaction detected (PLIP) NO2.4: 7 residues within 4Å: Chain A: W.259, A.260, T.261, G.262, K.263, N.266 Chain C: Q.272 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.263, A:N.266, C:Q.272 Water bridges: A:V.258, A:V.258, A:T.261 NO2.5: 4 residues within 4Å: Chain A: R.244, D.245 Chain C: R.247, N.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.245, A:D.245 NO2.6: 1 residues within 4Å: Chain A: R.48 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.48 NO2.7: 2 residues within 4Å: Chain A: T.165, R.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.234, A:R.234 Water bridges: A:T.165 NO2.8: 4 residues within 4Å: Chain A: K.119, T.121 Chain C: R.290, L.324 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.119, C:R.290, C:R.290 NO2.11: 8 residues within 4Å: Chain A: H.249, I.251, H.300, L.302 Chain B: D.92, H.94, H.129 Ligands: CU.10 No protein-ligand interaction detected (PLIP) NO2.12: 7 residues within 4Å: Chain A: Q.272 Chain B: W.259, A.260, T.261, G.262, K.263, N.266 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.261, B:K.263, B:N.266, A:Q.272 Water bridges: B:V.258, B:V.258, B:T.261 NO2.13: 4 residues within 4Å: Chain A: R.247, N.301 Chain B: R.244, D.245 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.245, B:D.245 NO2.14: 1 residues within 4Å: Chain B: R.48 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.48 NO2.15: 2 residues within 4Å: Chain B: T.165, R.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.234, B:R.234 Water bridges: B:T.165 NO2.16: 4 residues within 4Å: Chain A: R.290, L.324 Chain B: K.119, T.121 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.290, A:R.290, B:K.119 Water bridges: A:D.323 NO2.19: 8 residues within 4Å: Chain B: H.249, I.251, H.300, L.302 Chain C: D.92, H.94, H.129 Ligands: CU.18 No protein-ligand interaction detected (PLIP) NO2.20: 7 residues within 4Å: Chain B: Q.272 Chain C: W.259, A.260, T.261, G.262, K.263, N.266 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:Q.272, C:T.261, C:K.263, C:N.266 Water bridges: C:V.258, C:V.258, C:T.261 NO2.21: 4 residues within 4Å: Chain B: R.247, N.301 Chain C: R.244, D.245 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.245, C:D.245 NO2.22: 1 residues within 4Å: Chain C: R.48 1 PLIP interactions: 1 interactions with chain C Water bridges: C:R.48 NO2.23: 2 residues within 4Å: Chain C: T.165, R.234 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.234, C:R.234 Water bridges: C:T.165 NO2.24: 4 residues within 4Å: Chain B: R.290, L.324 Chain C: K.119, T.121 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.119, B:R.290, B:R.290 Water bridges: B:D.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horrell, S. et al., Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal. Iucrj (2016)

Release Date

2016-07-13

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase

Related Entries With Identical Sequence