SMTL ID : 5d4j.1

Chloride-bound form of a copper nitrite reductase from Alcaligenes faecals

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.93, C.134, H.143, M.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.93, A:C.134, A:H.143 CU.2: 5 residues within 4Å: Chain A: D.96, H.98, H.133 Chain C: H.304 Ligands: CL.14 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.98, A:H.133, C:H.304 CU.8: 4 residues within 4Å: Chain B: H.93, C.134, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.93, B:C.134, B:H.143 CU.9: 5 residues within 4Å: Chain A: H.304 Chain B: D.96, H.98, H.133 Ligands: CL.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.98, B:H.133, A:H.304 CU.15: 4 residues within 4Å: Chain C: H.93, C.134, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.93, C:C.134, C:H.143 CU.16: 5 residues within 4Å: Chain B: H.304 Chain C: D.96, H.98, H.133 Ligands: CL.10 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Metal complexes: B:H.304, C:H.98, C:H.133

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

CL.3: 6 residues within 4Å: Chain A: I.255, H.304 Chain B: D.96, H.98, H.133 Ligands: CU.9 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain B: I.255, H.304 Chain C: D.96, H.98, H.133 Ligands: CU.16 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain A: D.96, H.98, H.133 Chain C: H.253, I.255, H.304 Ligands: CU.2 Ligand excluded by PLIP

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: F.22, V.23, K.172, I.173, Y.174 Ligands: ACY.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.23, A:V.23, A:I.173 GOL.5: 5 residues within 4Å: Chain A: I.50, D.51, D.52, A.221, V.222 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.50 GOL.6: 7 residues within 4Å: Chain A: Y.191, T.214, H.215, V.222, E.311, L.312 Chain B: R.209 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.311, B:R.209, B:R.209 Water bridges: A:Y.191 GOL.11: 8 residues within 4Å: Chain B: D.51, Y.191, T.214, H.215, V.222, E.311, L.312 Chain C: R.209 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:E.311, B:L.312, C:R.209, C:R.209 Water bridges: B:D.51, B:T.55 GOL.12: 4 residues within 4Å: Chain B: W.324, D.326, T.330, S.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.330, B:S.331 GOL.17: 5 residues within 4Å: Chain A: L.104, A.135, V.140 Chain C: I.255, A.300 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.317 GOL.18: 4 residues within 4Å: Chain C: W.324, D.326, T.330, S.331 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.330, C:S.331 GOL.19: 9 residues within 4Å: Chain A: T.210, L.211, T.212 Chain B: T.210, L.211, T.212 Chain C: T.210, L.211, T.212 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.210, A:L.211 GOL.20: 3 residues within 4Å: Chain C: V.49, D.51, D.52 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.51 GOL.21: 7 residues within 4Å: Chain C: V.57, H.58, S.146, Y.182, P.184, A.200, T.204 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.58, C:H.58, C:V.145, C:T.204

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.7: 3 residues within 4Å: Chain A: H.26, D.171 Ligands: GOL.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.28 Salt bridges: A:H.26 ACY.13: 10 residues within 4Å: Chain A: F.310, E.311 Chain B: G.138, M.139, V.140, P.141, W.142, Y.201, V.205, M.208 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.141 Hydrogen bonds: B:M.139, B:W.142, A:E.311 Water bridges: B:Y.201 ACY.22: 3 residues within 4Å: Chain C: H.26, Q.28, D.171 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.26, C:Q.28 Salt bridges: C:H.26

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-09

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Copper-containing nitrite reductase

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