SMTL ID : 6l46.1

High-resolution neutron and X-ray joint refined structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans

Coordinates

PDB Format Compare

Method

NEUTRON DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 7 residues within 4Å: Chain A: W.63, H.95, S.96, C.135, T.137, H.143, M.148 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.95, A:C.135, A:H.143 CU.2: 9 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, H.294, F.296 Ligands: CU.4, NA.5, CL.6 7 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:H.294, A:H.100, A:H.134, H2O.1, H2O.1, H2O.11, H2O.11 CU.3: 3 residues within 4Å: Chain A: V.36, H.42, H.83 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.11, H2O.11 CU.4: 8 residues within 4Å: Chain A: D.98, H.100 Chain B: H.244, V.245, V.246, G.247 Ligands: CU.2, NA.5 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.244, H2O.1, H2O.1, H2O.6, H2O.6 CU.8: 7 residues within 4Å: Chain B: W.63, H.95, S.96, C.135, T.137, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.95, B:C.135, B:H.143 CU.9: 9 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, H.294, F.296 Ligands: CU.11, NA.12, CL.13 7 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: B:H.100, B:H.134, C:H.294, H2O.19, H2O.19, H2O.29, H2O.29 CU.10: 3 residues within 4Å: Chain B: V.36, H.42, H.83 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.29, H2O.29 CU.11: 8 residues within 4Å: Chain B: D.98, H.100 Chain C: H.244, V.245, V.246, G.247 Ligands: CU.9, NA.12 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:H.244, H2O.19, H2O.19, H2O.23, H2O.23 CU.15: 7 residues within 4Å: Chain C: W.63, H.95, S.96, C.135, T.137, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.95, C:C.135, C:H.143 CU.16: 9 residues within 4Å: Chain A: H.244, H.294, F.296 Chain C: D.98, H.100, H.134 Ligands: CU.18, NA.19, CL.20 7 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, A:H.294, H2O.36, H2O.36, H2O.47, H2O.47 CU.17: 3 residues within 4Å: Chain C: V.36, H.42, H.83 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.46, H2O.46 CU.18: 8 residues within 4Å: Chain A: H.244, V.245, V.246, G.247 Chain C: D.98, H.100 Ligands: CU.16, NA.19 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.244, H2O.36, H2O.36, H2O.41, H2O.41

3 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: D.98, H.134 Chain B: V.246 Ligands: CU.2, CU.4, CL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.98 NA.12: 6 residues within 4Å: Chain B: D.98, H.134 Chain C: V.246 Ligands: CU.9, CU.11, CL.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.98 NA.19: 6 residues within 4Å: Chain A: V.246 Chain C: D.98, H.134 Ligands: CU.16, CU.18, CL.20 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.98

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

CL.6: 8 residues within 4Å: Chain A: H.134 Chain B: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2, NA.5 Ligand excluded by PLIP CL.13: 8 residues within 4Å: Chain B: H.134 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.9, NA.12 Ligand excluded by PLIP CL.20: 8 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain C: H.134 Ligands: CU.16, NA.19 Ligand excluded by PLIP

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 7 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.163, A:V.166 Hydrogen bonds: A:E.169, A:E.169 MPD.14: 7 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.163, B:V.166 Hydrogen bonds: B:E.169, B:E.169 MPD.21: 7 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.163, C:V.166 Hydrogen bonds: C:E.169, C:E.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2020-02-12

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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