SMTL ID : 4ysr.1

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 16.6 MGy

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.95, C.135, 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: 4 residues within 4Å: Chain A: D.98, H.100, H.134 Chain C: H.294 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.294, A:H.100, A:H.134, H2O.9 CU.3: 2 residues within 4Å: Chain A: H.42, H.83 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.10 CU.4: 1 residues within 4Å: Chain A: H.39 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.39 CU.5: 1 residues within 4Å: Chain A: D.167 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.167, A:D.167, H2O.1 CU.6: 3 residues within 4Å: Chain A: T.248, V.249 Chain B: H.103 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:T.248, A:V.249, B:H.103, H2O.2 CU.7: 2 residues within 4Å: Chain A: P.191, E.239 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.239, H2O.3, H2O.4 CU.10: 4 residues within 4Å: Chain B: H.95, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.95, B:C.135, B:H.143 CU.11: 4 residues within 4Å: Chain A: H.294 Chain B: D.98, H.100, H.134 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.100, B:H.134, A:H.294, H2O.21 CU.12: 2 residues within 4Å: Chain B: H.42, H.83 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.21 CU.13: 1 residues within 4Å: Chain B: H.39 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.39 CU.14: 1 residues within 4Å: Chain B: D.167 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.167, B:D.167, H2O.13 CU.15: 3 residues within 4Å: Chain B: T.248, V.249 Chain C: H.103 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.103, B:T.248, B:V.249, H2O.14 CU.16: 2 residues within 4Å: Chain B: P.191, E.239 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.239, H2O.15, H2O.16 CU.19: 4 residues within 4Å: Chain C: H.95, C.135, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.95, C:C.135, C:H.143 CU.20: 4 residues within 4Å: Chain B: H.294 Chain C: D.98, H.100, H.134 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.294, C:H.100, C:H.134, H2O.33 CU.21: 2 residues within 4Å: Chain C: H.42, H.83 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.33 CU.22: 1 residues within 4Å: Chain C: H.39 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.39 CU.23: 1 residues within 4Å: Chain C: D.167 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.167, C:D.167, H2O.24 CU.24: 3 residues within 4Å: Chain A: H.103 Chain C: T.248, V.249 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:T.248, C:V.249, A:H.103, H2O.25 CU.25: 2 residues within 4Å: Chain C: P.191, E.239 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.239, H2O.27, H2O.27

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

MPD.8: 6 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.163, A:V.166 Hydrogen bonds: A:E.169 Water bridges: A:E.169, A:E.169 MPD.17: 6 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:D.163, B:V.166 Hydrogen bonds: B:E.169 Water bridges: B:E.169, B:E.169 MPD.26: 6 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:D.163, C:V.166 Hydrogen bonds: C:E.169 Water bridges: C:E.169, C:E.169

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 6 residues within 4Å: Chain A: D.55, Y.193, T.212, Q.300, K.301, G.302 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.300 SO4.18: 6 residues within 4Å: Chain B: D.55, Y.193, T.212, Q.300, K.301, G.302 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.300 SO4.27: 6 residues within 4Å: Chain C: D.55, Y.193, T.212, Q.300, K.301, G.302 1 PLIP interactions: 1 interactions with chain C Water bridges: C:Q.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography. J.Biochem. (2016)

Release Date

2016-02-24

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase

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