SMTL ID : 3wi9.1

Crystal structure of copper nitrite reductase from Geobacillus kaustophilus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.96, C.136, H.144, M.149 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.96, A:C.136, A:H.144 CU.2: 5 residues within 4Å: Chain A: D.99, H.101, H.135 Chain B: H.245, H.295 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.101, A:H.135, B:H.295, H2O.9, H2O.9 CU.11: 4 residues within 4Å: Chain B: H.96, C.136, H.144, M.149 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.96, B:C.136, B:H.144 CU.12: 5 residues within 4Å: Chain B: D.99, H.101, H.135 Chain C: H.245, H.295 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:H.101, B:H.135, C:H.295, H2O.22, H2O.22 CU.21: 4 residues within 4Å: Chain C: H.96, C.136, H.144, M.149 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.96, C:C.136, C:H.144 CU.22: 5 residues within 4Å: Chain A: H.245, H.295 Chain C: D.99, H.101, H.135 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.101, C:H.135, A:H.295, H2O.35, H2O.35

9 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: V.37, H.43, H.84 Ligands: ZN.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.84, H2O.6 ZN.4: 4 residues within 4Å: Chain A: H.43, H.84 Ligands: ZN.3, ACY.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.43, ACY.8 ZN.5: 1 residues within 4Å: Chain A: D.168 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.168, H2O.3, H2O.4, H2O.4, H2O.7, H2O.8 ZN.13: 4 residues within 4Å: Chain B: V.37, H.43, H.84 Ligands: ZN.14 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.84, H2O.19 ZN.14: 4 residues within 4Å: Chain B: H.43, H.84 Ligands: ZN.13, ACY.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.43 ZN.15: 1 residues within 4Å: Chain B: D.168 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.168, H2O.15, H2O.16, H2O.17, H2O.20, H2O.20 ZN.23: 4 residues within 4Å: Chain C: V.37, H.43, H.84 Ligands: ZN.24 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.84, H2O.31 ZN.24: 4 residues within 4Å: Chain C: H.43, H.84 Ligands: ZN.23, ACY.28 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.43, ACY.28 ZN.25: 1 residues within 4Å: Chain C: D.168 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.168, H2O.28, H2O.29, H2O.30, H2O.33, H2O.33

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

NA.6: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.218 NA.7: 1 residues within 4Å: Chain A: E.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.240 Water bridges: A:N.298 NA.16: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.218 NA.17: 1 residues within 4Å: Chain B: E.240 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.240 Water bridges: B:N.298 NA.26: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.218 NA.27: 1 residues within 4Å: Chain C: E.240 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.240 Water bridges: C:N.298

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

ACY.8: 4 residues within 4Å: Chain A: H.43, H.84, T.121 Ligands: ZN.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.121 Water bridges: A:H.84, A:H.84 Salt bridges: A:H.43, A:H.84 ACY.18: 4 residues within 4Å: Chain B: H.43, H.84, T.121 Ligands: ZN.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.121 Water bridges: B:H.84, B:H.84 Salt bridges: B:H.43, B:H.84 ACY.28: 4 residues within 4Å: Chain C: H.43, H.84, T.121 Ligands: ZN.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.121 Water bridges: C:H.84, C:H.84 Salt bridges: C:H.43, C:H.84

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

MPD.9: 6 residues within 4Å: Chain A: D.164, V.167, D.168, R.169, E.170, R.230 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.164, A:V.167 Hydrogen bonds: A:D.168, A:E.170 Water bridges: A:E.170, A:Y.232 MPD.19: 6 residues within 4Å: Chain B: D.164, V.167, D.168, R.169, E.170, R.230 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.164, B:V.167 Hydrogen bonds: B:D.168, B:E.170 Water bridges: B:E.170, B:Y.232 MPD.29: 6 residues within 4Å: Chain C: D.164, V.167, D.168, R.169, E.170, R.230 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:D.164, C:V.167 Hydrogen bonds: C:D.168, C:E.170 Water bridges: C:E.170, C:Y.232

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

SO4.10: 3 residues within 4Å: Chain A: K.23, G.24, K.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.24 Water bridges: A:K.62, A:K.62 Salt bridges: A:K.23, A:K.62 SO4.20: 3 residues within 4Å: Chain B: K.23, G.24, K.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.24 Water bridges: B:K.62, B:K.62 Salt bridges: B:K.23, B:K.62 SO4.30: 3 residues within 4Å: Chain C: K.23, G.24, K.62 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.24 Water bridges: C:K.62, C:K.62 Salt bridges: C:K.23, C:K.62

Links

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Citation

Fukuda, Y. et al., Structural and functional characterization of the Geobacillus copper nitrite reductase: involvement of the unique N-terminal region in the interprotein electron transfer with its redox partner. Biochim.Biophys.Acta (2014)

Release Date

2014-07-23

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase