SMTL ID : 3x1e.1

Structure of copper-containing nitrite reductase from Geobacillus thermodenitrificans without chloride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 4 residues within 4Å: Chain A: H.124, C.164, H.172, M.177 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.124, A:C.164, A:H.172 CU.2: 6 residues within 4Å: Chain A: D.127, H.129, H.163 Chain C: H.273, H.323 Ligands: CU.7 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.323, A:H.129, A:H.163, H2O.1, H2O.14 CU.3: 2 residues within 4Å: Chain A: H.71, H.112 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.71, A:H.112, H2O.2, H2O.11 CU.4: 1 residues within 4Å: Chain A: H.68 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.68, H2O.14 CU.5: 1 residues within 4Å: Chain A: D.196 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.196, H2O.10, H2O.10, H2O.13, H2O.14 CU.6: 2 residues within 4Å: Chain A: P.220, E.268 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.268, H2O.13, H2O.14, H2O.15 CU.7: 7 residues within 4Å: Chain A: D.127, H.129 Chain C: H.273, V.274, V.275, G.276 Ligands: CU.2 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.273, H2O.13, H2O.14 CU.8: 3 residues within 4Å: Chain A: T.277, V.278 Chain B: H.132 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:T.277, A:V.278, B:H.132, H2O.2 CU.9: 1 residues within 4Å: Chain A: H.291 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.291, H2O.8 CU.13: 4 residues within 4Å: Chain B: H.124, C.164, H.172, M.177 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.124, B:C.164, B:H.172 CU.14: 6 residues within 4Å: Chain A: H.273, H.323 Chain B: D.127, H.129, H.163 Ligands: CU.19 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.129, B:H.163, A:H.323, H2O.15, H2O.28 CU.15: 2 residues within 4Å: Chain B: H.71, H.112 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.71, B:H.112, H2O.17, H2O.25 CU.16: 1 residues within 4Å: Chain B: H.68 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.68, H2O.29 CU.17: 1 residues within 4Å: Chain B: D.196 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.196, H2O.24, H2O.24, H2O.27, H2O.29 CU.18: 2 residues within 4Å: Chain B: P.220, E.268 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.268, H2O.27, H2O.28, H2O.29 CU.19: 7 residues within 4Å: Chain A: H.273, V.274, V.275, G.276 Chain B: D.127, H.129 Ligands: CU.14 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.273, H2O.28, H2O.28 CU.20: 3 residues within 4Å: Chain B: T.277, V.278 Chain C: H.132 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:T.277, B:V.278, C:H.132, H2O.17 CU.21: 1 residues within 4Å: Chain B: H.291 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.291, H2O.23 CU.25: 4 residues within 4Å: Chain C: H.124, C.164, H.172, M.177 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.124, C:C.164, C:H.172 CU.26: 6 residues within 4Å: Chain B: H.273, H.323 Chain C: D.127, H.129, H.163 Ligands: CU.31 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.129, C:H.163, B:H.323, H2O.30, H2O.43 CU.27: 2 residues within 4Å: Chain C: H.71, H.112 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.71, C:H.112, H2O.31, H2O.40 CU.28: 1 residues within 4Å: Chain C: H.68 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.68 CU.29: 1 residues within 4Å: Chain C: D.196 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.196, H2O.39, H2O.39, H2O.42, H2O.44 CU.30: 2 residues within 4Å: Chain C: P.220, E.268 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.268, H2O.42, H2O.43, H2O.44 CU.31: 7 residues within 4Å: Chain B: H.273, V.274, V.275, G.276 Chain C: D.127, H.129 Ligands: CU.26 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.273, H2O.43, H2O.43 CU.32: 3 residues within 4Å: Chain A: H.132 Chain C: T.277, V.278 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.132, C:T.277, C:V.278, H2O.31 CU.33: 1 residues within 4Å: Chain C: H.291 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.291, H2O.38

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

MPD.10: 6 residues within 4Å: Chain A: D.192, V.195, D.196, R.197, E.198, R.258 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.195 Water bridges: A:E.198, A:E.198 MPD.11: 3 residues within 4Å: Chain A: K.51, G.52, K.90 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.51 Hydrogen bonds: A:G.52, A:K.90 MPD.22: 6 residues within 4Å: Chain B: D.192, V.195, D.196, R.197, E.198, R.258 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.195 Water bridges: B:E.198, B:E.198 MPD.23: 3 residues within 4Å: Chain B: K.51, G.52, K.90 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.51 Hydrogen bonds: B:G.52, B:K.90 MPD.34: 6 residues within 4Å: Chain C: D.192, V.195, D.196, R.197, E.198, R.258 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.195 Water bridges: C:E.198, C:E.198 MPD.35: 3 residues within 4Å: Chain C: K.51, G.52, K.90 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.51 Hydrogen bonds: C:G.52, C:K.90

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

SO4.12: 5 residues within 4Å: Chain A: Y.222, T.241, Q.329, K.330, G.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.329 Water bridges: A:Q.329 SO4.24: 5 residues within 4Å: Chain B: Y.222, T.241, Q.329, K.330, G.331 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.329 Water bridges: B:Q.329 SO4.36: 5 residues within 4Å: Chain C: Y.222, T.241, Q.329, K.330, G.331 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.329 Water bridges: C:Q.329

Links

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Citation

Fukuda, Y. et al., Structural evidence of the flexibility of the CuM site. To be Published

Release Date

2015-11-18

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase