SMTL ID : 3x1g.1

H294M mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans showing two coordination geometries at the T2Cu site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

18 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: 5 residues within 4Å: Chain A: D.127, H.129, H.163 Chain C: H.273, M.323 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.129, A:H.163, H2O.15 CU.3: 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.15 CU.4: 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.11, H2O.11, H2O.13, H2O.15 CU.5: 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.5 CU.6: 3 residues within 4Å: Chain A: P.220, E.268, H.327 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.268, A:H.327, H2O.16, H2O.17 CU.10: 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.11: 5 residues within 4Å: Chain A: H.273, M.323 Chain B: D.127, H.129, H.163 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.129, B:H.163, H2O.31 CU.12: 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.31 CU.13: 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.27, H2O.27, H2O.29, H2O.31 CU.14: 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.18, H2O.21 CU.15: 3 residues within 4Å: Chain B: P.220, E.268, H.327 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.268, B:H.327, H2O.33, H2O.33 CU.19: 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.20: 5 residues within 4Å: Chain B: H.273, M.323 Chain C: D.127, H.129, H.163 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.129, C:H.163, H2O.47 CU.21: 1 residues within 4Å: Chain C: H.68 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.68, H2O.48 CU.22: 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.44, H2O.44, H2O.46, H2O.48 CU.23: 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.34, H2O.38 CU.24: 3 residues within 4Å: Chain C: P.220, E.268, H.327 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.268, C:H.327, H2O.49, H2O.50

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

ACY.7: 6 residues within 4Å: Chain A: D.127, H.163, G.165, V.169 Chain C: V.275 Ligands: ACY.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.169 Hydrogen bonds: A:D.127 Salt bridges: A:H.163 ACY.8: 4 residues within 4Å: Chain C: P.319, V.333, M.335 Ligands: ACY.7 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.333 ACY.16: 6 residues within 4Å: Chain A: V.275 Chain B: D.127, H.163, G.165, V.169 Ligands: ACY.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.169 Hydrogen bonds: B:D.127 Salt bridges: B:H.163 ACY.17: 4 residues within 4Å: Chain A: P.319, V.333, M.335 Ligands: ACY.16 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.333 ACY.25: 6 residues within 4Å: Chain B: V.275 Chain C: D.127, H.163, G.165, V.169 Ligands: ACY.26 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.169 Hydrogen bonds: C:D.127 Salt bridges: C:H.163 ACY.26: 4 residues within 4Å: Chain B: P.319, V.333, M.335 Ligands: ACY.25 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.333

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

MPD.9: 6 residues within 4Å: Chain A: D.192, V.195, D.196, R.197, E.198, R.258 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.192, A:V.195 Hydrogen bonds: A:E.198 Water bridges: A:D.196, A:E.198, A:E.198, A:E.198 MPD.18: 6 residues within 4Å: Chain B: D.192, V.195, D.196, R.197, E.198, R.258 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.192, B:V.195 Hydrogen bonds: B:E.198 Water bridges: B:D.196, B:E.198, B:E.198, B:E.198 MPD.27: 6 residues within 4Å: Chain C: D.192, V.195, D.196, R.197, E.198, R.258 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.192, C:V.195 Hydrogen bonds: C:E.198 Water bridges: C:D.196, C:E.198, C:E.198, C:E.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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

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