SMTL ID : 3x1f.1

H294M mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-trimer

Ligands

21 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: 4 residues within 4Å: Chain A: H.129, H.163 Chain B: 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.14 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.13 CU.4: 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.3, H2O.5 CU.5: 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.2, H2O.14 CU.6: 2 residues within 4Å: Chain A: D.196 Ligands: ACY.12 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.196, A:D.196, H2O.1, H2O.9, H2O.13 CU.7: 5 residues within 4Å: Chain A: M.299 Chain B: M.299 Chain C: M.299 Ligands: CU.20, CU.33 No protein-ligand interaction detected (PLIP) CU.14: 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.15: 4 residues within 4Å: Chain B: H.129, H.163 Chain C: H.273, M.323 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.129, B:H.163, H2O.28 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.27 CU.17: 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.19 CU.18: 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.16, H2O.28 CU.19: 2 residues within 4Å: Chain B: D.196 Ligands: ACY.25 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.196, B:D.196, H2O.15, H2O.23, H2O.27 CU.20: 5 residues within 4Å: Chain A: M.299 Chain B: M.299 Chain C: M.299 Ligands: CU.7, CU.33 No protein-ligand interaction detected (PLIP) CU.27: 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.28: 4 residues within 4Å: Chain A: H.273, M.323 Chain C: 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.42 CU.29: 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.41 CU.30: 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.33 CU.31: 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.30, H2O.42 CU.32: 2 residues within 4Å: Chain C: D.196 Ligands: ACY.38 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.196, C:D.196, H2O.29, H2O.37, H2O.41 CU.33: 5 residues within 4Å: Chain A: M.299 Chain B: M.299 Chain C: M.299 Ligands: CU.7, CU.20 No protein-ligand interaction detected (PLIP)

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

ACY.8: 6 residues within 4Å: Chain A: D.127, H.163, G.165, V.169 Chain B: V.275 Ligands: ACY.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.169 Salt bridges: A:H.163 ACY.9: 1 residues within 4Å: Ligands: ACY.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.167 ACY.12: 5 residues within 4Å: Chain A: D.196, V.253, G.254, E.255 Ligands: CU.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.255, A:K.256 ACY.13: 5 residues within 4Å: Chain A: K.156, P.157, N.287, N.289 Chain B: Q.293 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:K.156 Hydrogen bonds: A:N.287, A:N.289, B:Q.293 Salt bridges: A:K.156 ACY.21: 6 residues within 4Å: Chain B: D.127, H.163, G.165, V.169 Chain C: V.275 Ligands: ACY.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.169 Salt bridges: B:H.163 ACY.22: 1 residues within 4Å: Ligands: ACY.21 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.167 ACY.25: 5 residues within 4Å: Chain B: D.196, V.253, G.254, E.255 Ligands: CU.19 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.255, B:K.256 ACY.26: 5 residues within 4Å: Chain B: K.156, P.157, N.287, N.289 Chain C: Q.293 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:K.156 Hydrogen bonds: B:N.287, B:N.289, C:Q.293 Salt bridges: B:K.156 ACY.34: 6 residues within 4Å: Chain A: V.275 Chain C: D.127, H.163, G.165, V.169 Ligands: ACY.35 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.169 Salt bridges: C:H.163 ACY.35: 1 residues within 4Å: Ligands: ACY.34 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.167 ACY.38: 5 residues within 4Å: Chain C: D.196, V.253, G.254, E.255 Ligands: CU.32 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.255, C:K.256 ACY.39: 5 residues within 4Å: Chain A: Q.293 Chain C: K.156, P.157, N.287, N.289 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:K.156 Hydrogen bonds: C:N.287, C:N.289, A:Q.293 Salt bridges: C:K.156 Water bridges: A:D.280

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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.192, A:V.195 Hydrogen bonds: A:D.196, A:E.198 Water bridges: A:E.198, A:Y.260 MPD.11: 7 residues within 4Å: Chain A: D.84, S.221, Y.222, T.241, Q.329, K.330, G.331 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.222, A:K.330 Water bridges: A:T.241, A:T.241 MPD.23: 6 residues within 4Å: Chain B: D.192, V.195, D.196, R.197, E.198, R.258 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:D.192, B:V.195 Hydrogen bonds: B:D.196, B:E.198 Water bridges: B:E.198, B:Y.260 MPD.24: 7 residues within 4Å: Chain B: D.84, S.221, Y.222, T.241, Q.329, K.330, G.331 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.222, B:K.330 Water bridges: B:T.241, B:T.241 MPD.36: 6 residues within 4Å: Chain C: D.192, V.195, D.196, R.197, E.198, R.258 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:D.192, C:V.195 Hydrogen bonds: C:D.196, C:E.198 Water bridges: C:E.198, C:Y.260 MPD.37: 7 residues within 4Å: Chain C: D.84, S.221, Y.222, T.241, Q.329, K.330, G.331 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.222, C:K.330 Water bridges: C:T.241, C:T.241

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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