SMTL ID : 5ytl.1

Crystal structure of Geobacillus thermodenitrificans copper-containing nitrite reductase determined with an anaerobically manipulated crystal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-trimer

Ligands

15 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: 5 residues within 4Å: Chain A: D.98, H.100, H.134 Chain C: H.244, H.294 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.100, A:H.134, C:H.294, H2O.5 CU.3: 2 residues within 4Å: Chain A: H.42, H.83 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.1, H2O.9 CU.4: 5 residues within 4Å: Chain A: M.270 Chain B: M.270 Chain C: M.270 Ligands: CU.12, CU.20 No protein-ligand interaction detected (PLIP) CU.5: 1 residues within 4Å: Chain A: D.167 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.167, A:D.167, H2O.1, H2O.1 CU.9: 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.10: 5 residues within 4Å: Chain A: H.244, 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.17 CU.11: 2 residues within 4Å: Chain B: H.42, H.83 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.12, H2O.21 CU.12: 5 residues within 4Å: Chain A: M.270 Chain B: M.270 Chain C: M.270 Ligands: CU.4, CU.20 No protein-ligand interaction detected (PLIP) CU.13: 1 residues within 4Å: Chain B: D.167 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.167, B:D.167, H2O.12, H2O.13 CU.17: 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.18: 5 residues within 4Å: Chain B: H.244, H.294 Chain C: D.98, H.100, H.134 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, B:H.294, H2O.29 CU.19: 2 residues within 4Å: Chain C: H.42, H.83 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.24, H2O.33 CU.20: 5 residues within 4Å: Chain A: M.270 Chain B: M.270 Chain C: M.270 Ligands: CU.4, CU.12 No protein-ligand interaction detected (PLIP) CU.21: 1 residues within 4Å: Chain C: D.167 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.167, C:D.167, H2O.24, H2O.24

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 6 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.163, A:R.229 Water bridges: A:V.166 MRD.14: 6 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.163, B:R.229 Water bridges: B:V.166 MRD.22: 6 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.163, C:R.229 Water bridges: C:V.166

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

MPD.7: 4 residues within 4Å: Chain A: K.22, G.23, D.51, K.61 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.22 Hydrogen bonds: A:K.22 MPD.15: 4 residues within 4Å: Chain B: K.22, G.23, D.51, K.61 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.22 Hydrogen bonds: B:K.22 MPD.23: 4 residues within 4Å: Chain C: K.22, G.23, D.51, K.61 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.22 Hydrogen bonds: C:K.22

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

ACY.8: 3 residues within 4Å: Chain A: R.168, L.221, A.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.221 Salt bridges: A:R.168 ACY.16: 3 residues within 4Å: Chain B: R.168, L.221, A.222 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.221 Salt bridges: B:R.168 ACY.24: 3 residues within 4Å: Chain C: R.168, L.221, A.222 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.221 Salt bridges: C:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Crystallographic study of dioxygen chemistry in a copper-containing nitrite reductase from Geobacillus thermodenitrificans. Acta Crystallogr D Struct Biol (2018)

Release Date

2018-08-22

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase

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