SMTL ID : 5ytm.1

C135A mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans determined by in-ouse source

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.95, A:H.143 CU.2: 5 residues within 4Å: Chain A: D.98, H.100, H.134 Chain C: H.244, H.294 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.134, C:H.294, H2O.1, H2O.10 CU.3: 2 residues within 4Å: Chain A: H.42, H.83 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.42, A:H.83, H2O.10 CU.4: 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.5 CU.10: 5 residues within 4Å: Chain B: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.95, B:H.143 CU.11: 5 residues within 4Å: Chain A: H.244, H.294 Chain B: D.98, H.100, H.134 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.294, B:H.100, B:H.134, H2O.14, H2O.24 CU.12: 2 residues within 4Å: Chain B: H.42, H.83 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.42, B:H.83, H2O.24 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.14, H2O.19 CU.19: 5 residues within 4Å: Chain C: W.63, H.95, A.135, H.143, M.148 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.95, C:H.143 CU.20: 5 residues within 4Å: Chain B: H.244, H.294 Chain C: D.98, H.100, H.134 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, B:H.294, H2O.28, H2O.38 CU.21: 2 residues within 4Å: Chain C: H.42, H.83 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.42, C:H.83, H2O.37 CU.22: 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.28, H2O.32

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

ACY.5: 3 residues within 4Å: Chain A: Y.180, N.181, D.182 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.180, A:D.182, A:D.182 ACY.6: 4 residues within 4Å: Chain A: H.103, N.126, K.127 Chain C: T.284 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.126 Salt bridges: A:H.103, A:K.127 ACY.14: 3 residues within 4Å: Chain B: Y.180, N.181, D.182 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Y.180, B:D.182, B:D.182 ACY.15: 4 residues within 4Å: Chain A: T.284 Chain B: H.103, N.126, K.127 3 PLIP interactions: 3 interactions with chain B Water bridges: B:N.126 Salt bridges: B:H.103, B:K.127 ACY.23: 3 residues within 4Å: Chain C: Y.180, N.181, D.182 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Y.180, C:D.182, C:D.182 ACY.24: 4 residues within 4Å: Chain B: T.284 Chain C: H.103, N.126, K.127 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.126 Salt bridges: C:H.103, C:K.127

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

MRD.7: 6 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.166 Hydrogen bonds: A:D.163, A:R.229 Water bridges: A:E.169, A:E.169, A:Y.231 MRD.16: 6 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.166 Hydrogen bonds: B:D.163, B:R.229 Water bridges: B:E.169, B:E.169, B:Y.231 MRD.25: 6 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:V.166 Hydrogen bonds: C:D.163, C:R.229 Water bridges: C:E.169, C:E.169, C:Y.231

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

SO4.8: 5 residues within 4Å: Chain A: H.262 Chain B: H.262 Chain C: H.262 Ligands: SO4.17, SO4.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.262 SO4.9: 5 residues within 4Å: Chain C: D.55, T.212, Q.300, K.301, G.302 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.55, C:Q.300 Water bridges: C:Q.300 SO4.17: 5 residues within 4Å: Chain A: H.262 Chain B: H.262 Chain C: H.262 Ligands: SO4.8, SO4.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.262 SO4.18: 5 residues within 4Å: Chain A: D.55, T.212, Q.300, K.301, G.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.55, A:Q.300 Water bridges: A:Q.300 SO4.26: 5 residues within 4Å: Chain A: H.262 Chain B: H.262 Chain C: H.262 Ligands: SO4.8, SO4.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.262 SO4.27: 5 residues within 4Å: Chain B: D.55, T.212, Q.300, K.301, G.302 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.55, B:Q.300 Water bridges: B:Q.300

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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