SMTL ID : 9kws.1

D98N mutant of a copper-containing nitrite reductase from Geobacillus thermodenitrificans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 7 residues within 4Å: Chain A: W.63, H.95, S.96, C.135, T.137, 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: 7 residues within 4Å: Chain A: N.98, H.100, H.134 Chain C: H.244, H.294, F.296 Ligands: CL.8 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Metal complexes: A:H.100, A:H.134, C:H.294 CU.5: 3 residues within 4Å: Chain A: V.36, 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.12 CU.6: 2 residues within 4Å: Chain A: P.38, H.39 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.39, H2O.8, H2O.10, H2O.11 CU.7: 3 residues within 4Å: Chain A: D.167, E.226, K.227 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.167, A:D.167, H2O.1, H2O.1, H2O.6 CU.11: 7 residues within 4Å: Chain B: W.63, H.95, S.96, C.135, T.137, H.143, M.148 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.95, B:C.135, B:H.143 CU.12: 7 residues within 4Å: Chain A: H.244, H.294, F.296 Chain B: N.98, H.100, H.134 Ligands: CL.18 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.100, B:H.134, A:H.294 CU.15: 3 residues within 4Å: Chain B: V.36, 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.28 CU.16: 2 residues within 4Å: Chain B: P.38, H.39 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.39, H2O.24, H2O.26, H2O.27 CU.17: 3 residues within 4Å: Chain B: D.167, E.226, K.227 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.167, B:D.167, H2O.17, H2O.18, H2O.23 CU.21: 7 residues within 4Å: Chain C: W.63, H.95, S.96, C.135, T.137, H.143, M.148 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.95, C:C.135, C:H.143 CU.22: 7 residues within 4Å: Chain B: H.244, H.294, F.296 Chain C: N.98, H.100, H.134 Ligands: CL.28 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Metal complexes: C:H.100, C:H.134, B:H.294 CU.25: 3 residues within 4Å: Chain C: V.36, 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.45 CU.26: 2 residues within 4Å: Chain C: P.38, H.39 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.39, H2O.41, H2O.43, H2O.44 CU.27: 3 residues within 4Å: Chain C: D.167, E.226, K.227 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.167, C:D.167, H2O.33, H2O.34, H2O.39

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

MPD.3: 7 residues within 4Å: Chain A: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.163, A:V.166 Hydrogen bonds: A:E.169 Water bridges: A:D.167, A:E.169, A:E.169, A:E.169 MPD.13: 7 residues within 4Å: Chain B: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:D.163, B:V.166 Hydrogen bonds: B:E.169 Water bridges: B:D.167, B:E.169, B:E.169, B:E.169 MPD.23: 7 residues within 4Å: Chain C: D.163, V.166, D.167, R.168, E.169, R.229, Y.231 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:D.163, C:V.166 Hydrogen bonds: C:E.169 Water bridges: C:D.167, C:E.169, C:E.169, C:E.169

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

ACY.4: 5 residues within 4Å: Chain A: H.103, N.126, K.127 Chain C: T.282, T.284 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.126, A:N.126 Salt bridges: A:H.103, A:K.127 ACY.14: 5 residues within 4Å: Chain A: T.282, T.284 Chain B: H.103, N.126, K.127 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.126, B:N.126 Salt bridges: B:H.103, B:K.127 ACY.24: 5 residues within 4Å: Chain B: T.282, T.284 Chain C: H.103, N.126, K.127 4 PLIP interactions: 4 interactions with chain C Water bridges: C:N.126, C:N.126 Salt bridges: C:H.103, C:K.127

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 9 residues within 4Å: Chain A: N.98, H.100, H.134 Chain C: H.244, V.246, V.292, H.294, F.296 Ligands: CU.2 Ligand excluded by PLIP CL.18: 9 residues within 4Å: Chain A: H.244, V.246, V.292, H.294, F.296 Chain B: N.98, H.100, H.134 Ligands: CU.12 Ligand excluded by PLIP CL.28: 9 residues within 4Å: Chain B: H.244, V.246, V.292, H.294, F.296 Chain C: N.98, H.100, H.134 Ligands: CU.22 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.9: 5 residues within 4Å: Chain A: V.190, P.191, E.239, H.298 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.239 NA.10: 5 residues within 4Å: Chain A: V.190, P.191, E.239 Chain C: N.297 Ligands: NA.9 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:E.239, A:E.239, C:N.297 NA.19: 5 residues within 4Å: Chain B: V.190, P.191, E.239, H.298 Ligands: NA.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.239 NA.20: 5 residues within 4Å: Chain A: N.297 Chain B: V.190, P.191, E.239 Ligands: NA.19 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:E.239, B:E.239, A:N.297 NA.29: 5 residues within 4Å: Chain C: V.190, P.191, E.239, H.298 Ligands: NA.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.239 NA.30: 5 residues within 4Å: Chain B: N.297 Chain C: V.190, P.191, E.239 Ligands: NA.29 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:E.239, C:E.239, B:N.297

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Structural basis of cuproenzyme nitrite reduction at the level of a single hydrogen atom. J.Biol.Chem. (2025)

Release Date

2025-06-11

Peptides

Copper-containing nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Copper-containing nitrite reductase