SMTL ID : 4ysd.1

Room temperature structure of copper nitrite reductase from Geobacillus thermodenitrificans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-trimer

Ligands

36 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: 6 residues within 4Å: Chain A: D.98, H.100, H.134 Chain B: H.244, H.294 Ligands: CU.11 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.134, B:H.294, H2O.1, H2O.7 CU.3: 2 residues within 4Å: Chain A: D.55, T.212 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.55, A:D.55, H2O.1, H2O.2 CU.4: 1 residues within 4Å: Chain A: H.39 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.39, H2O.7 CU.5: 2 residues within 4Å: Chain A: D.167 Ligands: ACY.13 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.167, H2O.1, H2O.1, H2O.1, H2O.2 CU.6: 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.5, H2O.7 CU.7: 5 residues within 4Å: Chain A: M.270 Chain B: M.270 Chain C: M.270 Ligands: CU.20, CU.33 No protein-ligand interaction detected (PLIP) CU.8: 4 residues within 4Å: Chain A: I.18, H.21, W.63, Y.180 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.21, H2O.8 CU.9: 3 residues within 4Å: Chain A: P.191, E.239, H.298 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.239, A:H.298, H2O.7 CU.10: 2 residues within 4Å: Chain A: E.169, Y.231 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.169, A:E.169, H2O.3 CU.11: 6 residues within 4Å: Chain A: D.98, H.100 Chain B: H.244, V.246, G.247 Ligands: CU.2 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.244, H2O.1, H2O.5 CU.12: 1 residues within 4Å: Chain A: E.239 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.239, H2O.6, H2O.6, H2O.8 CU.14: 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.15: 6 residues within 4Å: Chain B: D.98, H.100, H.134 Chain C: H.244, H.294 Ligands: CU.24 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: B:H.100, B:H.134, C:H.294, H2O.9, H2O.16 CU.16: 2 residues within 4Å: Chain B: D.55, T.212 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.55, B:D.55, H2O.9, H2O.10 CU.17: 1 residues within 4Å: Chain B: H.39 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.39, H2O.15 CU.18: 2 residues within 4Å: Chain B: D.167 Ligands: ACY.26 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.167, H2O.9, H2O.9, H2O.9, H2O.10 CU.19: 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.13, H2O.16 CU.20: 5 residues within 4Å: Chain A: M.270 Chain B: M.270 Chain C: M.270 Ligands: CU.7, CU.33 No protein-ligand interaction detected (PLIP) CU.21: 4 residues within 4Å: Chain B: I.18, H.21, W.63, Y.180 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.21, H2O.16 CU.22: 3 residues within 4Å: Chain B: P.191, E.239, H.298 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.239, B:H.298, H2O.15 CU.23: 2 residues within 4Å: Chain B: E.169, Y.231 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.169, B:E.169, H2O.11 CU.24: 6 residues within 4Å: Chain B: D.98, H.100 Chain C: H.244, V.246, G.247 Ligands: CU.15 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.244, H2O.9, H2O.13 CU.25: 1 residues within 4Å: Chain B: E.239 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.239, H2O.14, H2O.14, H2O.16 CU.27: 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.28: 6 residues within 4Å: Chain A: H.244, H.294 Chain C: D.98, H.100, H.134 Ligands: CU.37 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:H.100, C:H.134, A:H.294, H2O.17, H2O.24 CU.29: 2 residues within 4Å: Chain C: D.55, T.212 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.55, C:D.55, H2O.18, H2O.18 CU.30: 1 residues within 4Å: Chain C: H.39 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.39, H2O.24 CU.31: 2 residues within 4Å: Chain C: D.167 Ligands: ACY.39 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.167, H2O.17, H2O.17, H2O.17, H2O.18 CU.32: 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.21, H2O.24 CU.33: 5 residues within 4Å: Chain A: M.270 Chain B: M.270 Chain C: M.270 Ligands: CU.7, CU.20 No protein-ligand interaction detected (PLIP) CU.34: 4 residues within 4Å: Chain C: I.18, H.21, W.63, Y.180 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.21, H2O.24 CU.35: 3 residues within 4Å: Chain C: P.191, E.239, H.298 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.239, C:H.298, H2O.23 CU.36: 2 residues within 4Å: Chain C: E.169, Y.231 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.169, C:E.169, H2O.19 CU.37: 6 residues within 4Å: Chain A: H.244, V.246, G.247 Chain C: D.98, H.100 Ligands: CU.28 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.244, H2O.17, H2O.21 CU.38: 1 residues within 4Å: Chain C: E.239 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.239, H2O.22, H2O.22, H2O.24

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

ACY.13: 3 residues within 4Å: Chain A: E.165, D.167 Ligands: CU.5 No protein-ligand interaction detected (PLIP) ACY.26: 3 residues within 4Å: Chain B: E.165, D.167 Ligands: CU.18 No protein-ligand interaction detected (PLIP) ACY.39: 3 residues within 4Å: Chain C: E.165, D.167 Ligands: CU.31 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, Y. et al., Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography. J.Biochem. (2016)

Release Date

2016-02-24

Peptides

Nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Nitrite reductase

Related Entries With Identical Sequence