SMTL ID : 6sji.1

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus mutant with His 482 replaced by Gln

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

CU.1: 3 residues within 4Å: Chain A: H.128, D.236, H.303 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.128, A:D.236, A:D.236, A:H.303, H2O.10 CU.2: 3 residues within 4Å: Chain A: K.25, H.57, H.450 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.57, A:H.450, H2O.5, H2O.6 CU.5: 3 residues within 4Å: Chain B: H.128, D.236, H.303 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.128, B:D.236, B:D.236, B:H.303, H2O.19 CU.6: 3 residues within 4Å: Chain B: K.25, H.57, H.450 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.57, B:H.450, H2O.13, H2O.19 CU.7: 3 residues within 4Å: Chain C: H.128, D.236, H.303 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.128, C:D.236, C:D.236, C:H.303 CU.8: 3 residues within 4Å: Chain C: K.25, H.57, H.450 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.57, C:H.450, H2O.28, H2O.29 CU.9: 3 residues within 4Å: Chain D: H.128, D.236, H.303 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.128, D:D.236, D:D.236, D:H.303, H2O.44 CU.10: 3 residues within 4Å: Chain D: K.25, H.57, H.450 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.57, D:H.450, H2O.36, H2O.38 CU.11: 1 residues within 4Å: Chain D: H.333 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:H.333

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

SO4.3: 3 residues within 4Å: Chain A: K.105, Q.114, R.115 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.114, A:R.115, A:R.115 Water bridges: A:K.105, A:K.105, A:K.105 Salt bridges: A:K.105 SO4.4: 6 residues within 4Å: Chain A: G.50, D.51, T.52, C.53, G.96, K.100 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.50, A:T.52, A:C.53 Water bridges: A:E.97, A:K.100, A:K.100 Salt bridges: A:K.100 SO4.12: 5 residues within 4Å: Chain D: G.50, D.51, T.52, C.53, K.100 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:T.52, D:T.52, D:C.53 Water bridges: D:E.97, D:G.98, D:K.100, D:K.100 Salt bridges: D:K.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tikhonova, T.V. et al., Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2019-09-18

Peptides

thiocyanate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
J

D
K

thiocyanate dehydrogenase