SMTL ID : 2xts.1

Crystal Structure of the Sulfane Dehydrogenase SoxCD from Paracoccus pantotrophus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MTE: PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER(Non-covalent)

MTE.1: 23 residues within 4Å: Chain A: F.72, E.73, R.74, H.75, H.76, C.118, C.120, H.144, G.173, D.175, S.177, N.179, E.206, H.207, R.212, G.220, N.221, W.223, V.224, K.225, W.226, Y.246 Ligands: 2MO.2 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.74, A:R.74, A:R.74, A:H.76, A:S.177, A:S.177, A:N.179, A:R.212, A:W.223, A:K.225, A:K.225 Water bridges: A:S.77, A:D.175 Salt bridges: A:H.144, A:D.175, A:H.207, A:R.212, A:K.225 pi-Cation interactions: A:K.225 MTE.12: 23 residues within 4Å: Chain C: F.72, E.73, R.74, H.75, H.76, C.118, C.120, H.144, G.173, D.175, S.177, N.179, E.206, H.207, R.212, G.220, N.221, W.223, V.224, K.225, W.226, Y.246 Ligands: 2MO.13 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:R.74, C:R.74, C:R.74, C:H.76, C:S.177, C:S.177, C:N.179, C:R.212, C:W.223, C:K.225, C:K.225 Water bridges: C:S.77 Salt bridges: C:H.144, C:D.175, C:H.207, C:R.212, C:K.225 pi-Cation interactions: C:K.225

2 x 2MO: MOLYBDENUM (IV)OXIDE(Non-covalent)

2MO.2: 7 residues within 4Å: Chain A: R.74, C.120, A.121, G.220, N.221, Y.246 Ligands: MTE.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.74, A:A.121, A:N.221 2MO.13: 7 residues within 4Å: Chain C: R.74, C.120, A.121, G.220, N.221, Y.246 Ligands: MTE.12 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.74, C:A.121, C:N.221, C:Y.246

2 x CO: COBALT (II) ION(Non-covalent)

CO.3: 3 residues within 4Å: Chain A: E.219, T.259, H.369 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.219, A:T.259, A:T.259, A:H.369, H2O.12, H2O.12 CO.14: 3 residues within 4Å: Chain C: E.219, T.259, H.369 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.219, C:T.259, C:T.259, C:H.369, H2O.31, H2O.31

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: T.354, K.355, D.356, I.373, T.375, E.388, I.389 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.354, A:K.355, A:D.356, A:I.373, A:I.389 Water bridges: A:T.375, A:T.375 GOL.5: 6 residues within 4Å: Chain A: H.59, L.61, T.269, S.270, S.287 Chain C: R.111 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:R.111, C:R.111, A:T.269, A:S.270 Water bridges: A:S.270 GOL.6: 3 residues within 4Å: Chain A: G.129, R.364 Ligands: GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.129, A:R.364 Water bridges: A:N.365, A:N.365 GOL.10: 6 residues within 4Å: Chain B: D.67, G.68, L.70, S.81, P.141, N.142 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.68, B:P.141 Water bridges: B:L.70, B:G.80 GOL.11: 6 residues within 4Å: Chain A: G.129, G.130, A.131, Q.132 Chain B: K.176 Ligands: GOL.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.129, A:A.131, A:Q.132, B:K.176 GOL.15: 7 residues within 4Å: Chain C: T.354, K.355, D.356, I.373, T.375, E.388, I.389 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.355, C:D.356, C:D.356, C:I.373, C:T.375, C:I.389 GOL.16: 6 residues within 4Å: Chain A: R.111 Chain C: H.59, L.61, T.269, S.270, S.287 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.269, C:T.269, C:S.270, A:R.111, A:R.111 GOL.22: 7 residues within 4Å: Chain C: K.38, Q.40 Chain D: E.186, D.187, P.188, A.193, G.194 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:K.38, C:Q.40, D:D.187, D:D.187, D:G.194 Water bridges: C:Q.40 GOL.23: 5 residues within 4Å: Chain D: D.67, G.68, S.81, P.141, N.142 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.68, D:P.141 Water bridges: D:D.67, D:D.67, D:L.70, D:N.142

2 x HEC: HEME C(Covalent)

HEC.7: 20 residues within 4Å: Chain A: S.51, H.76, R.240, S.244 Chain B: N.45, C.46, S.48, C.49, H.50, W.60, P.61, L.63, W.83, Y.92, V.93, M.97, P.98, F.99, L.105, I.113 31 PLIP interactions: 21 interactions with chain B, 10 interactions with chain A, Hydrophobic interactions: B:W.60, B:W.60, B:P.61, B:L.63, B:L.63, B:W.83, B:Y.92, B:V.93, B:V.93, B:M.97, B:P.98, B:P.98, B:F.99, B:F.99, B:L.105, B:I.113 Water bridges: B:V.62, B:W.83, B:Y.92, B:Y.92, A:R.240, A:R.240, A:K.245, A:K.245 Metal complexes: B:H.50 Hydrogen bonds: A:S.51, A:S.244 Salt bridges: A:H.76, A:R.240, A:R.240, A:K.245 HEC.17: 22 residues within 4Å: Chain C: E.47, S.51, H.76, R.240, S.244 Chain D: F.42, N.45, C.46, S.48, C.49, H.50, W.60, P.61, L.63, W.83, Y.92, V.93, M.97, P.98, F.99, L.105, I.113 31 PLIP interactions: 20 interactions with chain D, 11 interactions with chain C, Hydrophobic interactions: D:F.42, D:W.60, D:W.60, D:P.61, D:L.63, D:L.63, D:W.83, D:Y.92, D:V.93, D:V.93, D:M.97, D:P.98, D:P.98, D:F.99, D:F.99, D:L.105, D:I.113 Water bridges: D:V.62, D:W.83, C:R.240, C:R.240, C:K.245, C:K.245 Metal complexes: D:H.50 Hydrogen bonds: C:S.51, C:H.76, C:S.244 Salt bridges: C:H.76, C:R.240, C:R.240, C:K.245

6 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain B: G.190 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:G.190, H2O.3, H2O.5, H2O.5, H2O.18 CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.19: 1 residues within 4Å: Chain D: E.12 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.12, H2O.31 CA.20: 1 residues within 4Å: Chain D: T.104 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.104, H2O.34, H2O.34, H2O.34 CA.21: 1 residues within 4Å: Chain D: G.190 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:G.190, H2O.23, H2O.23, H2O.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zander, U. et al., Structural Basis for the Oxidation of Protein-Bound Sulfur by the Sulfur Cycle Molybdohemo-Enzyme Sulfane Dehydrogenase Soxcd. J.Biol.Chem. (2011)

Release Date

2010-12-08

Peptides

SULFITE DEHYDROGENASE: AC
CYTOCHROME: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

SULFITE DEHYDROGENASE

CYTOCHROME