SMTL ID : 3or1.1

Crystal structure of dissimilatory sulfite reductase I (DsrI)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x SO3: SULFITE ION(Non-covalent)

SO3.1: 6 residues within 4Å: Chain A: R.101, R.172, K.213, K.215 Chain C: C.104 Ligands: SRM.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.101, A:R.101, A:R.172, A:R.172, A:K.213, A:K.213, A:K.215 Water bridges: A:T.136, A:T.136, A:G.168 SO3.8: 6 residues within 4Å: Chain D: R.101, R.172, K.213, K.215 Chain F: C.104 Ligands: SRM.9 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.101, D:R.101, D:R.172, D:R.172, D:K.213, D:K.213, D:K.215

4 x SRM: SIROHEME(Non-covalent)

SRM.2: 33 residues within 4Å: Chain A: I.81, R.83, R.101, G.134, S.135, T.136, G.137, D.138, Y.212, K.213, K.215, K.217, R.231, K.332, A.333, V.335, R.376, R.378 Chain B: R.71, H.144, T.145, Q.146, Y.150, C.151, H.152, N.191, C.193, G.194, T.266 Chain C: G.103, C.104 Ligands: SO3.1, SF4.6 38 PLIP interactions: 30 interactions with chain A, 7 interactions with chain B, 1 interactions with chain C, Hydrogen bonds: A:S.135, A:S.135, A:T.136, A:G.137, A:D.138, A:Y.212, A:A.333, B:Q.146 Water bridges: A:R.83, A:R.83, A:R.101, A:T.136, A:V.335, A:R.378, B:N.191, C:G.103 Salt bridges: A:R.83, A:R.83, A:R.101, A:K.213, A:K.213, A:K.213, A:K.215, A:K.215, A:K.217, A:R.231, A:K.332, A:R.376, A:R.378, A:R.378, B:R.71, B:H.152 pi-Cation interactions: A:R.101, A:K.213, A:K.215 Hydrophobic interactions: B:Q.146, B:N.191 Metal complexes: B:C.193 SRM.5: 34 residues within 4Å: Chain A: C.177, L.178, R.182, C.183, E.184, F.185, N.223, G.224, C.225, N.262, N.311 Chain B: H.44, I.46, L.52, H.54, R.66, R.94, T.96, T.97, R.98, N.100, E.102, G.134, T.135, G.136, S.140, I.181, R.183, K.288, I.289, S.290, R.292, R.336 Ligands: SF4.4 43 PLIP interactions: 36 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.52, B:T.96, B:R.98, B:R.183, A:L.178, A:F.185, A:N.223 Hydrogen bonds: B:T.97, B:N.100, B:G.136, B:S.140, B:R.183, B:C.198, B:I.289, B:S.290, B:S.290, B:S.290, A:L.178, A:N.262, A:N.311 Water bridges: B:R.94, B:T.97, B:R.98, B:R.98, B:G.134, B:R.183, B:K.288, B:R.292, B:R.336, A:R.231 Salt bridges: B:H.44, B:H.54, B:R.66, B:R.66, B:R.94, B:R.98, B:R.183, B:K.288, B:R.292, B:R.292, B:R.336, B:R.336 pi-Cation interactions: B:R.183 SRM.9: 32 residues within 4Å: Chain D: I.81, R.83, R.101, G.134, S.135, T.136, G.137, D.138, Y.212, K.213, K.215, K.217, R.231, K.332, A.333, V.335, R.376, R.378 Chain E: R.71, H.144, T.145, Q.146, Y.150, C.151, H.152, N.191, C.193, G.194 Chain F: G.103, C.104 Ligands: SO3.8, SF4.13 37 PLIP interactions: 29 interactions with chain D, 7 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: D:A.333, E:T.145, E:Q.146, E:N.191 Hydrogen bonds: D:G.134, D:S.135, D:S.135, D:T.136, D:G.137, D:D.138, D:Y.212, D:A.333 Water bridges: D:R.83, D:R.83, D:R.101, D:V.335, D:R.378, E:N.191, F:G.103 Salt bridges: D:R.83, D:R.83, D:R.101, D:K.213, D:K.213, D:K.215, D:K.215, D:K.217, D:R.231, D:K.332, D:R.376, D:R.378, D:R.378, E:R.71, E:H.152 pi-Cation interactions: D:K.213, D:K.215 Metal complexes: E:C.193 SRM.12: 34 residues within 4Å: Chain D: C.177, L.178, R.182, C.183, E.184, F.185, N.223, G.224, C.225, N.262, N.311 Chain E: H.44, I.46, L.52, H.54, R.66, R.94, T.96, T.97, R.98, N.100, E.102, G.134, T.135, G.136, S.140, I.181, R.183, K.288, I.289, S.290, R.292, R.336 Ligands: SF4.11 41 PLIP interactions: 34 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:R.98, E:R.183, E:I.289, D:L.178, D:F.185, D:N.223 Hydrogen bonds: E:T.97, E:N.100, E:G.136, E:S.140, E:R.183, E:I.289, E:S.290, E:S.290, E:S.290, D:L.178, D:N.262, D:N.311 Water bridges: E:R.94, E:G.134, E:R.183, E:C.198, E:R.292, E:R.292, E:R.292, E:R.292, E:R.336, E:R.336, D:R.231 Salt bridges: E:H.44, E:H.54, E:R.66, E:R.66, E:R.94, E:R.98, E:R.183, E:R.292, E:R.292, E:R.336, E:R.336 pi-Cation interactions: E:R.183

8 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.3: 11 residues within 4Å: Chain A: C.284, P.285, C.288, M.289, C.303, T.304, R.305, C.306, M.307, H.308, C.309 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.284, A:C.303, A:C.306, A:C.309 SF4.4: 13 residues within 4Å: Chain A: C.177, L.178, G.179, C.183, F.185, A.186, D.219, G.220, C.221, N.223, G.224, C.225 Ligands: SRM.5 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.219 Metal complexes: A:C.177, A:C.183, A:C.221, A:C.225 SF4.6: 10 residues within 4Å: Chain B: T.145, Q.146, C.151, T.153, P.154, C.188, C.189, N.191, C.193 Ligands: SRM.2 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.151, B:C.188, B:C.189, B:C.193 SF4.7: 12 residues within 4Å: Chain B: P.211, C.231, T.233, A.235, V.236, I.253, C.258, M.259, Y.260, C.261, G.262, C.264 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.231, B:C.258, B:C.261, B:C.264 SF4.10: 13 residues within 4Å: Chain D: I.244, C.284, P.285, C.288, M.289, I.298, C.303, T.304, R.305, C.306, M.307, H.308, C.309 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.284, D:C.303, D:C.306, D:C.309 SF4.11: 12 residues within 4Å: Chain D: C.177, L.178, C.183, F.185, A.186, D.219, G.220, C.221, N.223, G.224, C.225 Ligands: SRM.12 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:D.219 Metal complexes: D:C.177, D:C.183, D:C.221, D:C.225 SF4.13: 10 residues within 4Å: Chain E: T.145, Q.146, C.151, T.153, P.154, C.188, C.189, N.191, C.193 Ligands: SRM.9 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.151, E:C.188, E:C.189, E:C.193 SF4.14: 14 residues within 4Å: Chain E: P.211, A.230, C.231, T.233, A.235, V.236, I.253, C.258, M.259, Y.260, C.261, G.262, N.263, C.264 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.231, E:C.258, E:C.261, E:C.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, Y.C. et al., Structure insights into the enzyme catalysis from comparison of three forms of dissimilatory sulfite reductase from Desulfovibrio gigas. To be Published

Release Date

2010-09-22

Peptides

Sulfite reductase alpha: AD
Sulfite reductase beta: BE
Sulfite reductase gama: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Sulfite reductase alpha

Sulfite reductase beta

Sulfite reductase gama