SMTL ID : 3or2.1

Crystal structure of dissimilatory sulfite reductase II (DsrII)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: C.282, P.283, C.286, M.287, C.301, T.302, R.303, C.304, M.305, H.306, C.307 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.282, A:C.301, A:C.304, A:C.307 SF4.2: 12 residues within 4Å: Chain A: C.175, L.176, C.181, F.183, A.184, D.217, G.218, C.219, N.221, G.222, C.223 Ligands: SRM.6 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.217 Metal complexes: A:C.175, A:C.181, A:C.219, A:C.223 SF4.7: 10 residues within 4Å: Chain B: T.144, Q.145, C.150, T.152, P.153, C.187, C.188, N.190, C.192 Ligands: SRM.4 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.150, B:C.188, B:C.192 SF4.8: 14 residues within 4Å: Chain B: P.210, A.229, C.230, T.232, A.234, V.235, I.252, C.257, M.258, Y.259, C.260, G.261, C.263, L.272 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.230, B:C.257, B:C.260, B:C.263 SF4.9: 13 residues within 4Å: Chain D: C.282, P.283, T.284, C.286, M.287, I.296, C.301, T.302, R.303, C.304, M.305, H.306, C.307 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.282, D:C.301, D:C.304, D:C.307 SF4.10: 12 residues within 4Å: Chain D: C.175, L.176, C.181, F.183, A.184, D.217, G.218, C.219, N.221, G.222, C.223 Ligands: SRM.14 5 PLIP interactions: 5 interactions with chain D, Salt bridges: D:D.217 Metal complexes: D:C.175, D:C.181, D:C.219, D:C.223 SF4.15: 12 residues within 4Å: Chain E: T.144, Q.145, C.150, T.152, P.153, A.186, C.187, C.188, N.190, M.191, C.192 Ligands: SRM.12 3 PLIP interactions: 3 interactions with chain E, Metal complexes: E:C.150, E:C.188, E:C.192 SF4.16: 12 residues within 4Å: Chain E: P.210, A.229, C.230, T.232, V.235, I.252, C.257, M.258, Y.259, C.260, G.261, C.263 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.230, E:C.257, E:C.260, E:C.263

4 x SO3: SULFITE ION(Non-covalent)

SO3.3: 7 residues within 4Å: Chain A: K.64, H.65, G.66, G.67 Chain C: E.14, D.15, K.99 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.99, A:H.65 Salt bridges: C:E.14, C:D.15 Water bridges: A:K.64 SO3.5: 6 residues within 4Å: Chain A: R.99, T.134, R.170, K.211, K.213 Ligands: SRM.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.99, A:R.99, A:T.134, A:R.170, A:R.170, A:K.211, A:K.213 SO3.11: 6 residues within 4Å: Chain D: K.64, H.65, G.66, G.67 Chain F: E.14, K.99 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:D.13, F:K.99, F:K.99, D:H.65 Salt bridges: F:E.14, F:D.15 SO3.13: 6 residues within 4Å: Chain D: R.99, R.170, K.211, K.213 Chain F: C.103 Ligands: SRM.12 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.99, D:R.99, D:R.170, D:R.170, D:K.211, D:K.213 Water bridges: D:T.134, D:T.134

4 x SRM: SIROHEME(Non-covalent)

SRM.4: 31 residues within 4Å: Chain A: I.79, R.81, R.99, G.132, S.133, T.134, G.135, D.136, Y.210, K.211, K.213, K.215, R.229, K.330, A.331, V.333, R.376 Chain B: R.70, H.143, T.144, Q.145, Y.149, C.150, H.151, N.190, C.192, G.193 Chain C: G.102, C.103 Ligands: SO3.5, SF4.7 42 PLIP interactions: 34 interactions with chain A, 6 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: A:A.331, A:V.333, B:N.190 Hydrogen bonds: A:G.132, A:S.133, A:S.133, A:T.134, A:G.135, A:D.136, A:D.136, A:Y.210, A:A.331, B:Q.145, C:C.103 Water bridges: A:R.81, A:R.81, A:R.99, A:R.99, A:R.99, A:T.134, A:V.333, A:R.376, B:N.190, C:G.102 Salt bridges: A:R.81, A:R.81, A:R.99, A:K.211, A:K.211, A:K.211, A:K.213, A:K.213, A:K.215, A:R.229, A:K.330, A:R.376, A:R.376, B:R.70, B:H.151 pi-Cation interactions: A:K.211, A:K.213 Metal complexes: B:C.192 SRM.6: 33 residues within 4Å: Chain A: C.175, L.176, R.180, C.181, E.182, F.183, N.221, G.222, C.223, N.260, N.309 Chain B: H.43, I.45, L.51, H.53, R.65, R.93, T.95, T.96, R.97, N.99, E.101, G.133, T.134, S.139, I.180, R.182, K.287, I.288, S.289, R.291, R.335 Ligands: SF4.2 39 PLIP interactions: 33 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.51, B:R.97, B:I.180, B:R.182, B:I.288, A:F.183, A:N.221 Hydrogen bonds: B:T.96, B:N.99, B:S.139, B:R.182, B:I.288, B:S.289, B:S.289, B:S.289, A:L.176, A:N.260, A:N.309 Water bridges: B:R.93, B:T.96, B:G.133, B:R.182, B:C.197, B:R.335, B:R.335, A:R.229 Salt bridges: B:H.43, B:H.53, B:R.65, B:R.65, B:R.93, B:R.97, B:R.182, B:K.287, B:R.291, B:R.291, B:R.335, B:R.335 pi-Cation interactions: B:R.182 SRM.12: 32 residues within 4Å: Chain D: I.79, R.81, R.99, G.132, S.133, T.134, G.135, D.136, Y.210, K.211, K.213, K.215, R.229, K.330, A.331, V.333, R.374, R.376 Chain E: R.70, H.143, T.144, Q.145, Y.149, C.150, H.151, N.190, C.192, G.193 Chain F: G.102, C.103 Ligands: SO3.13, SF4.15 36 PLIP interactions: 7 interactions with chain E, 28 interactions with chain D, 1 interactions with chain F, Hydrophobic interactions: E:T.144, E:Q.145, E:N.190 Water bridges: E:N.190, D:R.81, D:R.81, D:R.99, D:V.333, D:R.376 Salt bridges: E:R.70, E:H.151, D:R.81, D:R.81, D:R.99, D:K.211, D:K.211, D:K.213, D:K.213, D:K.215, D:R.229, D:K.330, D:R.374, D:R.376, D:R.376 Metal complexes: E:C.192 Hydrogen bonds: D:G.132, D:S.133, D:S.133, D:T.134, D:G.135, D:D.136, D:Y.210, D:A.331, F:C.103 pi-Cation interactions: D:K.211, D:K.213 SRM.14: 34 residues within 4Å: Chain D: C.175, L.176, R.180, C.181, E.182, F.183, N.221, G.222, C.223, N.260, N.309 Chain E: H.43, I.45, L.51, H.53, R.65, R.93, T.95, T.96, R.97, N.99, E.101, G.133, T.134, G.135, S.139, I.180, R.182, K.287, I.288, S.289, R.291, R.335 Ligands: SF4.10 41 PLIP interactions: 34 interactions with chain E, 7 interactions with chain D Hydrophobic interactions: E:L.51, E:R.97, E:I.180, E:R.182, E:I.288, D:L.176, D:N.221 Hydrogen bonds: E:T.96, E:N.99, E:G.135, E:S.139, E:R.182, E:I.288, E:S.289, E:S.289, E:S.289, D:L.176, D:N.260, D:N.309 Water bridges: E:R.93, E:G.133, E:R.182, E:C.197, E:K.287, E:R.291, E:R.291, E:R.335, D:R.229, D:R.229 Salt bridges: E:H.43, E:H.53, E:R.65, E:R.65, E:R.93, E:R.97, E:R.182, E:R.291, E:R.291, E:R.335, E:R.335 pi-Cation interactions: E:R.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, Y.C. et al., Dissimilatory Sulfite Reductase, Sulfate Reduction. To be Published

Release Date

2010-09-22

Peptides

Sulfite redcutase subunit alpha: AD
Sulfite redcutase subunit beta: BE
Sulfite redcutase subunit gama: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Sulfite redcutase subunit alpha

Sulfite redcutase subunit beta

Sulfite redcutase subunit gama