SMTL ID : 2xsj.1

Structure of desulforubidin from Desulfomicrobium norvegicum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-2-2-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: C.284, P.285, T.286, 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 SF4.2: 11 residues within 4Å: Chain A: C.177, C.183, W.185, A.186, D.219, G.220, C.221, N.223, G.224, C.225 Ligands: SRM.3 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 SF4.4: 11 residues within 4Å: Chain B: A.230, C.231, P.232, I.236, I.258, C.263, M.264, F.265, C.266, G.267, C.269 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:C.231, B:C.263, B:C.266, B:C.269, SF4.4, SF4.4 SF4.5: 11 residues within 4Å: Chain B: T.145, Q.146, C.151, T.153, P.154, C.188, C.189, N.191, M.192, C.193 Ligands: SRM.6 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:C.151, B:C.188, B:C.189, B:C.193, SF4.5, SF4.5 SF4.8: 11 residues within 4Å: Chain D: 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 D, Metal complexes: D:C.284, D:C.303, D:C.306, D:C.309 SF4.9: 10 residues within 4Å: Chain D: C.177, C.183, W.185, A.186, G.220, C.221, N.223, G.224, C.225 Ligands: SRM.10 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 SF4.11: 10 residues within 4Å: Chain E: C.231, V.233, I.236, I.258, C.263, M.264, F.265, C.266, G.267, C.269 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.231, E:C.263, E:C.266, E:C.269 SF4.12: 11 residues within 4Å: Chain E: T.145, Q.146, C.151, T.153, P.154, C.188, C.189, N.191, M.192, C.193 Ligands: SRM.13 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.151, E:C.188, E:C.189, E:C.193

4 x SRM: SIROHEME(Non-covalent)(Covalent)

SRM.3: 33 residues within 4Å: Chain A: C.177, L.178, R.182, C.183, E.184, W.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, T.140, R.183, K.293, V.294, S.295, R.297, R.341 Ligands: SF4.2 38 PLIP interactions: 28 interactions with chain B, 9 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: B:L.52, B:R.98, B:V.294, A:L.178, A:W.185, A:N.223, A:N.311 Hydrogen bonds: B:T.97, B:N.100, B:G.136, B:T.140, B:C.198, B:V.294, B:S.295, A:L.178, A:N.262 Water bridges: B:H.54, B:G.134, B:Q.181, B:R.183, B:R.297, B:R.341, A:R.182, 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:R.183, B:R.297, B:R.297, B:R.341, B:R.341 Metal complexes: A:C.225, H2O.12 SRM.6: 34 residues within 4Å: Chain A: I.81, R.83, R.101, G.134, A.135, T.136, G.137, D.138, Y.212, K.213, K.215, K.217, R.231, K.332, A.333, I.335, R.376, R.378 Chain B: R.71, H.144, T.145, Q.146, H.150, C.151, H.152, N.191, M.192, C.193, G.194, T.271 Chain C: G.103, C.104 Ligands: SF4.5, SO3.7 37 PLIP interactions: 7 interactions with chain B, 29 interactions with chain A, 1 interactions with chain C, Hydrophobic interactions: B:Q.146, B:N.191, A:A.135 Hydrogen bonds: B:Q.146, A:G.134, A:A.135, A:T.136, A:G.137, A:D.138, A:Y.212, A:A.333, C:C.104 Salt bridges: B:R.71, B:H.150, B:H.152, A:R.83, A:R.83, A:R.101, 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 Metal complexes: B:C.193 Water bridges: A:R.83, A:R.83, A:R.101, A:N.131, A:I.335, A:R.378 pi-Cation interactions: A:K.213, A:K.215 SRM.10: 32 residues within 4Å: Chain D: C.177, L.178, R.182, C.183, E.184, W.185, N.223, G.224, C.225, N.262, N.311 Chain E: H.44, L.52, H.54, R.66, R.94, T.96, T.97, R.98, N.100, E.102, G.134, T.135, G.136, T.140, R.183, K.293, V.294, S.295, R.297, R.341 Ligands: SF4.9 37 PLIP interactions: 28 interactions with chain E, 8 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: E:L.52, E:R.98, E:V.294, D:W.185, D:N.223, D:N.311 Hydrogen bonds: E:T.97, E:N.100, E:N.100, E:G.136, E:T.140, E:C.198, E:V.294, E:S.295, D:L.178, D:N.262 Water bridges: E:H.54, E:R.98, E:G.134, E:R.183, E:R.341, D:R.182, 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.183, E:R.297, E:R.297, E:R.341, E:R.341 Metal complexes: D:C.225, H2O.32 SRM.13: 34 residues within 4Å: Chain D: I.81, R.83, R.101, G.134, A.135, T.136, G.137, D.138, Y.212, K.213, K.215, K.217, R.231, K.332, A.333, I.335, R.376, R.378 Chain E: R.71, H.144, T.145, Q.146, H.150, C.151, H.152, N.191, M.192, C.193, G.194, T.271 Chain F: G.103, C.104 Ligands: SF4.12, SO3.14 35 PLIP interactions: 28 interactions with chain D, 6 interactions with chain E, 1 interactions with chain F, Hydrogen bonds: D:G.134, D:A.135, D:T.136, D:G.137, D:D.138, D:Y.212, D:A.333, F:C.104 Water bridges: D:R.83, D:R.83, D:N.131, D:I.335, D:L.336, D:R.378, E:Q.146 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.150, E:H.152 pi-Cation interactions: D:K.213, D:K.215 Hydrophobic interactions: E:N.191 Metal complexes: E:C.193

2 x SO3: SULFITE ION(Non-covalent)

SO3.7: 6 residues within 4Å: Chain A: R.101, R.172, K.213, K.215 Chain C: C.104 Ligands: SRM.6 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.101, A:R.101, A:T.136, A:R.172, A:R.172, A:K.213, A:K.215 Water bridges: C:C.104 SO3.14: 6 residues within 4Å: Chain D: R.101, R.172, K.213, K.215 Chain F: C.104 Ligands: SRM.13 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.101, D:R.101, D:T.136, D:R.172, D:R.172, D:K.213, D:K.213, D:K.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oliveira, T.F. et al., Structural Insights Into Dissimilatory Sulfite Reductases: Structure of Desulforubidin from Desulfomicrobium Norvegicum. Front.Microbiol. (2011)

Release Date

2011-08-24

Peptides

SULFITE REDUCTASE ALPHA SUBUNIT: AD
SULFITE REDUCTASE BETA SUBUNIT: BE
SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

SULFITE REDUCTASE ALPHA SUBUNIT

SULFITE REDUCTASE BETA SUBUNIT

SULFUR RELAY PROTEIN, TUSE/DSRC/DSVC FAMILY