SMTL ID : 1eu1.1

THE CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES DIMETHYLSULFOXIDE REDUCTASE REVEALS TWO DISTINCT MOLYBDENUM COORDINATION ENVIRONMENTS.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

3 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 1 residues within 4Å: Chain A: R.509 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.509, A:R.509, A:R.509, A:R.509 Salt bridges: A:R.509 GLC.2: 7 residues within 4Å: Chain A: M.9, K.18, W.32, D.33, K.34, E.565, I.567 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.18, A:D.33, A:K.34 Water bridges: A:E.7, A:E.7 GLC.3: 6 residues within 4Å: Chain A: R.401, D.404, V.743, G.744, K.747, Q.750 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.401, A:R.401, A:D.404, A:G.744, A:Q.750, A:Q.750 Water bridges: A:D.404, A:Y.422, A:D.742

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

SO4.4: 4 residues within 4Å: Chain A: Y.278, S.283, D.284, H.618 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.283 Water bridges: A:Y.278, A:S.283, A:H.618 Salt bridges: A:H.618

1 x CD: CADMIUM ION(Non-covalent)

CD.5: 2 residues within 4Å: Chain A: D.87, D.91 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.87, A:D.91, A:D.91

2 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.6: 35 residues within 4Å: Chain A: Y.114, G.115, W.116, K.117, S.118, C.125, Y.146, S.147, R.326, G.432, G.433, N.434, H.438, Q.440, Q.458, D.459, F.460, T.463, A.475, R.481, D.511, A.641, H.643, L.648, H.649, S.650, Q.651, E.715, N.737, G.754, Q.755 Ligands: MGD.7, 6MO.8, O.9, O.10 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:W.116, A:K.117, A:R.326, A:G.432, A:N.434, A:H.438, A:Q.440, A:Q.458, A:Q.458, A:R.481, A:R.481, A:H.643, A:L.648, A:S.650, A:Q.651, A:Q.651, A:N.737, A:N.737, A:Q.755 Water bridges: A:S.118, A:D.511, A:Q.651 Salt bridges: A:H.438, A:D.459, A:D.511, A:H.649 MGD.7: 37 residues within 4Å: Chain A: Q.41, W.116, S.147, A.185, A.186, D.187, K.190, T.191, E.193, I.194, I.220, N.221, P.222, V.223, T.225, P.240, Q.241, D.243, G.321, W.322, S.323, I.324, R.326, M.327, H.359, V.640, S.642, H.643, P.644, K.645, R.647, L.648, H.649, Q.755 Ligands: MGD.6, 6MO.8, O.9 26 PLIP interactions: 26 interactions with chain A Hydrogen bonds: A:Q.41, A:A.185, A:K.190, A:T.191, A:I.220, A:I.220, A:N.221, A:Q.241, A:W.322, A:S.323, A:S.323, A:R.326, A:H.643, A:H.643, A:H.649, A:H.649, A:Q.755 Water bridges: A:T.191, A:T.191, A:D.243 Salt bridges: A:K.190, A:D.243, A:R.326, A:H.359, A:H.643, A:H.643

1 x 6MO: MOLYBDENUM(VI) ION(Non-covalent)

6MO.8: 8 residues within 4Å: Chain A: Y.114, Y.146, S.147 Ligands: MGD.6, MGD.7, O.9, O.10, EPE.11 No protein-ligand interaction detected (PLIP)

2 x O: OXYGEN ATOM(Non-covalent)

O.9: 8 residues within 4Å: Chain A: Y.114, W.116, S.147 Ligands: MGD.6, MGD.7, 6MO.8, O.10, EPE.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.114, A:W.116 O.10: 8 residues within 4Å: Chain A: Y.114, D.145, Y.146, S.147 Ligands: MGD.6, 6MO.8, O.9, EPE.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.114, A:Y.146, A:S.147

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 9 residues within 4Å: Chain A: Y.114, D.145, S.147, Y.165, W.196, Y.360 Ligands: 6MO.8, O.9, O.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.145 Water bridges: A:D.145, A:Y.165 Salt bridges: A:D.145

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H.K. et al., The 1.3 A Crystal Structure of Rhodobacter sphaeroides Dimethylsulfoxide Reductase Reveals Two Distinct Molybdenum Coordination Environments. J.Am.Chem.Soc. (2000)

Release Date

2000-08-02

Peptides

DIMETHYL SULFOXIDE REDUCTASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DIMETHYL SULFOXIDE REDUCTASE