SMTL ID : 5chc.3 (2 other biounits)

Crystal structure of the perchlorate reductase PcrAB - substrate analog SeO3 bound - from Azospira suillum PS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: H.32, C.36, G.38, A.39, C.40, H.42, G.73, C.74, G.77 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.78 Metal complexes: A:H.32, A:C.36, A:C.40, A:C.74 SF4.15: 10 residues within 4Å: Chain B: C.137, N.138, H.139, C.140, P.143, A.144, C.145, C.180, P.185, K.196 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.137, B:C.140, B:C.145, B:C.180 SF4.16: 12 residues within 4Å: Chain B: C.21, I.22, G.23, C.24, Q.25, C.27, R.47, V.49, P.134, C.216, V.217, G.218 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.21, B:C.24, B:C.27, B:C.216 SF4.17: 12 residues within 4Å: Chain B: Y.14, C.31, W.35, W.46, R.47, C.197, I.198, G.199, C.200, P.210, A.211, C.212 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.31, B:C.197, B:C.200, B:C.212

1 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.2: 5 residues within 4Å: Chain A: D.170, G.459 Ligands: MGD.3, MD1.4, BSY.8 Ligand excluded by PLIP

1 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.3: 40 residues within 4Å: Chain A: N.35, K.76, D.170, W.200, G.201, S.202, N.203, Q.206, T.207, R.208, I.228, S.229, P.230, D.231, N.233, P.247, G.248, D.250, G.421, G.422, G.423, T.424, W.427, Y.457, I.458, G.459, N.761, P.763, H.764, S.765, R.766, S.768, V.769, H.770, R.830, H.835, R.882 Ligands: MO.2, MD1.4, BSY.8 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:K.76, A:N.203, A:T.207, A:R.208, A:I.228, A:S.229, A:N.233, A:G.248, A:G.422, A:G.423, A:N.761, A:H.764, A:H.764, A:R.766, A:S.768, A:H.770, A:R.830, A:R.830 Water bridges: A:D.231, A:D.231 Salt bridges: A:D.250, A:R.882

1 x MD1: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER(Non-covalent)

MD1.4: 37 residues within 4Å: Chain A: L.33, N.35, P.138, Y.168, D.170, H.426, Y.536, R.537, G.538, N.539, Q.543, K.545, I.564, N.565, I.566, R.567, D.569, S.581, W.584, K.587, D.615, S.762, H.764, V.769, H.770, S.771, T.772, H.835, C.836, Q.849, C.852, Q.881, R.882 Ligands: MO.2, MGD.3, BSY.8, NA.11 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:Y.168, A:R.537, A:N.539, A:Q.543, A:K.545, A:I.564, A:N.565, A:R.567, A:D.569, A:D.569, A:S.581, A:K.587, A:K.587, A:S.762, A:S.762, A:S.762, A:H.764, A:V.769, A:H.770, A:S.771, A:T.772, A:Q.849, A:R.882 Water bridges: A:Y.136, A:Y.136, A:R.537 Salt bridges: A:D.615, A:H.770

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 8 residues within 4Å: Chain A: T.185, E.187, K.462, T.593, S.594, H.596, N.697, Y.708 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.185, A:K.462, A:N.697 Water bridges: A:T.593, A:T.593 EDO.7: 2 residues within 4Å: Chain A: R.96, D.576 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96 Water bridges: A:R.106 EDO.18: 9 residues within 4Å: Chain B: I.82, G.85, I.86, F.88, P.108, T.109, P.110, R.111, S.112 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.86, B:R.111, B:S.112 EDO.19: 6 residues within 4Å: Chain B: E.89, F.90, D.91, V.104, R.105, S.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.89, B:D.91

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: R.107, E.611 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.107 Water bridges: A:R.107, A:W.610, A:E.611

1 x BSY: BISELENITE ION(Non-covalent)

BSY.8: 13 residues within 4Å: Chain A: N.35, V.139, F.164, Y.165, Y.168, D.170, I.458, G.459, Q.460, W.461 Ligands: MO.2, MGD.3, MD1.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.35, A:G.459

1 x SO3: SULFITE ION(Non-covalent)

SO3.9: 4 residues within 4Å: Chain A: V.51, H.81, Y.85 Ligands: ZN.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.52

3 x NA: SODIUM ION(Non-functional Binders)

NA.10: 3 residues within 4Å: Chain A: H.88, N.776, V.777 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.777 Water bridges: A:N.776, A:L.778 NA.11: 8 residues within 4Å: Chain A: V.535, G.538, N.539, D.563, N.565, D.569, T.571 Ligands: MD1.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.538, A:N.565 NA.12: 2 residues within 4Å: Chain A: H.128, E.559 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.128

1 x ZN: ZINC ION(Non-covalent)

ZN.13: 3 residues within 4Å: Chain A: M.52, H.81 Ligands: SO3.9 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.81, H2O.15

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.14: 13 residues within 4Å: Chain B: C.149, P.150, N.151, I.154, I.165, C.170, K.171, G.172, A.173, Q.174, A.175, C.176, A.194 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.149, B:C.170, B:C.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Youngblut, M.D. et al., Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues. J.Biol.Chem. (2016)

Release Date

2016-03-09

Peptides

DMSO reductase family type II enzyme, molybdopterin subunit: A
DMSO reductase family type II enzyme, iron-sulfur subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

DMSO reductase family type II enzyme, molybdopterin subunit

DMSO reductase family type II enzyme, iron-sulfur subunit

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