SMTL ID : 3u52.1

X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: E.108, E.138, H.141, E.233 Ligands: FE.2, GOL.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.108, A:E.138, A:H.141, H2O.1 FE.2: 7 residues within 4Å: Chain A: Q.134, E.138, E.199, E.233, H.236 Ligands: FE.1, GOL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.199, A:E.233, A:E.233, A:H.236, H2O.3 FE.20: 6 residues within 4Å: Chain B: E.108, E.138, H.141, E.233 Ligands: FE.21, GOL.27 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.108, B:E.138, B:H.141, H2O.7 FE.21: 5 residues within 4Å: Chain B: E.138, E.199, E.233, H.236 Ligands: FE.20 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.199, B:E.233, B:E.233, B:H.236, H2O.7

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.399, C.402, C.432, C.436 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.399, A:C.402, A:C.432, A:C.436 ZN.22: 4 residues within 4Å: Chain B: C.399, C.402, C.432, C.436 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.399, B:C.402, B:C.432, B:C.436

2 x CU: COPPER (II) ION(Non-covalent)

CU.4: 3 residues within 4Å: Chain A: H.155, H.494 Chain C: I.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.155, A:H.494 CU.23: 3 residues within 4Å: Chain B: H.155, H.494 Chain D: E.11 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.155, B:H.494

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: L.107, E.108, A.111, E.138, I.194, F.198, E.199 Ligands: FE.1, FE.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.134, A:E.138 GOL.6: 9 residues within 4Å: Chain A: E.36, K.117, A.182, R.183, A.185, G.186, P.187, F.190 Chain C: W.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.36, A:G.186 Water bridges: A:Q.113 GOL.7: 8 residues within 4Å: Chain A: V.323, E.410, K.411, S.418, R.420, S.433, D.434 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.410, A:K.411, A:R.420, A:D.434, A:D.434 Water bridges: A:G.435 GOL.8: 10 residues within 4Å: Chain A: R.271, V.323, A.327, F.408, T.409, K.411, S.418, C.432, S.433 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.271, A:R.271, A:T.409, A:S.418, A:C.432 Water bridges: A:T.409 GOL.26: 5 residues within 4Å: Chain B: L.10, K.13, Y.14, L.17, R.55 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.10 GOL.27: 9 residues within 4Å: Chain B: L.107, E.108, A.111, Q.134, E.138, I.194, F.198, E.199 Ligands: FE.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.134, B:E.138 Water bridges: B:H.141 GOL.39: 1 residues within 4Å: Chain C: K.323 No protein-ligand interaction detected (PLIP) GOL.40: 6 residues within 4Å: Chain C: G.224, P.228, Y.257, E.316, L.317, R.320 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.257, C:Y.257, C:R.320 GOL.42: 8 residues within 4Å: Chain B: Q.449 Chain D: F.45, H.46, Y.47, R.48, P.49, T.56, L.57 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:H.46, D:L.57 Water bridges: D:R.48 GOL.44: 7 residues within 4Å: Chain F: V.3, N.4, A.5, Y.7, D.8, Y.9, K.10 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:A.5, F:Y.9, F:K.10

24 x XE: XENON(Non-covalent)

XE.9: 2 residues within 4Å: Chain A: F.100, M.211 Ligand excluded by PLIP XE.10: 3 residues within 4Å: Chain A: F.198, G.269, L.273 Ligand excluded by PLIP XE.11: 3 residues within 4Å: Chain A: F.339, I.404, P.405 Ligand excluded by PLIP XE.12: 3 residues within 4Å: Chain A: W.170, Y.342, P.396 Ligand excluded by PLIP XE.13: 3 residues within 4Å: Chain A: A.345, I.457, Y.475 Ligand excluded by PLIP XE.14: 5 residues within 4Å: Chain A: Q.344, N.392, N.393, L.395, L.467 Ligand excluded by PLIP XE.15: 1 residues within 4Å: Chain A: Q.344 Ligand excluded by PLIP XE.16: 4 residues within 4Å: Chain A: F.100, A.148, M.149, T.222 Ligand excluded by PLIP XE.17: 2 residues within 4Å: Chain A: S.197, F.266 Ligand excluded by PLIP XE.18: 4 residues within 4Å: Chain A: W.47, W.50, F.188, L.191 Ligand excluded by PLIP XE.19: 1 residues within 4Å: Chain A: W.23 Ligand excluded by PLIP XE.28: 2 residues within 4Å: Chain B: E.108, M.211 Ligand excluded by PLIP XE.29: 2 residues within 4Å: Chain B: I.104, L.275 Ligand excluded by PLIP XE.30: 4 residues within 4Å: Chain B: Y.171, L.275, F.339, I.404 Ligand excluded by PLIP XE.31: 4 residues within 4Å: Chain B: W.170, Y.342, L.395, P.396 Ligand excluded by PLIP XE.32: 3 residues within 4Å: Chain B: A.345, I.457, Y.475 Ligand excluded by PLIP XE.33: 4 residues within 4Å: Chain B: N.392, N.393, L.395, L.467 Ligand excluded by PLIP XE.34: 1 residues within 4Å: Chain B: Q.344 Ligand excluded by PLIP XE.35: 4 residues within 4Å: Chain B: Q.145, A.148, M.149, T.222 Ligand excluded by PLIP XE.36: 2 residues within 4Å: Chain B: S.197, F.266 Ligand excluded by PLIP XE.37: 3 residues within 4Å: Chain B: W.47, F.188, L.191 Ligand excluded by PLIP XE.38: 1 residues within 4Å: Chain B: W.23 Ligand excluded by PLIP XE.41: 2 residues within 4Å: Chain C: Y.227, Y.257 Ligand excluded by PLIP XE.43: 3 residues within 4Å: Chain D: Y.227, D.232, Y.257 Ligand excluded by PLIP

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.24: 15 residues within 4Å: Chain B: E.36, Q.113, G.114, K.117, V.118, A.182, R.183, A.185, G.186, P.187, F.190 Chain D: W.51, L.57, N.58, G.142 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:W.51, B:K.117, B:R.183 Hydrogen bonds: D:N.58, D:G.142 Salt bridges: B:R.183

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

EPE.25: 8 residues within 4Å: Chain B: Q.15, Y.16, R.19, D.20, W.47, S.48, G.124, A.125 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.15, B:D.20, B:A.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCormick, M.S. et al., Analysis of Substrate Access to Active Sites in Bacterial Multicomponent Monooxygenase Hydroxylases: X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1. Biochemistry (2011)

Release Date

2011-12-14

Peptides

Phenol hydroxylase component phN: AB
Phenol hydroxylase component phL: CD
Phenol hydroxylase component phO: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Phenol hydroxylase component phN

Phenol hydroxylase component phL

Phenol hydroxylase component phO

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