SMTL ID : 4yar.2 (1 other biounit)

2-Hydroxyethylphosphonate dioxygenase (HEPD) E176H

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

20 x CD: CADMIUM ION(Non-covalent)

CD.1: 2 residues within 4Å: Chain A: H.129, H.182 Ligand excluded by PLIP CD.2: 2 residues within 4Å: Chain A: D.66, R.107 Ligand excluded by PLIP CD.3: 1 residues within 4Å: Chain A: H.75 Ligand excluded by PLIP CD.4: 3 residues within 4Å: Chain A: E.131 Chain B: H.10 Ligands: ACT.25 Ligand excluded by PLIP CD.5: 2 residues within 4Å: Chain A: D.32, E.43 Ligand excluded by PLIP CD.6: 1 residues within 4Å: Chain A: H.94 Ligand excluded by PLIP CD.7: 5 residues within 4Å: Chain A: D.142, H.160, A.161, H.163 Ligands: ACT.13 Ligand excluded by PLIP CD.8: 2 residues within 4Å: Chain A: D.189 Ligands: CD.10 Ligand excluded by PLIP CD.9: 1 residues within 4Å: Chain A: E.80 Ligand excluded by PLIP CD.10: 2 residues within 4Å: Chain A: D.189 Ligands: CD.8 Ligand excluded by PLIP CD.14: 2 residues within 4Å: Chain B: H.129, H.182 Ligand excluded by PLIP CD.15: 2 residues within 4Å: Chain B: D.66, R.107 Ligand excluded by PLIP CD.16: 1 residues within 4Å: Chain B: H.75 Ligand excluded by PLIP CD.17: 3 residues within 4Å: Chain A: H.10 Chain B: E.131 Ligands: ACT.12 Ligand excluded by PLIP CD.18: 2 residues within 4Å: Chain B: D.32, E.43 Ligand excluded by PLIP CD.19: 1 residues within 4Å: Chain B: H.94 Ligand excluded by PLIP CD.20: 5 residues within 4Å: Chain B: D.142, H.160, A.161, H.163 Ligands: ACT.26 Ligand excluded by PLIP CD.21: 2 residues within 4Å: Chain B: D.189 Ligands: CD.23 Ligand excluded by PLIP CD.22: 1 residues within 4Å: Chain B: E.80 Ligand excluded by PLIP CD.23: 2 residues within 4Å: Chain B: D.189 Ligands: CD.21 Ligand excluded by PLIP

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

NA.11: 2 residues within 4Å: Chain A: Q.296, H.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.296, A:Q.296, A:K.302 NA.24: 2 residues within 4Å: Chain B: Q.296, H.330 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.296, B:Q.296, B:K.302 Water bridges: B:H.330

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 8 residues within 4Å: Chain A: A.9, H.10, N.13 Chain B: H.129, L.130, E.131, Y.179 Ligands: CD.17 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.130, B:Y.179 Hydrogen bonds: B:L.130, B:E.131 Salt bridges: A:H.10 ACT.13: 4 residues within 4Å: Chain A: D.142, H.160, H.163 Ligands: CD.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.160, A:H.163 ACT.25: 8 residues within 4Å: Chain A: H.129, L.130, E.131, Y.179 Chain B: A.9, H.10, N.13 Ligands: CD.4 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.130, A:Y.179 Hydrogen bonds: A:L.130, A:E.131 Water bridges: B:H.10, B:H.10, B:H.10 Salt bridges: B:H.10 ACT.26: 4 residues within 4Å: Chain B: D.142, H.160, H.163 Ligands: CD.20 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.160, B:H.163

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peck, S.C. et al., A Common Late-Stage Intermediate in Catalysis by 2-Hydroxyethyl-phosphonate Dioxygenase and Methylphosphonate Synthase. J.Am.Chem.Soc. (2015)

Release Date

2015-03-04

Peptides

2-hydroxyethylphosphonate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

2-hydroxyethylphosphonate dioxygenase

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