SMTL ID : 2no5.1 (1 other biounit)

Crystal Structure analysis of a Dehalogenase with intermediate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 1 residues within 4Å: Chain A: H.65 Ligand excluded by PLIP

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

SO4.2: 4 residues within 4Å: Chain A: R.61, Q.66, Q.72 Chain B: F.215 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.66, A:Q.72, A:Q.72 Salt bridges: A:R.61 SO4.3: 2 residues within 4Å: Chain A: R.83 Chain B: E.214 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.83 SO4.4: 7 residues within 4Å: Chain A: Y.107, P.108, D.109, R.206, S.224, L.225, S.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.109, A:S.224, A:L.225, A:S.226 Salt bridges: A:R.206 SO4.5: 2 residues within 4Å: Chain A: R.83, R.90 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.83, A:R.90 SO4.6: 2 residues within 4Å: Chain A: E.214 Chain B: R.83 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.83 Hydrogen bonds: A:E.214 SO4.7: 4 residues within 4Å: Chain A: H.29, Y.107, R.206, Q.207 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.107, A:Q.207 Water bridges: A:H.29, A:Q.207, A:Q.207 Salt bridges: A:H.29, A:R.206 SO4.9: 4 residues within 4Å: Chain B: N.131, D.132, E.133, D.155 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.131, B:E.133, B:D.155 SO4.10: 2 residues within 4Å: Chain B: R.83, R.90 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.83, B:R.90 SO4.11: 5 residues within 4Å: Chain A: F.215 Chain B: R.61, Q.66, Q.72, E.76 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.66, B:Q.72 Salt bridges: B:R.61 SO4.12: 6 residues within 4Å: Chain B: Y.107, P.108, D.109, R.206, S.224, L.225 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.109, B:D.109, B:L.225, B:S.226 Salt bridges: B:R.206 SO4.13: 2 residues within 4Å: Chain B: E.112, K.116 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.116 SO4.14: 4 residues within 4Å: Chain B: H.29, Y.107, R.206, Q.207 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.107 Water bridges: B:Y.107 Salt bridges: B:H.29, B:R.206 SO4.15: 5 residues within 4Å: Chain A: Q.52, R.53 Chain B: M.48 Ligands: CNR.16, CNR.17 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.53

3 x CNR: (2S)-2-CHLOROPROPANOIC ACID(Non-covalent)

CNR.8: 7 residues within 4Å: Chain A: R.51, L.55, N.187, A.188, W.189 Chain B: R.53, E.56 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.51 CNR.16: 5 residues within 4Å: Chain B: H.29, E.44, S.47, M.48 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.48 Salt bridges: B:H.29 CNR.17: 9 residues within 4Å: Chain A: R.53, E.56 Chain B: L.55, S.186, N.187, A.188, W.189, E.212 Ligands: SO4.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.56 Salt bridges: A:R.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidberger, J.W. et al., Crystal structures of the substrate free-enzyme, and reaction intermediate of the HAD superfamily member, haloacid dehalogenase DehIVa from Burkholderia cepacia MBA4. J.Mol.Biol. (2007)

Release Date

2007-09-25

Peptides

(S)-2-haloacid dehalogenase IVA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

(S)-2-haloacid dehalogenase IVA

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