SMTL ID : 3k2o.1

Structure of an oxygenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 3 residues within 4Å: Chain A: H.188, D.190, H.274 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.188, A:D.190, A:H.274, H2O.166, H2O.167, H2O.168 NI.7: 3 residues within 4Å: Chain B: H.188, D.190, H.274 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.188, B:D.190, B:H.274, H2O.330, H2O.338, H2O.340

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

NA.2: 3 residues within 4Å: Chain A: P.154, K.155 Ligands: CL.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.155 Water bridges: A:A.76, A:A.76 NA.12: 4 residues within 4Å: Chain B: F.156, F.157, T.158, D.159 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.159, B:D.159 Water bridges: B:D.160

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

CL.3: 1 residues within 4Å: Ligands: NA.2 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain B: K.5 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: N.198, T.286 Ligands: ACT.16 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: T.87, L.88, E.89 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: S.56, V.57, K.155 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: Q.98, K.99 Ligand excluded by PLIP

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 3 residues within 4Å: Chain A: S.110, K.112, S.137 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.110, A:S.137 Water bridges: A:S.137 Salt bridges: A:K.112 PO4.9: 5 residues within 4Å: Chain B: A.76, Q.77, E.78, W.80, K.152 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.78 Water bridges: B:N.75, B:E.78, B:K.155 PO4.15: 3 residues within 4Å: Chain B: S.110, K.112, S.137 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.110, B:S.110, B:S.110, B:S.137 Water bridges: B:S.110, B:S.137, B:S.137, B:H.141 Salt bridges: B:K.112

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

ACT.5: 5 residues within 4Å: Chain A: Y.132, T.185, N.198, K.205, V.276 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.276 Hydrogen bonds: A:T.185, A:N.198 Salt bridges: A:K.205 ACT.16: 5 residues within 4Å: Chain B: Y.132, T.185, N.198, K.205 Ligands: CL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.132, B:N.198 Salt bridges: B:K.205

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 7 residues within 4Å: Chain A: E.62, R.66, P.67 Chain B: Y.68, G.270, G.271, V.297 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mantri, M. et al., Crystal Structure of the 2-Oxoglutarate- and Fe(II)-Dependent Lysyl Hydroxylase JMJD6. J.Mol.Biol. (2010)

Release Date

2009-11-03

Peptides

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6