SMTL ID : 4y3o.1

Crystal structure of Ribosomal oxygenase NO66 in complex with substrate Rpl8 peptide and Ni(II) and cofactor N-oxalyglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-2-2-mer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.165, D.167, H.230 Ligands: OGA.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.165, A:D.167, A:H.230, H2O.2 NI.3: 4 residues within 4Å: Chain B: H.165, D.167, H.230 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.165, B:D.167, B:H.230, H2O.21

2 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.2: 10 residues within 4Å: Chain A: Y.153, F.162, H.165, D.167, W.182, H.230, A.232, H.242, T.244 Ligands: NI.1 12 PLIP interactions: 2 interactions with chain C, 10 interactions with chain A Water bridges: C:H.5, A:Y.153, A:T.155, A:F.162 Salt bridges: C:H.5, A:H.230, A:H.242, A:H.242 Hydrogen bonds: A:H.165, A:A.232, A:H.242, A:T.244 OGA.4: 11 residues within 4Å: Chain B: Y.153, F.162, H.165, D.167, K.180, W.182, H.230, A.232, H.242, T.244 Ligands: NI.3 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:F.162, B:H.242 Water bridges: B:S.120, B:S.120, B:K.180, B:K.180, B:K.180, D:H.5, D:H.5, D:H.5 Salt bridges: B:K.180, B:H.230, B:H.242, B:H.242, D:H.5

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: W.253 Chain B: P.280, A.301, F.302, K.305 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.305 GOL.6: 5 residues within 4Å: Chain A: D.285 Chain B: R.24, E.142, D.378, G.379 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.24 Water bridges: B:D.378, B:G.379, B:I.380, B:A.381 GOL.7: 8 residues within 4Å: Chain A: L.279, F.283, M.284 Chain B: G.145, S.146, N.251, R.326, F.330 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.326, B:R.326, B:F.330 Water bridges: B:M.147, B:N.251, B:N.251

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

ACT.8: 1 residues within 4Å: Chain B: F.430 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Structure of the JmjC domain-containing protein NO66 complexed with ribosomal protein Rpl8. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-10-07

Peptides

Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66: AB
Rpl8 peptide: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66

Rpl8 peptide

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