SMTL ID : 3pua.1

PHF2 Jumonji-NOG-Ni(II)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.190, D.192, Y.262 Ligands: OGA.14 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.190, A:D.192, A:Y.262, H2O.2

11 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: K.316, H.366, F.367, K.368, L.372 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.368, A:K.368 EDO.3: 2 residues within 4Å: Chain A: R.226, H.231 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.226 EDO.4: 3 residues within 4Å: Chain A: R.213, P.214, A.215 No protein-ligand interaction detected (PLIP) EDO.5: 4 residues within 4Å: Chain A: S.216, E.284, M.285, R.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.216, A:R.288 Water bridges: A:E.284, A:E.284, A:R.288 EDO.6: 4 residues within 4Å: Chain A: R.48, V.49, P.50, P.71 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.48 EDO.7: 4 residues within 4Å: Chain A: G.51, S.52, G.75, D.151 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52, A:D.151, A:D.151 Water bridges: A:I.152 EDO.8: 4 residues within 4Å: Chain A: Y.162, Y.313, H.317, E.320 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.317, A:E.320 Water bridges: A:K.316 EDO.9: 8 residues within 4Å: Chain A: V.174, Y.177, D.192, H.276, T.302, Q.303, F.304 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.177 Water bridges: A:S.193, A:T.302 EDO.10: 8 residues within 4Å: Chain A: T.134, Y.177, L.179, A.274, H.276, T.302 Ligands: EDO.9, OGA.14 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: S.124, T.125, N.126, R.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.126, A:R.127, A:R.127 EDO.12: 7 residues within 4Å: Chain A: F.39, P.40, A.237, V.240, D.241, K.242, C.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.237, A:C.243

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

CL.13: 5 residues within 4Å: Chain A: S.157, W.158, V.159, F.277, L.278 Ligand excluded by PLIP

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

OGA.14: 11 residues within 4Å: Chain A: L.179, T.187, H.190, D.192, Y.200, K.207, Y.262, T.264, H.276 Ligands: NI.1, EDO.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.187, A:Y.200, A:T.264, A:T.264 Water bridges: A:T.187 Salt bridges: A:K.207, A:H.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structural basis for human PHF2 Jumonji domain interaction with metal ions. J.Mol.Biol. (2011)

Release Date

2011-01-26

Peptides

PHD finger protein 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PHD finger protein 2

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