SMTL ID : 3pu8.2 (1 other biounit)

PHF2 Jumonji-NOG-Fe(II) complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

monomer

Ligands

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.1: 4 residues within 4Å: Chain A: T.134, Y.177, H.276 Ligands: OGA.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.192

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

EDO.2: 5 residues within 4Å: Chain A: S.139, K.171, P.172, K.173, T.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.139, A:S.139 Water bridges: A:V.174, A:V.174 EDO.3: 3 residues within 4Å: Chain A: R.213, P.214, A.215 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: H.366, F.367, K.368, L.372 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.368, A:K.368 Water bridges: A:K.316, A:H.366 EDO.5: 3 residues within 4Å: Chain A: K.116, E.117, D.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.120 Water bridges: A:K.116 EDO.6: 2 residues within 4Å: Chain A: E.160, N.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.160 EDO.7: 6 residues within 4Å: Chain A: K.155, L.156, W.158, Y.162, H.279, S.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.155, A:S.280, A:S.280 EDO.8: 5 residues within 4Å: Chain A: F.30, E.33, L.34, R.37, F.235 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.33 EDO.9: 9 residues within 4Å: Chain A: F.64, T.65, P.257, S.258, W.260, L.281, S.282, M.285 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.260 EDO.10: 7 residues within 4Å: Chain A: L.281, S.282, V.283, E.284, M.285 Ligands: EDO.9, EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.284, A:M.285 EDO.11: 10 residues within 4Å: Chain A: S.280, L.281, S.282, V.283, E.284, H.335, Q.338, G.339, I.342 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.281, A:V.283, A:E.284 EDO.12: 4 residues within 4Å: Chain A: R.127, R.129, V.182, K.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.127, A:R.127 EDO.13: 3 residues within 4Å: Chain A: D.120, Y.123, S.124 No protein-ligand interaction detected (PLIP)

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

OGA.14: 12 residues within 4Å: Chain A: L.179, C.181, T.187, H.190, D.192, Y.200, K.207, Y.262, T.264, H.276 Ligands: OXY.1, FE.16 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.187, A:D.192, A:Y.262 Water bridges: A:T.187, A:D.192, A:D.192, A:T.264 Salt bridges: A:K.207, A:H.276

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

CL.15: 5 residues within 4Å: Chain A: S.157, W.158, V.159, F.277, L.278 Ligand excluded by PLIP

1 x FE: FE (III) ION(Non-covalent)

FE.16: 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.35

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

SO4.17: 4 residues within 4Å: Chain A: D.74, G.75, L.76, G.77 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.75, A:G.75, A:G.77 Water bridges: A:L.76, A:L.76 SO4.18: 4 residues within 4Å: Chain A: S.216, I.219, M.285, R.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.216 Salt bridges: A:R.288

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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