SMTL ID : 4lt5.1

Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 4 residues within 4Å: Chain A: H.235, D.237, H.285 Ligands: OGA.13 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.235, A:D.237, A:H.285, H2O.1

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

EDO.2: 2 residues within 4Å: Chain A: Y.258, E.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.258 Water bridges: A:R.232 EDO.3: 5 residues within 4Å: Chain A: N.251, F.252, Q.253, N.254, Q.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.251, A:N.251, A:F.252, A:N.254, A:N.254 EDO.4: 4 residues within 4Å: Chain A: N.181, S.185, Y.207, L.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.185, A:Y.207 EDO.5: 2 residues within 4Å: Chain A: T.85, N.86 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.87, A:A.87 EDO.6: 2 residues within 4Å: Chain A: I.241, T.242 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: E.135, N.251, G.293, W.294 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.135 EDO.8: 2 residues within 4Å: Chain A: K.143, D.144 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.144, A:D.144 EDO.14: 2 residues within 4Å: Chain C: C.8, A.9 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: S.154 Chain B: G.9 Chain C: A.5, G.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.154, A:S.154

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

SO4.9: 3 residues within 4Å: Chain A: Q.82, S.83, N.120 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.82, A:S.83, A:N.120 Water bridges: A:S.83 SO4.10: 2 residues within 4Å: Chain A: P.123, K.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.124 Water bridges: A:E.125 SO4.11: 3 residues within 4Å: Chain A: S.192, S.193, R.194 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.193, A:R.194 Salt bridges: A:R.194 SO4.12: 4 residues within 4Å: Chain A: P.178, N.181, Y.207, N.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.181

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

OGA.13: 14 residues within 4Å: Chain A: N.220, R.230, I.231, H.235, D.237, L.246, Y.248, L.259, H.285, V.287, R.295, V.299 Chain C: C.6 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.220, A:Y.248 Water bridges: A:R.230 Salt bridges: A:R.230, A:H.235, A:R.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, H. et al., Structure of a Naegleria Tet-like dioxygenase in complex with 5-methylcytosine DNA. Nature (2014)

Release Date

2013-12-18

Peptides

Naegleria Tet-like dioxygenase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Naegleria Tet-like dioxygenase