SMTL ID : 4b21.1

Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 7 residues within 4Å: Chain A: S.70, D.75, W.161, M.165, F.169, D.181, T.183 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.70, A:S.70, A:D.75, A:T.183, A:T.183 Water bridges: A:T.78, A:E.187 BGC.5: 7 residues within 4Å: Chain D: S.70, D.75, W.161, M.165, F.169, D.181, T.183 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.70, D:S.70, D:D.75, D:T.183, D:T.183 Water bridges: D:T.78, D:E.187

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

PO4.2: 6 residues within 4Å: Chain A: Q.199, T.200, E.201 Chain E: G.7, A.8 Chain F: T.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.201 Water bridges: A:T.200, A:T.200 PO4.3: 8 residues within 4Å: Chain A: N.186, K.189, K.197 Chain D: K.189, S.195, S.196, K.197 Ligands: PO4.7 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:K.197, A:N.186 Water bridges: D:K.197, A:N.186 PO4.4: 4 residues within 4Å: Chain A: S.74 Chain C: G.7, T.8, A.9 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.74, A:S.74, A:S.74, A:D.75 PO4.6: 6 residues within 4Å: Chain B: G.7, A.8 Chain C: T.4 Chain D: Q.199, T.200, E.201 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.201 Water bridges: D:T.200, D:T.200 PO4.7: 8 residues within 4Å: Chain A: K.189, S.195, S.196, K.197 Chain D: N.186, K.189, K.197 Ligands: PO4.3 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:K.197, D:N.186 Water bridges: A:K.197, D:N.186 PO4.8: 4 residues within 4Å: Chain D: S.74 Chain F: G.7, T.8, A.9 4 PLIP interactions: 4 interactions with chain D Water bridges: D:S.74, D:S.74, D:S.74, D:D.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dalhus, B. et al., Sculpting of DNA at Abasic Sites by DNA Glycosylase Homolog Mag2. Structure (2013)

Release Date

2013-01-09

Peptides

PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2: AD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

PROBABLE DNA-3-METHYLADENINE GLYCOSYLASE 2

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