SMTL ID : 3ubt.1 (2 other biounits)

Crystal Structure of C71S Mutant of DNA Cytosine-5 Methyltransferase M.HaeIII Bound to DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

2 x DT- DG- DG- DC- DC- DA: 5'-D(*TP*GP*GP*CP*CP*A)-3'(Non-covalent)

DT-DG-DG-DC-DC-DA.1: 13 residues within 4Å: Chain A: S.219, T.220, I.221, S.224, R.225, R.243, Q.244 Ligands: DT-DG-DG-DC-DC-DA.2, DT-DG-DG-DC-DC-DA.2, DT-DG-DG-DC-DC-DA.2, DT-DG-DG-DC-DC-DA.2, DT-DG-DG-DC-DC-DA.2, DT-DG-DG-DC-DC-DA.2 Protein-ligand interaction information (PLIP) not available DT-DG-DG-DC-DC-DA.2: 15 residues within 4Å: Chain A: R.155, I.221, R.225, R.227, R.229, F.236, T.237, Q.239, Q.244 Ligands: DT-DG-DG-DC-DC-DA.1, DT-DG-DG-DC-DC-DA.1, DT-DG-DG-DC-DC-DA.1, DT-DG-DG-DC-DC-DA.1, DT-DG-DG-DC-DC-DA.1, CL.3 Protein-ligand interaction information (PLIP) not available

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

CL.3: 2 residues within 4Å: Chain A: S.241 Ligands: DT-DG-DG-DC-DC-DA.2 Ligand excluded by PLIP

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 9 residues within 4Å: Chain A: F.7, E.29, Y.30, D.31, G.49, D.50, I.51, P.70, L.90 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.29, A:D.31, A:D.50, A:D.50, A:I.51, A:K.89 Water bridges: A:Y.30, A:Y.30 ATP.5: 3 residues within 4Å: Chain A: S.258, K.259, N.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.258, A:K.259, A:N.260, A:N.260

1 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.6: 4 residues within 4Å: Chain A: K.182, W.186, W.231, N.232 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.182, A:N.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Didovyk, A. et al., Structural origins of DNA target selection and nucleobase extrusion by a DNA Cytosine methyltransferase. J.Biol.Chem. (2012)

Release Date

2012-10-03

Peptides

Modification methylase HaeIII: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Y

Modification methylase HaeIII

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