SMTL ID : 2z6q.1

Ternary structure of Arg165Ala M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

1 x DT- DG- DA- DT- DA- DG: DNA (5'-D(*DTP*DGP*DAP*DTP*DAP*DG)-3')(Non-covalent)

DT-DG-DA-DT-DA-DG.1: 17 residues within 4Å: Chain A: G.7, C.8, T.9, A.10, T.11, C.12 Chain B: I.86, S.87, K.162, T.226, R.228, Q.237, R.240, Y.242, I.249, T.250 Ligands: DCZ.3 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DT- DA- DT- DC: DNA (5'-D(*DGP*DCP*DTP*DAP*DTP*DC)-3')(Non-covalent)

DG-DC-DT-DA-DT-DC.2: 18 residues within 4Å: Chain A: G.1, A.2, T.3, A.4, G.5, C.6, G.7 Chain B: Q.82, S.85, S.87, G.88, K.89, R.97, Q.237, Y.254, G.255, G.256 Ligands: DCZ.3 Protein-ligand interaction information (PLIP) not available

1 x DCZ: 2'-DEOXYCYTIDINE(Non-covalent)

DCZ.3: 16 residues within 4Å: Chain B: C.81, S.85, E.119, N.120, V.121, R.163, E.164, A.165, T.250, L.251, S.252, A.253, G.303, N.304 Ligands: DT-DG-DA-DT-DA-DG.1, DG-DC-DT-DA-DT-DC.2 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.121 Hydrogen bonds: B:E.119, B:R.163, B:R.163, B:A.253 pi-Cation interactions: B:R.163

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 20 residues within 4Å: Chain B: F.18, A.19, G.20, L.21, G.23, F.24, N.39, E.40, W.41, D.42, D.60, I.61, T.62, G.78, P.80, L.100, Y.285, N.304, S.305, V.306 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:F.18, B:L.21, B:G.23, B:W.41, B:D.60, B:I.61, B:T.62, B:Y.285, B:V.306 Water bridges: B:F.24, B:F.24, B:D.42, B:G.78, B:N.304, B:N.304 pi-Stacking: B:F.18, B:F.18, B:W.41, B:W.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shieh, F.K. et al., The role of Arg165 towards base flipping, base stabilization and catalysis in M.HhaI. J.Mol.Biol. (2006)

Release Date

2007-08-28

Peptides

Modification methylase HhaI: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Modification methylase HhaI