SMTL ID : 2c7r.1

HhaI DNA methyltransferase (T250G mutant) complex with oligonucleotide containing 2-aminopurine as a target base (GPGC:GMGC) and SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: F.18, A.19, G.20, L.21, G.22, G.23, N.39, E.40, W.41, D.42, D.60, I.61, G.78, P.80, L.100, Y.285, N.304, S.305, V.306 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:F.18, A:L.21, A:G.22, A:G.23, A:W.41, A:D.42, A:D.60, A:I.61, A:V.306 Water bridges: A:F.18, A:F.24, A:F.24, A:D.42, A:N.304, A:N.304 pi-Stacking: A:F.18, A:F.18, A:W.41, A:W.41

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

SO4.2: 2 residues within 4Å: Chain A: P.198, D.199 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.199 Water bridges: A:D.199, A:S.200, A:N.268 SO4.3: 3 residues within 4Å: Chain A: P.286, D.287, S.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.287, A:S.288, A:S.288 SO4.4: 1 residues within 4Å: Chain A: K.290 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.290 SO4.5: 4 residues within 4Å: Chain A: L.196, L.197, P.198, R.281 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.281 SO4.6: 2 residues within 4Å: Chain A: K.114, R.172 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.114, A:R.172 Salt bridges: A:K.114, A:R.172 SO4.7: 3 residues within 4Å: Chain A: I.219, E.220, Q.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.220, A:Q.221 Water bridges: A:Q.221 SO4.8: 3 residues within 4Å: Chain A: E.47, M.51, P.293 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.47

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 7 residues within 4Å: Chain A: K.150, V.151, L.152, N.153, D.156, Y.157, P.185 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.153, A:N.153, A:D.156, A:Y.157 Water bridges: A:K.150, A:K.150, A:N.153, A:Y.157 GOL.10: 5 residues within 4Å: Chain A: E.3, I.4, K.5, D.6, Y.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.3, A:K.5, A:D.6, A:D.6, A:Y.316 GOL.11: 3 residues within 4Å: Chain A: K.325, P.326, Y.327 No protein-ligand interaction detected (PLIP) GOL.12: 8 residues within 4Å: Chain A: Q.237, G.238, I.249, G.250, S.252, K.261, T.262, G.263 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.238, A:S.252, A:K.261 Water bridges: A:Q.237, A:R.240, A:Y.242, A:S.252 GOL.13: 3 residues within 4Å: Chain A: D.199, S.200, E.203 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neely, R.K. et al., Time-Resolved Fluorescence of 2-Aminopurine as a Probe of Base Flipping in M.HhaI-DNA Complexes. Nucleic Acids Res. (2005)

Release Date

2005-12-14

Peptides

MODIFICATION METHYLASE HHAI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

MODIFICATION METHYLASE HHAI

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