SMTL ID : 3g00.1

Mth0212 in complex with a 9bp blunt end dsDNA at 1.7 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

1 x DC- DG- DT- DA- DT- DT- DA- DC- DG: 5'-D(*CP*GP*TP*AP*TP*TP*AP*CP*G)-3'(Non-covalent)

DC-DG-DT-DA-DT-DT-DA-DC-DG.1: 31 residues within 4Å: Chain A: N.12, G.13, L.14, R.15, A.16, R.19, K.20, K.40, Q.45, K.66, G.67, Y.208, R.209 Chain B: E.38, R.65, Y.68, R.96, N.114, M.117, R.209 Ligands: DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2, MPD.10, PO4.11 Protein-ligand interaction information (PLIP) not available

1 x DC- DG- DT- DA- DU- DT- DA- DC- DG: 5'-D(*CP*GP*TP*AP*UP*TP*AP*CP*G)-3'(Non-covalent)

DC-DG-DT-DA-DU-DT-DA-DC-DG.2: 30 residues within 4Å: Chain A: R.65, Y.68, N.114, M.117, R.209 Chain B: N.12, G.13, L.14, R.15, A.16, R.19, K.20, K.40, Q.45, K.66, G.67, Y.208, R.209, R.211 Ligands: DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, DC-DG-DT-DA-DT-DT-DA-DC-DG.1, GOL.5, PO4.8 Protein-ligand interaction information (PLIP) not available

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

PO4.3: 6 residues within 4Å: Chain A: R.57, F.59, P.79, S.80, S.81, L.82 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.57 Water bridges: A:L.82, A:L.82 PO4.4: 4 residues within 4Å: Chain A: E.44, Q.45, L.46, P.47 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.44 PO4.8: 7 residues within 4Å: Chain A: N.10, N.12, E.38, W.205, D.247, H.248 Ligands: DC-DG-DT-DA-DU-DT-DA-DC-DG.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.10, A:E.38, A:E.38, A:N.151 Water bridges: A:N.12, A:N.114, A:N.153, A:D.247 Salt bridges: A:H.248 PO4.11: 7 residues within 4Å: Chain B: N.10, N.12, E.38, W.205, D.247, H.248 Ligands: DC-DG-DT-DA-DT-DT-DA-DC-DG.1 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.10, B:N.12, B:N.151 Water bridges: B:N.12, B:N.114, B:N.153, B:N.153, B:H.248 Salt bridges: B:H.248

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: R.65, Y.68, E.94, M.117, R.121 Ligands: DC-DG-DT-DA-DU-DT-DA-DC-DG.2, DC-DG-DT-DA-DU-DT-DA-DC-DG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.65 Water bridges: A:R.121 GOL.6: 6 residues within 4Å: Chain A: R.140, G.143, R.144, N.145, N.227, E.229 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.144, A:N.145 GOL.9: 5 residues within 4Å: Chain B: K.20, W.25, D.242, V.243, M.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.244 Water bridges: B:W.25, B:W.25

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.7: 5 residues within 4Å: Chain A: K.20, G.21, W.25, E.28, M.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.21 MPD.10: 6 residues within 4Å: Chain B: R.65, Y.68, E.94, M.117, R.121 Ligands: DC-DG-DT-DA-DT-DT-DA-DC-DG.1 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.68 Hydrogen bonds: B:R.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lakomek, K. et al., Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA. J.Mol.Biol. (2010)

Release Date

2010-03-09

Peptides

Exodeoxyribonuclease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Exodeoxyribonuclease

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