SMTL ID : 3g3c.1

Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.04 Å

Oligo State

homo-dimer

Ligands

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

DC-DG-DT-DA-DC-DT-DA.1: 30 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, Y.111, N.114, M.117, R.209 Ligands: DT-DA-UPS-DT-DA-DC-DG.2, DT-DA-UPS-DT-DA-DC-DG.2, DT-DA-UPS-DT-DA-DC-DG.2, DT-DA-UPS-DT-DA-DC-DG.2, DT-DA-UPS-DT-DA-DC-DG.2, DT-DA-UPS-DT-DA-DC-DG.2, DT-DA-UPS-DT-DA-DC-DG.2, PO4.6, MG.7 Protein-ligand interaction information (PLIP) not available

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

DT-DA-UPS-DT-DA-DC-DG.2: 28 residues within 4Å: Chain A: E.38, R.65, Y.68, Y.111, N.114, M.117, R.209 Chain B: N.12, G.13, R.15, A.16, R.19, K.20, K.40, Q.45, K.66, G.67, Y.208, R.209 Ligands: DC-DG-DT-DA-DC-DT-DA.1, DC-DG-DT-DA-DC-DT-DA.1, DC-DG-DT-DA-DC-DT-DA.1, DC-DG-DT-DA-DC-DT-DA.1, DC-DG-DT-DA-DC-DT-DA.1, DC-DG-DT-DA-DC-DT-DA.1, DC-DG-DT-DA-DC-DT-DA.1, PO4.3, MG.4 No protein-ligand interaction detected (PLIP)

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

PO4.3: 9 residues within 4Å: Chain A: N.10, E.38, Y.111, N.114, D.151, N.153, H.248 Ligands: DT-DA-UPS-DT-DA-DC-DG.2, MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.10, A:D.151, A:N.153 Salt bridges: A:H.248 PO4.6: 10 residues within 4Å: Chain B: N.10, E.38, Y.111, N.114, D.151, N.153, L.221, H.248 Ligands: DC-DG-DT-DA-DC-DT-DA.1, MG.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.10, B:Y.111, B:N.153, B:N.153, B:N.153 Salt bridges: B:H.248

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: N.12, E.38, D.247 Ligands: DT-DA-UPS-DT-DA-DC-DG.2, PO4.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.38 MG.7: 6 residues within 4Å: Chain B: N.10, N.12, E.38, D.247 Ligands: DC-DG-DT-DA-DC-DT-DA.1, PO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.38

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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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