SMTL ID : 3g2c.1

Mth0212 in complex with a short ssDNA (CGTA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

DC-DG-DT-DA.1: 15 residues within 4Å: Chain A: Y.208, R.209, R.211 Chain B: K.116, R.163, N.167, V.170, W.205, S.207, R.209, T.210, R.215, V.217, W.219 Ligands: GOL.13 Protein-ligand interaction information (PLIP) not available

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: W.9, K.20, G.21, F.22, V.243, M.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.20, A:M.244, A:M.244 GOL.3: 5 residues within 4Å: Chain A: W.25, E.28, E.29, L.240, V.243 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.28, A:E.29 Water bridges: A:D.242, A:V.243 GOL.4: 1 residues within 4Å: Chain A: D.242 No protein-ligand interaction detected (PLIP) GOL.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.6: 5 residues within 4Å: Chain A: E.158, I.159, L.161, P.164, P.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.161 GOL.10: 2 residues within 4Å: Chain A: F.86, R.138 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.138 GOL.13: 3 residues within 4Å: Chain B: T.210, R.215 Ligands: DC-DG-DT-DA.1 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: N.12, E.38 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.38, A:E.38 MG.11: 5 residues within 4Å: Chain B: N.10, N.12, E.38, D.247 Ligands: PO4.12 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.38

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

PO4.8: 8 residues within 4Å: Chain A: N.10, E.38, Y.111, N.114, D.151, N.153, H.248 Ligands: MG.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.10, A:Y.111, A:N.114, A:N.153, A:N.153 Salt bridges: A:H.248 PO4.9: 3 residues within 4Å: Chain A: R.157, E.158, R.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.158, A:E.158, A:R.178 PO4.12: 8 residues within 4Å: Chain B: N.10, E.38, Y.111, N.114, D.151, N.153, H.248 Ligands: MG.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.10, B:Y.111, B:N.114, B:D.151, B:N.153 Salt bridges: B:H.248

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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