SMTL ID : 1oup.2 (1 other biounit)

Crystal structure of the periplasmic endonuclease Vvn complexed with octamer double stranded DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

DG-DC-DG-DA-DT-DC.1: 14 residues within 4Å: Chain A: R.54, W.67, W.76, N.109, G.110, S.113, N.114 Ligands: DG-DC.2, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3 Protein-ligand interaction information (PLIP) not available

1 x DG- DC: 5'-D(P*GP*C)-3'(Non-covalent)

DG-DC.2: 13 residues within 4Å: Chain A: F.6, K.10, R.57, E.59, W.60, R.81, K.82, N.109 Ligands: DG-DC-DG-DA-DT-DC.1, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3, DG-DC-DG-DA-DT-DC-DG-DC.3, CA.4 Protein-ligand interaction information (PLIP) not available

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

DG-DC-DG-DA-DT-DC-DG-DC.3: 14 residues within 4Å: Chain A: R.49, K.50, Q.51, K.82, F.137, K.138 Ligands: DG-DC-DG-DA-DT-DC.1, DG-DC-DG-DA-DT-DC.1, DG-DC-DG-DA-DT-DC.1, DG-DC-DG-DA-DT-DC.1, DG-DC-DG-DA-DT-DC.1, DG-DC-DG-DA-DT-DC.1, DG-DC.2, DG-DC.2 Protein-ligand interaction information (PLIP) not available

1 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: E.61, A.62, N.109 Ligands: DG-DC.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.61, H2O.1, H2O.2, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, C.-L. et al., DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. Embo J. (2003)

Release Date

2003-08-05

Peptides

Nuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nuclease

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