SMTL ID : 1rvc.1

MG2+ BINDING TO THE ACTIVE SITE OF ECO RV ENDONUCLEASE: A CRYSTALLOGRAPHIC STUDY OF COMPLEXES WITH SUBSTRATE AND PRODUCT DNA AT 2 ANGSTROMS RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x DA- DA- DA- DG- DA- DT: DNA (5'-D(*AP*AP*AP*GP*AP*T)-3')(Non-covalent)

DA-DA-DA-DG-DA-DT.1: 23 residues within 4Å: Chain A: N.69, G.108, T.110, S.111, F.112, K.118, N.119, T.185, R.220 Chain B: L.179, S.182, G.183, N.184, T.185, T.221, S.222, R.225 Ligands: DA-DT-DC-DT-DT.2, DA-DT-DC-DT-DT.4, DA-DT-DC-DT-DT.4, DA-DT-DC-DT-DT.4, DA-DT-DC-DT-DT.4, DA-DT-DC-DT-DT.4 Protein-ligand interaction information (PLIP) not available DA-DA-DA-DG-DA-DT.3: 22 residues within 4Å: Chain A: L.179, S.182, G.183, N.184, T.185, T.221, S.222, R.225 Chain B: N.69, G.108, T.110, S.111, F.112, K.118, N.119, T.185 Ligands: DA-DT-DC-DT-DT.2, DA-DT-DC-DT-DT.2, DA-DT-DC-DT-DT.2, DA-DT-DC-DT-DT.2, DA-DT-DC-DT-DT.2, DA-DT-DC-DT-DT.4 Protein-ligand interaction information (PLIP) not available

2 x DA- DT- DC- DT- DT: DNA (5'-D(*AP*TP*CP*TP*T)-3')(Non-covalent)

DA-DT-DC-DT-DT.2: 29 residues within 4Å: Chain A: T.36, S.40, E.44, Q.68, D.73, I.90, K.91, T.92, T.93, Y.94, T.105, G.181, S.182, T.185, N.187 Chain B: K.37, Q.67, Q.68, N.69 Ligands: DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.3, DA-DA-DA-DG-DA-DT.3, DA-DA-DA-DG-DA-DT.3, DA-DA-DA-DG-DA-DT.3, DA-DA-DA-DG-DA-DT.3, DA-DA-DA-DG-DA-DT.3, DA-DT-DC-DT-DT.4, MG.5, MG.7 Protein-ligand interaction information (PLIP) not available DA-DT-DC-DT-DT.4: 29 residues within 4Å: Chain A: K.37, Q.67, Q.68, N.69 Chain B: T.36, S.40, E.44, Q.68, D.73, K.91, T.92, T.93, Y.94, T.105, R.139, G.181, S.182, T.185, N.187 Ligands: DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DA-DA-DG-DA-DT.1, DA-DT-DC-DT-DT.2, DA-DA-DA-DG-DA-DT.3, MG.6, MG.8 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: Q.68 Chain B: K.37 Ligands: DA-DT-DC-DT-DT.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:Q.68, H2O.1, H2O.1, H2O.1, H2O.5 MG.6: 2 residues within 4Å: Chain B: Q.68 Ligands: DA-DT-DC-DT-DT.4 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:Q.68, H2O.2, H2O.5, H2O.8, H2O.8 MG.7: 4 residues within 4Å: Chain A: E.44, D.73, I.90 Ligands: DA-DT-DC-DT-DT.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:D.73, A:D.73, H2O.1, H2O.5 MG.8: 4 residues within 4Å: Chain B: E.44, D.73, I.90 Ligands: DA-DT-DC-DT-DT.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.44, B:D.73, B:D.73, H2O.2, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kostrewa, D. et al., Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution. Biochemistry (1995)

Release Date

1995-01-26

Peptides

PROTEIN (ECO RV (E.C.3.1.21.4)): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROTEIN (ECO RV (E.C.3.1.21.4))

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