SMTL ID : 1sx5.1

K38A EcoRV bound to cleaved DNA and Mn2+: P1 crystal form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

DA-DA-DA-DG-DA-DT.1: 22 residues within 4Å: Chain A: N.69, G.108, T.110, S.111, F.112, K.118, N.119, T.185 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.221, S.222, R.225 Chain B: N.69, H.70, 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: 5'-D(P*AP*TP*CP*TP*T)-3'(Non-covalent)

DA-DT-DC-DT-DT.2: 27 residues within 4Å: Chain A: T.36, E.44, D.73, K.91, T.92, T.93, Y.94, T.105, G.181, S.182, T.185, N.187 Chain B: D.35, Q.68, N.69, H.70 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, MN.5, MN.6, MN.11 Protein-ligand interaction information (PLIP) not available DA-DT-DC-DT-DT.4: 29 residues within 4Å: Chain A: Q.67, Q.68, N.69, H.70 Chain B: T.36, S.40, D.73, D.89, I.90, K.91, T.92, T.93, Y.94, T.105, 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, MN.9, MN.10, MN.13 Protein-ligand interaction information (PLIP) not available

9 x MN: MANGANESE (II) ION(Non-covalent)

MN.5: 4 residues within 4Å: Chain A: E.44, D.73 Ligands: DA-DT-DC-DT-DT.2, MN.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:D.73, H2O.6, H2O.7 MN.6: 5 residues within 4Å: Chain A: E.44, D.73, I.90 Ligands: DA-DT-DC-DT-DT.2, MN.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.44, A:D.73, A:I.90, H2O.1, H2O.1 MN.7: 1 residues within 4Å: Chain A: H.192 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.192, H2O.5, H2O.9, H2O.9 MN.8: 2 residues within 4Å: Chain A: H.194, D.197 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.194, A:D.197, H2O.3 MN.9: 3 residues within 4Å: Chain A: Q.67, H.70 Ligands: DA-DT-DC-DT-DT.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.70, H2O.2, H2O.2 MN.10: 6 residues within 4Å: Chain B: E.44, D.73, D.89, I.90 Ligands: DA-DT-DC-DT-DT.4, MN.13 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.73, B:D.89, B:I.90 MN.11: 2 residues within 4Å: Chain B: H.70 Ligands: DA-DT-DC-DT-DT.2 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.70, H2O.1, H2O.1, H2O.9, H2O.12 MN.12: 2 residues within 4Å: Chain B: H.194, D.197 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.194, B:D.197 MN.13: 4 residues within 4Å: Chain B: E.44, D.73 Ligands: DA-DT-DC-DT-DT.4, MN.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.44, B:E.44, B:D.73, H2O.15, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, N.C. et al., DNA cleavage by EcoRV endonuclease: Two metal ions in three metal ion binding sites. Biochemistry (2004)

Release Date

2004-04-06

Peptides

Type II restriction enzyme EcoRV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Type II restriction enzyme EcoRV

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