SMTL ID : 3a4k.2 (1 other biounit)

Crystal structural analysis of HindIII restriction endonuclease in complex with cognate DNA and divalent cations at 2.17 angstrom resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 Å

Oligo State

homo-dimer

Ligands

2 x DG- DC- DC- DA: DNA (5'-D(*GP*CP*CP*A)-3')(Non-covalent)

DG-DC-DC-DA.1: 20 residues within 4Å: Chain A: G.91, N.92, K.127, W.134 Chain B: A.120, N.122, Q.123, P.151, T.152, T.153, K.154, S.155, Q.156 Ligands: DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, MG.5 Protein-ligand interaction information (PLIP) not available DG-DC-DC-DA.3: 22 residues within 4Å: Chain A: A.120, N.122, Q.123, P.151, T.152, T.153, K.154, S.155, Q.156 Chain B: R.90, G.91, N.92, D.95, K.127, W.134 Ligands: DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.4, MG.8 Protein-ligand interaction information (PLIP) not available

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

DA-DG-DC-DT-DT-DG-DG-DC.2: 41 residues within 4Å: Chain A: L.51, S.58, E.62, S.66, D.95, D.110, A.111, K.112, S.113, F.114, R.115, S.117, R.118, T.119, A.120, N.122, D.125, K.127 Chain B: F.22, K.23, S.58, S.59, T.60, K.63, R.90, N.122, K.124, N.278, K.282 Ligands: DG-DC-DC-DA.1, DG-DC-DC-DA.3, DG-DC-DC-DA.3, DG-DC-DC-DA.3, DG-DC-DC-DA.3, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, DA-DG-DC-DT-DT-DG-DG-DC.4, MG.5, MN.6 Protein-ligand interaction information (PLIP) not available DA-DG-DC-DT-DT-DG-DG-DC.4: 41 residues within 4Å: Chain A: F.22, S.58, S.59, T.60, K.63, E.88, N.122, K.124, N.278, K.282 Chain B: L.51, S.58, E.62, S.66, D.95, D.110, A.111, K.112, S.113, F.114, R.115, S.117, R.118, T.119, A.120, N.122, K.124, D.125, K.127 Ligands: DG-DC-DC-DA.1, DG-DC-DC-DA.1, DG-DC-DC-DA.1, DG-DC-DC-DA.1, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DA-DG-DC-DT-DT-DG-DG-DC.2, DG-DC-DC-DA.3, MG.8, MN.9 Protein-ligand interaction information (PLIP) not available

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.95 Ligands: DG-DC-DC-DA.1, DA-DG-DC-DT-DT-DG-DG-DC.2, MN.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.95, H2O.4, H2O.9 MG.8: 5 residues within 4Å: Chain B: A.93, D.95 Ligands: DG-DC-DC-DA.3, DA-DG-DC-DT-DT-DG-DG-DC.4, MN.9 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.95, H2O.9, H2O.10, H2O.10

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

MN.6: 5 residues within 4Å: Chain A: D.95, D.110, A.111 Ligands: DA-DG-DC-DT-DT-DG-DG-DC.2, MG.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.95, A:D.110, A:A.111, H2O.5 MN.9: 5 residues within 4Å: Chain B: D.95, D.110, A.111 Ligands: DA-DG-DC-DT-DT-DG-DG-DC.4, MG.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.95, B:D.110, B:A.111, H2O.9

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: D.163, S.201, T.204, S.205, V.206, A.209 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.206 ACT.11: 7 residues within 4Å: Chain B: L.162, D.163, S.201, T.204, S.205, V.206, A.209 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.209

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain B: K.203, T.204, N.211, N.212, F.213, D.216 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.203, B:D.208, B:N.211, B:N.212 Water bridges: B:Q.200, B:T.204, B:D.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watanabe, N. et al., Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations. Acta Crystallogr.,Sect.D (2009)

Release Date

2009-10-20

Peptides

Type-2 restriction enzyme HindIII: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Type-2 restriction enzyme HindIII

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