SMTL ID : 4i2i.1

Binary complex of mouse TdT with AP5A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x AP5: BIS(ADENOSINE)-5'-PENTAPHOSPHATE(Non-covalent)

AP5.1: 16 residues within 4Å: Chain A: G.222, G.223, R.226, G.231, H.232, D.233, D.235, F.295, D.324, G.339, W.340, G.342, R.344, E.347 Ligands: ZN.2, MG.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.223, A:H.232, A:D.233, A:E.347 Water bridges: A:T.230, A:D.233, A:D.235 Salt bridges: A:R.226, A:H.232, A:H.232, A:R.344

7 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.233, D.235, D.324 Ligands: AP5.1, MG.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.233, A:D.235, A:D.324 ZN.3: 1 residues within 4Å: Chain A: H.306 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.306, H2O.4, H2O.4, H2O.4 ZN.4: 2 residues within 4Å: Chain A: E.197, H.302 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.197, A:H.302, H2O.4, H2O.7 ZN.5: 1 residues within 4Å: Chain A: H.356 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.356, H2O.5 ZN.6: 1 residues within 4Å: Chain A: E.154 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.154, H2O.4 ZN.7: 2 residues within 4Å: Chain A: D.363, H.365 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.363, A:D.363, A:H.365, H2O.3 ZN.8: 2 residues within 4Å: Chain A: D.69, C.78 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.69, A:C.78

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: D.233, D.235 Ligands: AP5.1, ZN.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gouge, J. et al., Structures of Intermediates along the Catalytic Cycle of Terminal Deoxynucleotidyltransferase: Dynamical Aspects of the Two-Metal Ion Mechanism. J.Mol.Biol. (2013)

Release Date

2013-07-24

Peptides

DNA nucleotidylexotransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA nucleotidylexotransferase

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