SMTL ID : 4i2h.1

Ternary complex of mouse TdT with ssDNA and AMPcPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

monomer

Ligands

1 x DA- DA: 5'-D(P*AP*AP*AP*AP*A)-3'(Non-covalent)

DA-DA.1: 9 residues within 4Å: Chain A: V.145, F.146, G.147, V.148, G.149, L.150, K.151, T.152 Ligands: NA.3 Protein-ligand interaction information (PLIP) not available

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.233, D.235 Ligands: APC.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: T.143, V.145, V.148 Ligands: DA-DA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.143, A:V.148

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.233, D.235, D.324 Ligands: APC.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.233, A:D.235, A:D.235, A:D.324 ZN.5: 2 residues within 4Å: Chain A: D.363, H.365 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.363, A:H.365

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.6: 16 residues within 4Å: Chain A: G.222, G.223, R.226, G.231, H.232, D.233, D.235, D.289, G.339, W.340, G.342, R.344, E.347, N.364 Ligands: MG.2, ZN.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.223, A:R.226, A:R.226, A:H.232, A:D.233, A:D.289, A:D.289, A:T.341, A:N.364 Water bridges: A:D.233, A:R.344 pi-Stacking: A:W.340, A:W.340

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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