SMTL ID : 4i2c.1

Ternary complex of mouse TdT with ssDNA and AMPcPP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

DA-DA-DA.1: 12 residues within 4Å: Chain A: V.145, G.147, V.148, G.149, L.150, K.151, T.152, M.178, F.295, R.322 Ligands: NA.2, APC.3 Protein-ligand interaction information (PLIP) not available

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

NA.2: 5 residues within 4Å: Chain A: T.143, V.145, V.148 Ligands: DA-DA-DA.1, DA-DA-DA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.145, A:V.148

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

APC.3: 15 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 Ligands: DA-DA-DA.1, MN.4, MN.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.223, A:R.226, A:R.226, A:H.232, A:D.233, A:D.324 Water bridges: A:N.364 Salt bridges: A:H.232 pi-Stacking: A:W.340

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

MN.4: 5 residues within 4Å: Chain A: D.233, D.235, D.324 Ligands: APC.3, MN.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, A:D.324, H2O.11 MN.5: 4 residues within 4Å: Chain A: D.233, D.235 Ligands: APC.3, MN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.11

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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