SMTL ID : 4i27.1

Ternary complex of mouse TdT with ssDNA and incoming nucleotide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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

DA-DA-DA-DA-DA-2DT.1: 20 residues within 4Å: Chain A: V.145, F.146, G.147, V.148, G.149, L.150, K.151, T.152, M.178, H.232, D.233, L.271, A.287, L.288, F.295, R.322, D.324, W.340 Ligands: D3T.3, NA.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.340 Salt bridges: A:H.232, A:R.322

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.232, D.233, D.235 Ligands: D3T.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.233, A:D.235, H2O.8

1 x D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

D3T.3: 16 residues within 4Å: Chain A: G.222, G.223, R.226, K.228, T.230, G.231, H.232, D.233, D.235, G.339, W.340, G.342, E.347, R.351 Ligands: DA-DA-DA-DA-DA-2DT.1, MG.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.347 Hydrogen bonds: A:G.223, A:H.232, A:D.233, A:D.235, A:R.351 Water bridges: A:F.224, A:F.224, A:R.226, A:E.347 Salt bridges: A:R.226, A:K.228, A:K.228, A:H.232, A:H.232

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

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

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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