SMTL ID : 4ebc.1

Conformationally Restrained North-methanocarba-2'-deoxyadenosine Corrects the Error-Prone Nature of Human DNA Polymerase Iota

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x DA- DG- DG- DA- DC- DC- DOC: 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'(Non-covalent)

DA-DG-DG-DA-DC-DC-DOC.1: 21 residues within 4Å: Chain A: E.127, K.207, G.241, I.242, G.243, Y.244, K.245, T.246, E.358, S.359, R.360, Q.361 Ligands: DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, 0OH.3, CA.5 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.207 Salt bridges: A:K.207

1 x DC- DT- DG- DG- DG- DT- DC- DC- DT: 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'(Non-covalent)

DC-DT-DG-DG-DG-DT-DC-DC-DT.2: 28 residues within 4Å: Chain A: Q.59, K.60, Y.61, L.62, L.78, E.97, L.99, P.299, Q.300, S.301, F.302, S.303, E.304, E.305, D.306, S.307, R.331, R.347, R.357 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, DA-DG-DG-DA-DC-DC-DOC.1, 0OH.3, GOL.7 Protein-ligand interaction information (PLIP) not available

1 x 0OH: North-methanocarba-2'-deoxyadenosine triphosphate(Non-covalent)

0OH.3: 19 residues within 4Å: Chain A: D.34, D.36, C.37, F.38, Y.39, V.64, T.65, Y.68, R.71, K.77, L.78, D.126, E.127, K.214 Ligands: DA-DG-DG-DA-DC-DC-DOC.1, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2, CA.4, CA.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:F.38, A:Y.39, A:Y.39 Hydrogen bonds: A:C.37, A:F.38, A:Y.39, A:T.65, A:Y.68, A:Y.68, A:E.127 Water bridges: A:Q.59, A:K.77, A:K.77, A:K.214, A:K.214 Salt bridges: A:R.71, A:R.71, A:K.77, A:K.77, A:K.77, A:K.214

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: D.34, L.35, D.126 Ligands: 0OH.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.34, A:L.35, A:D.126 CA.5: 4 residues within 4Å: Chain A: K.237, I.239, I.242 Ligands: DA-DG-DG-DA-DC-DC-DOC.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.237, H2O.1, H2O.2, H2O.3 CA.6: 3 residues within 4Å: Chain A: D.34, E.127 Ligands: 0OH.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.34, A:E.127, H2O.1

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 8 residues within 4Å: Chain A: E.97, D.98, L.99, E.304, E.305, S.327 Ligands: DC-DT-DG-DG-DG-DT-DC-DC-DT.2, DC-DT-DG-DG-DG-DT-DC-DC-DT.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.99, A:E.305, A:S.327, A:S.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ketkar, A. et al., A Nucleotide-Analogue-Induced Gain of Function Corrects the Error-Prone Nature of Human DNA Polymerase iota. J.Am.Chem.Soc. (2012)

Release Date

2012-06-13

Peptides

DNA polymerase iota: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase iota

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