SMTL ID : 3pnc.1

Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x DC- DA- DG- DT- DA- DG: 5'-D(*CP*AP*GP*TP*AP*G)-3'(Non-covalent)

DC-DA-DG-DT-DA-DG.1: 26 residues within 4Å: Chain A: I.100, W.101, G.102, A.103, G.104, T.105, K.106, T.107, D.188, L.228, R.242, D.244, Y.259, F.260 Chain B: C.5, T.6, T.7, A.8, C.9, T.10, G.11 Ligands: 1GC.3, NA.5, NA.6, TRS.7, NA.8 Protein-ligand interaction information (PLIP) not available

1 x DG- DC- DC- DG: 5'-D(*GP*CP*CP*G)-3'(Non-covalent)

DG-DC-DC-DG.2: 16 residues within 4Å: Chain A: W.33, R.34, G.37, Y.38, I.61, P.62, G.63, I.64, G.65, K.66, R.67, M.68 Chain B: C.1, G.2, G.3, C.4 Protein-ligand interaction information (PLIP) not available

1 x 1GC: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine(Non-covalent)

1GC.3: 22 residues within 4Å: Chain A: R.145, G.175, S.176, R.179, C.184, G.185, D.186, D.188, Y.259, F.260, T.261, G.262, S.263, A.264, N.267, R.271 Chain B: C.5 Ligands: DC-DA-DG-DT-DA-DG.1, MG.4, NA.5, TRS.7, NA.8 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.176, A:S.176, A:R.179, A:R.179, A:G.185, A:D.186, A:N.267, A:R.271 Water bridges: A:R.145, A:R.145, A:R.145, A:A.264, A:R.268 Salt bridges: A:R.145

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.186, D.188 Ligands: 1GC.3, NA.5, TRS.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.186, A:D.188, H2O.6

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

NA.5: 7 residues within 4Å: Chain A: D.186, D.188, D.244 Ligands: DC-DA-DG-DT-DA-DG.1, 1GC.3, MG.4, TRS.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.188 NA.6: 6 residues within 4Å: Chain A: S.98, I.100, W.101, G.102, A.103 Ligands: DC-DA-DG-DT-DA-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.100, A:G.102, A:A.103 NA.8: 2 residues within 4Å: Ligands: DC-DA-DG-DT-DA-DG.1, 1GC.3 No protein-ligand interaction detected (PLIP)

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 8 residues within 4Å: Chain A: W.101, G.185, D.186, R.242 Ligands: DC-DA-DG-DT-DA-DG.1, 1GC.3, MG.4, NA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.242, A:R.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bebenek, K. et al., Replication infidelity via a mismatch with Watson-Crick geometry. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-02-02

Peptides

DNA polymerase lambda: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA polymerase lambda

Related Entries With Identical Sequence