5j2f.1 | SWISS-MODEL Template Library

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SMTL ID : 5j2f.1

Ternary complex crystal structure of DNA polymerase Beta with G:A mismatch at the primer terminus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: Downstream Primer Strand(Non-covalent)

DG-DT-DC-DG-DG.1:

18 residues within 4Å:

Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.6

5 PLIP interactions:

5 interactions with chain A

Hydrogen bonds: A:R.283
Water bridges: A:N.37, A:N.37
Salt bridges: A:K.280
pi-Stacking: A:H.34

1 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.2:

18 residues within 4Å:

Chain A: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, S.275, D.276, N.279
Chain B: A.6
Chain C: A.10
Ligands: MG.3, MG.4

14 PLIP interactions:

14 interactions with chain A

Hydrophobic interactions: A:D.276
Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:D.190, A:D.192, A:N.279
Water bridges: A:R.149, A:S.180, A:D.276, A:D.276

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: DUP.2, MG.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.2
MG.4:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: A.10 Ligands: DUP.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.3

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

NA.5:	5 residues within 4Å: Chain A: T.101, V.103, G.105, I.106 Chain C: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.105, A:I.106, A:I.106
NA.6:	4 residues within 4Å: Chain A: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.62, A:V.65 Water bridges: A:K.60

5 x CL: CHLORIDE ION(Non-functional Binders)

CL.7:	5 residues within 4Å: Chain A: D.263, Q.264, Y.266, C.267, V.313 Ligand excluded by PLIP
CL.8:	4 residues within 4Å: Chain A: A.32, I.33, H.34, K.35 Ligand excluded by PLIP
CL.9:	3 residues within 4Å: Chain A: K.81, L.82, R.89 Ligand excluded by PLIP
CL.10:	3 residues within 4Å: Chain A: N.294, T.297, R.299 Ligand excluded by PLIP
CL.11:	5 residues within 4Å: Chain A: K.234, R.258, Y.271, F.272 Chain C: A.10 Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Structures of DNA Polymerase Mispaired DNA Termini Transitioning to Pre-catalytic Complexes Support an Induced-Fit Fidelity Mechanism. Structure (2016)

Release Date

2016-10-26

Peptides

DNA polymerase beta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

DNA polymerase beta

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