6g2q.1 | SWISS-MODEL Template Library

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SMTL ID : 6g2q.1

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHCL (S-isomer), beta, gamma dTTP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

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

17 residues within 4Å:

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

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:R.283
Salt bridges: C:K.280
pi-Stacking: C:H.34

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

NA.2:	7 residues within 4Å: Chain B: G.9 Chain C: T.101, R.102, V.103, S.104, G.105, I.106 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.105, C:I.106
NA.6:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.62
NA.7:	5 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: EJH.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.192

1 x EJH: [(~{S})-chloranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphonic acid(Non-covalent)

EJH.3:

19 residues within 4Å:

Chain A: A.6
Chain B: C.10
Chain C: R.149, 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
Ligands: MG.4, NA.7

12 PLIP interactions:

12 interactions with chain C

Hydrophobic interactions: C:D.276
Hydrogen bonds: C:R.149, C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:D.192, C:N.279
Water bridges: C:R.254, C:R.254, C:D.276

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4:

3 residues within 4Å:

Chain C: D.190, D.192
Ligands: EJH.3

3 PLIP interactions:

2 interactions with chain C, 1 Ligand-Water interactions

Metal complexes: C:D.190, C:D.192, H₂O.4

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

CL.5:

4 residues within 4Å:

Chain C: A.32, I.33, H.34, K.35

Ligand excluded by PLIP

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry (2018)

Release Date

2018-07-04

Peptides

DNA polymerase beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
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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