6cr9.1 | SWISS-MODEL Template Library

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SMTL ID : 6cr9.1

Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CFCL, beta, gamma dATP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 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: C.1, C.2, G.3, A.4, C.5
Chain C: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Ligands: NA.5

6 PLIP interactions:

6 interactions with chain C

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

1 x VA5: 9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine(Non-covalent)

VA5.2:

19 residues within 4Å:

Chain A: T.6, G.7
Chain B: C.10
Chain C: 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.3, NA.6

13 PLIP interactions:

13 interactions with chain C

Hydrogen bonds: C:S.180, C:R.183, C:R.183, C:G.189, C:D.190, C:F.272, C:N.279
Water bridges: C:R.149, C:R.149, C:D.276, C:D.276, C:D.276
Halogen bonds: C:R.183

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3:

4 residues within 4Å:

Chain C: D.190, D.192
Ligands: VA5.2, NA.6

3 PLIP interactions:

2 interactions with chain C, 1 Ligand-Water interactions

Metal complexes: C:D.190, C:D.192, H₂O.7

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

NA.4:	6 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, S.104, G.105, I.106 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.105, C:I.106, C:I.106
NA.5:	4 residues within 4Å: Chain C: K.60, L.62, V.65 Ligands: DG-DT-DC-DG-DG.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.60, C:V.65 Water bridges: C:K.60
NA.6:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: VA5.2, MG.3 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.256

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

CL.7:

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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