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SMTL ID : 9icg.1

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DCTP (1 MILLIMOLAR) AND ZNCL2 (1 MILLIMOLAR)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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

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

14 residues within 4Å:

Chain A: S.229, K.230, G.231, E.232, T.233, K.234, Y.296
Ligands: DT-DC-DT-DA-DA-DT-DG.2, DT-DC-DT-DA-DA-DT-DG.2, DT-DC-DT-DA-DA-DT-DG.2, DT-DC-DT-DA-DA-DT-DG.2, DT-DC-DT-DA-DA-DT-DG.2, DT-DC-DT-DA-DA-DT-DG.2, DT-DC-DT-DA-DA-DT-DG.2

Protein-ligand interaction information (PLIP) not available

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

DT-DC-DT-DA-DA-DT-DG.2:

21 residues within 4Å:

Chain A: V.103, S.104, G.105, I.106, G.107, P.108, S.109, A.110, K.234, R.254, D.256
Ligands: DC-DA-DT-DT-DA-DG-DA-DA.1, DC-DA-DT-DT-DA-DG-DA-DA.1, DC-DA-DT-DT-DA-DG-DA-DA.1, DC-DA-DT-DT-DA-DG-DA-DA.1, DC-DA-DT-DT-DA-DG-DA-DA.1, DC-DA-DT-DT-DA-DG-DA-DA.1, DC-DA-DT-DT-DA-DG-DA-DA.1, ZN.4, NA.5, DCP.8

Protein-ligand interaction information (PLIP) not available

3 x ZN: ZINC ION(Non-covalent)

ZN.3:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: ZN.4, DCP.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.190, A:D.192
ZN.4:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DT-DC-DT-DA-DA-DT-DG.2, ZN.3, DCP.8 No protein-ligand interaction detected (PLIP)
ZN.7:	1 residues within 4Å: Chain A: H.51 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.51

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

NA.5:	7 residues within 4Å: Chain A: T.101, R.102, V.103, S.104, G.105, I.106 Ligands: DT-DC-DT-DA-DA-DT-DG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.102, A:G.105, A:I.106
NA.6:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x DCP: 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

DCP.8:

16 residues within 4Å:

Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, T.273, G.274, D.276
Ligands: DT-DC-DT-DA-DA-DT-DG.2, ZN.3, ZN.4

10 PLIP interactions:

10 interactions with chain A

Hydrogen bonds: A:S.180, A:S.180, A:S.180, A:G.189, A:D.190, A:D.190
Water bridges: A:F.181, A:F.272
Salt bridges: A:R.149, A:R.183

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pelletier, H. et al., Characterization of the metal ion binding helix-hairpin-helix motifs in human DNA polymerase beta by X-ray structural analysis. Biochemistry (1996)

Release Date

1996-11-15

Peptides

PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7)): 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

PROTEIN (DNA POLYMERASE BETA (E.C.2.7.7.7))

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Background

Transparent

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