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SMTL ID : 8ick.1

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF DATP (1 MILLIMOLAR), MGCL2 (5 MILLIMOLAR), AND MNCL2 (5 MILLIMOLAR)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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: N.133, S.229, K.230, G.231, E.232, T.233, K.234
Ligands: DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2

Protein-ligand interaction information (PLIP) not available

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

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

23 residues within 4Å:

Chain A: V.103, S.104, G.105, I.106, G.107, P.108, S.109, A.110, D.192, K.234, R.254, Y.271, F.272
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, MN.3, MN.4, NA.5

Protein-ligand interaction information (PLIP) not available

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.3:	5 residues within 4Å: Chain A: D.190, D.192 Ligands: DT-DC-DT-DA-DA-DT-DG-DA.2, MN.4, DTP.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.190
MN.4:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DT-DC-DT-DA-DA-DT-DG-DA.2, DT-DC-DT-DA-DA-DT-DG-DA.2, MN.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.190, A:D.192, A:D.256

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-DA.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.102, A:G.105, A:I.106
NA.6:	4 residues within 4Å: Chain A: K.60, K.61, L.62, V.65 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

1 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.7:

8 residues within 4Å:

Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190
Ligands: MN.3

9 PLIP interactions:

9 interactions with chain A

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Pelletier, H. et al., A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta. 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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Cartoon
Tube
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Lines
Ball+Stick
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Hyperball
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Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

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Extreme

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