2fmp.1 | SWISS-MODEL Template Library

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SMTL ID : 2fmp.1

DNA Polymerase beta with a terminated gapped DNA substrate and ddCTP with sodium in the catalytic site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: 5'-D(P*GP*TP*CP*GP*G)-3'(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

8 PLIP interactions:

8 interactions with chain C

Hydrogen bonds: C:N.279, C:K.280, C:R.283, C:R.283, C:R.283
Water bridges: C:N.37
Salt bridges: C:K.280
pi-Stacking: C:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

4 residues within 4Å:

Chain C: D.190, D.192
Ligands: NA.3, DCT.8

4 PLIP interactions:

2 interactions with chain C, 2 Ligand-Water interactions

Metal complexes: C:D.190, C:D.192, H₂O.6, H₂O.6

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

NA.3:	6 residues within 4Å: Chain B: C.10 Chain C: D.190, D.192, D.256 Ligands: MG.2, DCT.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.190
NA.4:	5 residues within 4Å: Chain B: G.9 Chain C: T.101, V.103, 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 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.60, C:V.65
NA.6:	2 residues within 4Å: Chain C: R.126 Ligands: NA.7 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.126, C:E.129
NA.7:	1 residues within 4Å: Ligands: NA.6 No protein-ligand interaction detected (PLIP)

1 x DCT: 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE(Non-covalent)

DCT.8:

16 residues within 4Å:

Chain A: G.6
Chain B: C.10
Chain C: G.179, S.180, R.183, S.188, G.189, D.190, D.192, Y.271, F.272, G.274, D.276, N.279
Ligands: MG.2, NA.3

13 PLIP interactions:

13 interactions with chain C

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Batra, V.K. et al., Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure (2006)

Release Date

2006-04-25

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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