4lvs.1 | SWISS-MODEL Template Library

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SMTL ID : 4lvs.1

DNA polymerase beta mismatched substrate complex with Mn2+, 2.5 min

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

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

18 residues within 4Å:

Chain A: H.34, K.35, A.38, Y.39, L.62, P.63, G.64, V.65, G.66, T.67, K.68, I.69
Chain C: C.1, C.2, G.3, A.4, C.5
Ligands: NA.7

4 PLIP interactions:

4 interactions with chain A

Hydrogen bonds: A:R.283, A:R.283
Water bridges: A:H.34
pi-Stacking: A:H.34

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

DTP.2:

20 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, S.275, D.276, N.279
Chain B: C.10
Chain C: G.6, G.7
Ligands: MN.3, MN.4

7 PLIP interactions:

7 interactions with chain A

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

6 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.3:	5 residues within 4Å: Chain A: D.190, D.192, D.256 Ligands: DTP.2, MN.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.1, H₂O.6
MN.4:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: DTP.2, MN.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.1
MN.5:	1 residues within 4Å: Chain A: D.124 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.124, H₂O.5, H₂O.5, H₂O.5, H₂O.5
MN.8:	2 residues within 4Å: Chain B: G.4, A.5 No protein-ligand interaction detected (PLIP)
MN.9:	1 residues within 4Å: Chain C: G.15 No protein-ligand interaction detected (PLIP)
MN.10:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.6:	6 residues within 4Å: Chain A: T.101, V.103, S.104, G.105, I.106 Chain B: G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.103, A:G.105, A:I.106
NA.7:	5 residues within 4Å: Chain A: K.60, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.65 Water bridges: A:K.60

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Freudenthal, B.D. et al., Observing a DNA polymerase choose right from wrong. Cell(Cambridge,Mass.) (2013)

Release Date

2013-09-04

Peptides

DNA polymerase beta: 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

DNA polymerase beta

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