4ymn.1 | SWISS-MODEL Template Library

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SMTL ID : 4ymn.1

Structure of human DNA polymerase beta complexed with N7BG in the template base paired with incoming non-hydrolyzable CTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

monomer

Ligands

1 x DG- DT- DC- DG- DG: DNA 5-mer (dn-primer)(Non-covalent)

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

19 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, K.72
Chain B: C.1, C.2, G.3, A.4, C.5
Ligands: NA.4

1 PLIP interactions:

1 interactions with chain A

pi-Stacking: A:H.34

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2:

2 residues within 4Å:

Chain A: D.190
Ligands: 0KX.5

2 PLIP interactions:

2 interactions with chain A

Metal complexes: A:D.190, A:D.190

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

NA.3:	4 residues within 4Å: Chain A: T.101, V.103, I.106 Chain C: G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.103, A:I.106
NA.4:	6 residues within 4Å: Chain A: K.60, K.61, L.62, P.63, V.65 Ligands: DG-DT-DC-DG-DG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.62

1 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.5:

14 residues within 4Å:

Chain A: R.149, G.179, S.180, R.183, S.188, G.189, D.190, Y.271, F.272, G.274, D.276
Chain B: X.6
Chain C: A.10
Ligands: MG.2

6 PLIP interactions:

6 interactions with chain A

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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Kou, Y. et al., Structural and kinetic studies of the effect of guanine-N7 alkylation and metal cofactors on DNA replication. Biochemistry (2018)

Release Date

2016-03-09

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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