4ymo.1 | SWISS-MODEL Template Library

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SMTL ID : 4ymo.1

Structure of human DNA polymerase beta complexed with N7BG in the template opposite to incoming non-hydrolyzable CTP WITH MANGANESE IN THE ACTIVE SITE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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:

17 residues within 4Å:

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

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:R.283
Water bridges: A:N.37
pi-Stacking: A:H.34

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

MN.2:	4 residues within 4Å: Chain A: D.190, D.192 Ligands: MN.3, 0KX.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, H₂O.3
MN.3:	6 residues within 4Å: Chain A: D.190, D.192, D.256 Chain C: A.10 Ligands: MN.2, 0KX.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.190, A:D.192, A:D.256, H₂O.7

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

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

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

0KX.6:

18 residues within 4Å:

Chain A: 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: X.6
Chain C: A.10
Ligands: MN.2, MN.3

13 PLIP interactions:

13 interactions with chain A

Hydrophobic interactions: A:D.276
Hydrogen bonds: A:S.180, A:S.180, A:R.183, A:R.183, A:G.189, A:D.190, A:N.279
Water bridges: A:R.149, A:R.149, A:S.188, A:D.190, A:D.276

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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