5u9h.1 | SWISS-MODEL Template Library

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SMTL ID : 5u9h.1

DNA polymerase beta product complex with inserted Sp-isomer of dCTP-alpha-S

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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:

17 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

7 PLIP interactions:

7 interactions with chain C

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

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

MN.2:	0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)
MN.4:	6 residues within 4Å: Chain B: C.10, X.11 Chain C: D.190, D.192, D.256 Ligands: MN.5 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.190, C:D.192, C:D.256, H₂O.6
MN.5:	5 residues within 4Å: Chain B: X.11 Chain C: D.190, D.192 Ligands: PPV.3, MN.4 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.190, C:D.192, H₂O.4
MN.6:	2 residues within 4Å: Chain C: D.145, H.252 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.145, C:H.252, H₂O.10, H₂O.11, H₂O.12

1 x PPV: PYROPHOSPHATE(Non-covalent)

PPV.3:

10 residues within 4Å:

Chain B: X.11
Chain C: R.149, G.179, S.180, R.183, S.188, G.189, D.190, D.192
Ligands: MN.5

11 PLIP interactions:

11 interactions with chain C

Hydrogen bonds: C:S.180, C:S.180, C:G.189, C:D.190, C:D.192
Water bridges: C:R.183, C:R.183, C:R.183, C:R.183
Salt bridges: C:R.149, C:R.183

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

NA.7:

6 residues within 4Å:

Chain B: G.9
Chain C: T.101, V.103, S.104, G.105, I.106

3 PLIP interactions:

3 interactions with chain C

Hydrogen bonds: C:G.105, C:I.106, C:I.106

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Perera, L. et al., Revealing the role of the product metal in DNA polymerase beta catalysis. Nucleic Acids Res. (2017)

Release Date

2017-02-08

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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