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Efficient and High Fidelity Incorporation of dCTP Opposite 7,8- Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4

Analyse Efficient and High Fidelity Incorporation of dCTP Opposite 7,8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2C28
Type: protein + DNA
Length: 371 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.27
Source: SULFOLOBUS SOLFATARICUS; SYNTHETIC CONSTRUCT
Molecule: DNA polymerase IV; 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP *TP*TP*C)-3'; 5'-D(TP*CP*AP*C…
EC: 2.7.7.7
UniProt: Q97W02
Ligands: DG, CA
Pockets: 2 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.27 · 3 distinct chains · 44% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA polymerase IV (EC 2.7.7.7)	protein	341	44% helix, 25% strand	Q97W02
P	5'-D(GPGPGPGPGPAPAPGPGPAP TPTP*C)-3'	dna	13	—	—
T	5'-D(TPCPAPC 8OGPGPAPAPTPCPCPTP TPCPCPCPCPC)-3'	dna	17	—	—

Ligands and binding sites

DG · 2'-deoxyguanosine-5'-monophosphate · ligand · chains A, T
CA · Calcium ion · metal · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1021	0.81	0.82	67	DG, CA
2	587	0.72	0.80	39	empty

Interfaces

3 interfaces between chains.

A–T · 991 Å² buried · 29 hydrogen bonds · protein-nucleic
P–T · 562 Å² buried · 55 hydrogen bonds · nucleic-nucleic
A–P · 555 Å² buried · 17 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

2C28 · Efficient and high fidelity incorporation of dctp opposite… · the same entry in another collection · chain A against A, TM-score 1.00
Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q97W02
Elsewhere: RCSB PDB 2C28 · PDBe 2C28 · UniProt Q97W02

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