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Sodium in active site of DNA polymerase beta

Analyse Sodium in active site of DNA polymerase beta in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2FMQ
Type: protein + DNA
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'…
EC: 2.7.7.7
UniProt: P06746
Ligands: DUP, NA, MG
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'- D(CPCPGPAPCPAPGPCPGPCPAPTPCPAPGPC)-3'	dna	16	—	—
C	5'-D(GPCPTPGPAPTPGPCPGPC)-3'	dna	10	—	—
D	5'-D(PGPTPCPGP*G)-3'	dna	5	—	—
A	DNA polymerase beta (EC 2.7.7.7)	protein	326	49% helix, 13% strand	P06746

Ligands and binding sites

DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · chains B, C, A
NA · Sodium ion · metal · 3 copies · chains C, A, D
MG · Magnesium ion · metal · 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	958	0.76	0.79	84	MG, DUP
2	219	0.58	0.80	25	empty

Interfaces

5 interfaces between chains.

B–A · 719 Å² buried · 13 hydrogen bonds · protein-nucleic
B–C · 466 Å² buried · 48 hydrogen bonds · nucleic-nucleic
D–A · 396 Å² buried · 11 hydrogen bonds · protein-nucleic
C–A · 366 Å² buried · 11 hydrogen bonds · protein-nucleic
B–D · 230 Å² buried · 19 hydrogen bonds · nucleic-nucleic

Compared structures

2FMQ · Sodium in active site of DNA Polymerase Beta · the same entry in another collection · chain B against B, TM-score 1.00
P06746 · AlphaFold monomer V2.0 prediction for DNA polymerase beta (P06746) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 P06746
Elsewhere: RCSB PDB 2FMQ · PDBe 2FMQ · UniProt P06746

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