Magnesium in PDB 7kt0: Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN), PDB code: 7kt0 was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.28 / 1.36
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.918, 68.568, 110.222, 90, 90, 90
R / Rfree (%)	16.1 / 17.9

The structure of Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN) also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN) (pdb code 7kt0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN), PDB code: 7kt0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:20.0 occ:0.93 OD2 A:ASP330 1.9 24.9 1.0 OD1 A:ASP332 2.0 23.1 1.0 O P:HOH101 2.0 28.5 1.0 O A:HOH626 2.1 26.4 1.0 OD2 A:ASP418 2.1 21.9 1.0 O1G A:DGT507 2.2 21.0 0.7 CG A:ASP330 2.9 26.2 1.0 CG A:ASP332 3.1 22.9 1.0 CG A:ASP418 3.3 18.5 1.0 OD1 A:ASP330 3.3 24.6 1.0 PG A:DGT507 3.4 22.9 0.4 O3' P:DA4 3.4 38.6 1.0 OD2 A:ASP332 3.5 21.6 1.0 O3G A:DGT507 3.6 25.5 0.6 MG A:MG509 3.6 18.6 0.7 CB A:ASP418 3.9 16.7 1.0 C5' P:DA4 4.0 23.9 1.0 O2G A:DGT507 4.0 29.2 0.6 OD1 A:ASP418 4.2 19.0 1.0 C4' P:DA4 4.2 23.5 1.0 CB A:ASP330 4.3 21.9 1.0 CB A:ASP332 4.4 17.1 1.0 C3' P:DA4 4.4 34.3 1.0 O5' A:DGT507 4.6 22.0 0.7 OP1 P:DA4 4.7 21.6 1.0 NH2 A:ARG416 4.7 17.1 1.0 O3B A:DGT507 4.8 23.5 0.6 O5' P:DA4 4.9 22.3 1.0 O1B A:DGT507 5.0 18.2 0.7

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Mu, Dgtp:at Ground State Ternary Complex, 50 Mm MG2+ (60MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:18.6 occ:0.72 OD1 A:ASP330 2.0 24.6 1.0 O1B A:DGT507 2.0 18.2 0.7 O5' A:DGT507 2.1 22.0 0.7 OD2 A:ASP332 2.1 21.6 1.0 O A:HOH654 2.1 22.9 1.0 O1G A:DGT507 2.2 21.0 0.7 CG A:ASP330 3.0 26.2 1.0 CG A:ASP332 3.1 22.9 1.0 PB A:DGT507 3.2 23.5 0.7 PG A:DGT507 3.3 22.9 0.4 PA A:DGT507 3.3 24.0 0.7 O3B A:DGT507 3.4 23.5 0.6 OD1 A:ASP332 3.4 23.1 1.0 OD2 A:ASP330 3.5 24.9 1.0 O3A A:DGT507 3.6 23.6 0.7 MG A:MG508 3.6 20.0 0.9 O A:ASP330 3.8 20.6 1.0 O2G A:DGT507 3.9 29.2 0.6 C A:ASP330 4.1 20.9 1.0 O A:HOH651 4.1 17.0 1.0 N A:GLY320 4.2 12.5 1.0 O1A A:DGT507 4.2 30.8 0.8 CB A:ASP330 4.3 21.9 1.0 O3G A:DGT507 4.4 25.5 0.6 N A:ASP330 4.5 18.5 1.0 O2A A:DGT507 4.5 30.6 0.7 CA A:ASP330 4.5 20.5 1.0 O2B A:DGT507 4.5 25.1 0.8 O A:HOH800 4.5 23.2 1.0 CB A:ASP332 4.5 17.1 1.0 O A:HOH626 4.6 26.4 1.0 N A:VAL331 4.6 19.1 1.0 CA A:GLY319 4.6 12.4 1.0 O P:HOH101 4.6 28.5 1.0 N A:ASP332 4.8 15.0 1.0 CA A:VAL331 4.9 17.3 1.0 C A:VAL331 4.9 16.8 1.0 C A:GLY319 5.0 12.6 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6