Magnesium in PDB 7ktk: Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)

All present enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN):
2.7.7.7;

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN), PDB code: 7ktk 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)	33.19 / 1.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.109, 61.775, 118.076, 90, 90, 90
R / Rfree (%)	14.3 / 16.8

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) (pdb code 7ktk). 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 (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN), PDB code: 7ktk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)


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 (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:16.0 occ:1.00 OD2 A:ASP330 2.0 17.3 1.0 OD2 A:ASP418 2.0 20.1 1.0 OD1 A:ASP332 2.1 15.8 1.0 O A:HOH706 2.1 22.1 1.0 O P:HOH106 2.1 19.6 1.0 O2A A:8DG501 2.3 16.1 1.0 CG A:ASP330 3.0 14.6 1.0 CG A:ASP332 3.1 15.2 1.0 CG A:ASP418 3.2 17.9 1.0 PA A:8DG501 3.4 18.0 1.0 OD1 A:ASP330 3.4 15.3 1.0 OD2 A:ASP332 3.6 15.7 1.0 MG A:MG503 3.6 15.7 1.0 O5' A:8DG501 3.7 21.0 1.0 O1A A:8DG501 3.8 21.5 1.0 CB A:ASP418 3.8 15.5 1.0 C5' A:8DG501 4.1 24.7 1.0 OD1 A:ASP418 4.2 18.1 1.0 CE1 A:HIS329 4.2 21.6 1.0 CB A:ASP330 4.3 14.0 1.0 NH2 A:ARG416 4.4 15.6 1.0 CB A:ASP332 4.4 13.9 1.0 OP1 P:DA4 4.4 16.0 0.8 O P:HOH112 4.6 32.6 0.7 O3A A:8DG501 4.8 17.8 1.0 O3G A:8DG501 4.8 19.3 1.0 NE2 A:HIS329 4.9 21.1 1.0 O1B A:8DG501 5.0 16.6 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)


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 (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:15.7 occ:1.00 OD1 A:ASP330 2.0 15.3 1.0 OD2 A:ASP332 2.0 15.7 1.0 O3G A:8DG501 2.1 19.3 1.0 O1B A:8DG501 2.1 16.6 1.0 O A:HOH707 2.1 16.5 1.0 O2A A:8DG501 2.1 16.1 1.0 CG A:ASP332 3.0 15.2 1.0 CG A:ASP330 3.1 14.6 1.0 PB A:8DG501 3.1 18.1 1.0 PA A:8DG501 3.3 18.0 1.0 PG A:8DG501 3.3 20.3 1.0 O3A A:8DG501 3.3 17.8 1.0 OD1 A:ASP332 3.4 15.8 1.0 OD2 A:ASP330 3.5 17.3 1.0 O3B A:8DG501 3.6 18.7 1.0 MG A:MG502 3.6 16.0 1.0 O A:ASP330 4.0 15.2 1.0 ND1 A:HIS329 4.1 21.3 1.0 O5' A:8DG501 4.2 21.0 1.0 O A:HOH689 4.2 15.2 1.0 O2G A:8DG501 4.2 31.2 1.0 C A:ASP330 4.2 13.9 1.0 N A:GLY320 4.3 13.8 1.0 CE1 A:HIS329 4.3 21.6 1.0 C5' A:8DG501 4.4 24.7 1.0 O A:HOH632 4.4 21.4 1.0 CB A:ASP330 4.4 14.0 1.0 CB A:ASP332 4.4 13.9 1.0 O1A A:8DG501 4.4 21.5 1.0 O1G A:8DG501 4.5 26.6 1.0 O2B A:8DG501 4.5 19.6 1.0 N A:ASP330 4.5 14.8 1.0 CA A:GLY319 4.6 13.2 1.0 CA A:ASP330 4.6 13.8 1.0 N A:ASP332 4.7 12.7 1.0 N A:VAL331 4.8 14.0 1.0 O P:HOH106 4.8 19.6 1.0 O A:HOH706 4.9 22.1 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