Magnesium in PDB 5tyf: Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min), PDB code: 5tyf 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)	25.13 / 1.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.994, 68.482, 110.702, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.5

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min) (pdb code 5tyf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min), PDB code: 5tyf:

Magnesium binding site 1 out of 1 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min)


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 Product Complex, 10 Mm MG2+ (270 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:17.4 occ:1.00 OP1 P:DT5 2.0 17.3 1.0 OD2 A:ASP332 2.0 17.6 1.0 OD1 A:ASP330 2.1 19.9 1.0 O12 A:GOA508 2.1 19.6 1.0 O A:HOH704 2.1 21.7 1.0 O2 A:GOA508 2.2 24.3 1.0 C1 A:GOA508 2.8 21.8 1.0 C2 A:GOA508 3.0 27.9 1.0 CG A:ASP330 3.1 24.9 1.0 CG A:ASP332 3.1 16.7 1.0 NA A:NA502 3.4 20.7 1.0 P P:DT5 3.4 19.0 1.0 OD2 A:ASP330 3.4 27.0 1.0 OD1 A:ASP332 3.5 16.1 1.0 O5' P:DT5 4.0 16.4 1.0 C5' P:DT5 4.0 16.5 1.0 O11 A:GOA508 4.0 19.5 1.0 O A:HOH812 4.1 24.2 1.0 O A:ASP330 4.2 20.1 1.0 O A:HOH613 4.2 17.2 1.0 OP2 P:DT5 4.3 18.0 1.0 O P:HOH101 4.3 43.3 1.0 N A:GLY320 4.3 16.7 1.0 O P:HOH112 4.3 21.5 1.0 O3' P:DA4 4.4 18.5 1.0 CB A:ASP332 4.4 14.1 1.0 CB A:ASP330 4.4 22.6 1.0 CA A:GLY319 4.5 17.6 1.0 O A:HOH708 4.5 29.7 1.0 C A:ASP330 4.5 20.7 1.0 N A:ASP332 5.0 15.3 1.0 CA A:ASP330 5.0 21.8 1.0 C A:GLY319 5.0 18.0 1.0

J.A.Jamsen, W.A.Beard, L.C.Pedersen, D.D.Shock, A.F.Moon, J.M.Krahn, K.Bebenek, T.A.Kunkel, S.H.Wilson. Time-Lapse Crystallography Snapshots of A Double-Strand Break Repair Polymerase in Action. Nat Commun V. 8 253 2017.
ISSN: ESSN 2041-1723
PubMed: 28811466
DOI: 10.1038/S41467-017-00271-7