Sodium in PDB 5tyg: Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min), PDB code: 5tyg 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)	34.99 / 1.73
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.998, 68.534, 110.747, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.5

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min) (pdb code 5tyg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min), PDB code: 5tyg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:26.2 occ:1.00 O A:VAL246 2.3 24.5 1.0 O A:THR241 2.4 26.8 1.0 O A:ILE243 2.4 25.1 1.0 O A:HOH829 2.4 33.1 1.0 O P:HOH215 2.5 25.2 1.0 OP1 P:DT3 2.6 26.5 1.0 C A:VAL246 3.4 24.0 1.0 C A:ILE243 3.4 29.9 1.0 C A:THR241 3.4 30.4 1.0 P P:DT3 3.7 24.7 1.0 N A:VAL246 3.7 25.8 1.0 OP2 P:DT3 3.8 23.5 1.0 O P:HOH209 3.8 48.9 1.0 CA A:VAL246 4.0 24.9 1.0 N A:ILE243 4.1 26.2 1.0 O A:HOH736 4.1 48.0 1.0 N A:GLY245 4.2 24.1 1.0 CA A:THR241 4.2 26.2 1.0 C A:GLN242 4.2 30.4 0.7 N A:PHE244 4.2 24.5 1.0 CA A:PHE244 4.3 27.2 1.0 C A:GLN242 4.3 30.4 0.3 O A:HOH855 4.4 41.0 1.0 CA A:ILE243 4.4 25.0 1.0 CB A:VAL246 4.4 24.9 1.0 N A:GLN242 4.4 28.1 0.3 N A:GLY247 4.4 27.7 1.0 N A:GLN242 4.4 27.2 0.7 CA A:GLN242 4.5 30.8 0.7 CA A:GLN242 4.5 31.5 0.3 O A:GLN242 4.5 29.3 0.7 C A:PHE244 4.6 26.0 1.0 O3' P:DG2 4.6 25.3 1.0 CA A:GLY247 4.7 26.1 1.0 O A:PHE240 4.7 25.5 1.0 C A:GLY245 4.7 25.5 1.0 O A:GLN242 4.9 33.7 0.3 CB A:THR241 4.9 25.6 1.0 O5' P:DT3 4.9 22.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (960 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:23.4 occ:1.00 OD1 A:ASP332 2.3 21.2 1.0 OD2 A:ASP418 2.3 25.2 1.0 OP1 P:DT5 2.4 20.0 1.0 O P:HOH212 2.4 26.5 1.0 OD1 A:ASP330 2.6 22.6 1.0 O3' P:DA4 2.7 19.9 1.0 P P:DT5 3.1 19.8 1.0 CG A:ASP332 3.2 21.1 1.0 CG A:ASP330 3.2 45.6 1.0 MG A:MG501 3.3 18.0 0.8 CG A:ASP418 3.3 27.3 1.0 OD2 A:ASP332 3.5 20.5 1.0 C3' P:DA4 3.9 20.0 1.0 C5' P:DA4 3.9 20.5 1.0 CB A:ASP330 3.9 28.6 1.0 OD2 A:ASP330 4.0 38.3 1.0 C4' P:DA4 4.0 19.6 1.0 CB A:ASP418 4.0 20.6 1.0 OP2 P:DT5 4.1 22.5 1.0 OD1 A:ASP418 4.3 22.3 1.0 O5' P:DT5 4.3 19.1 1.0 NH2 A:ARG416 4.4 22.1 1.0 C5' P:DT5 4.6 20.9 1.0 CB A:ASP332 4.6 18.7 1.0 O2 A:GOA508 4.6 23.1 0.9 O P:HOH202 4.6 36.0 0.8 O A:VAL331 4.7 19.5 1.0 OP1 P:DA4 4.8 21.7 1.0 O5' P:DA4 4.8 21.9 1.0 CZ3 A:TRP434 4.9 18.6 1.0 C A:VAL331 4.9 20.6 1.0 O A:HOH739 5.0 21.5 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