Sodium in PDB 5tyd: Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min)

All present enzymatic activity of Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min), PDB code: 5tyd 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)	34.94 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.891, 68.590, 110.476, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.2

The structure of Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min) (pdb code 5tyd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 Min), PDB code: 5tyd:

Sodium binding site 1 out of 1 in the Dna Polymerase Mu Reactant Complex, 10 Mm MG2+ (45 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 Reactant Complex, 10 Mm MG2+ (45 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:18.1 occ:1.00 O P:HOH215 2.3 20.6 1.0 O A:ILE243 2.3 15.9 1.0 O A:VAL246 2.4 19.2 1.0 O A:THR241 2.4 21.6 1.0 O A:HOH823 2.5 25.4 1.0 OP1 P:DT3 2.6 17.6 1.0 C A:ILE243 3.4 18.1 1.0 C A:VAL246 3.4 20.2 1.0 C A:THR241 3.5 23.8 1.0 P P:DT3 3.6 16.3 1.0 N A:VAL246 3.6 18.8 1.0 O P:HOH208 3.8 34.3 1.0 OP2 P:DT3 3.8 13.4 1.0 CA A:VAL246 4.0 18.8 1.0 N A:ILE243 4.0 22.3 1.0 O A:HOH736 4.1 33.9 1.0 N A:GLY245 4.1 14.7 1.0 C A:GLN242 4.1 26.9 1.0 N A:PHE244 4.1 15.5 1.0 CA A:THR241 4.2 20.7 1.0 CA A:PHE244 4.2 17.3 1.0 CA A:ILE243 4.3 18.8 1.0 CB A:VAL246 4.4 16.0 1.0 N A:GLN242 4.4 19.9 1.0 N A:GLY247 4.5 14.5 1.0 O A:GLN242 4.5 23.4 1.0 C A:PHE244 4.6 18.8 1.0 O3' P:DG2 4.6 16.7 1.0 CA A:GLN242 4.6 23.9 1.0 O A:HOH836 4.6 34.5 1.0 C A:GLY245 4.7 20.1 1.0 O A:PHE240 4.7 18.6 1.0 CA A:GLY247 4.8 16.0 1.0 O5' P:DT3 4.8 13.2 1.0 CB A:THR241 4.9 18.7 1.0 CA A:GLY245 5.0 18.9 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