Sodium 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:

Magnesium

(Mg)

1 atom

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 Min), PDB code: 5tyf:
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+ (270 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+ (270 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:20.7 occ:1.00 OD1 A:ASP332 2.2 16.1 1.0 OP1 P:DT5 2.4 17.3 1.0 OD2 A:ASP418 2.4 22.6 1.0 O P:HOH112 2.5 21.5 1.0 O3' P:DA4 2.6 18.5 1.0 OD1 A:ASP330 2.7 19.9 1.0 P P:DT5 3.0 19.0 1.0 CG A:ASP332 3.2 16.7 1.0 CG A:ASP330 3.3 24.9 1.0 MG A:MG501 3.4 17.4 1.0 CG A:ASP418 3.4 22.2 1.0 OD2 A:ASP332 3.4 17.6 1.0 C3' P:DA4 3.8 17.9 1.0 C4' P:DA4 3.9 18.9 1.0 C5' P:DA4 3.9 22.4 1.0 CB A:ASP418 4.0 20.1 1.0 OD2 A:ASP330 4.0 27.0 1.0 CB A:ASP330 4.0 22.6 1.0 OP2 P:DT5 4.0 18.0 1.0 O5' P:DT5 4.3 16.4 1.0 OD1 A:ASP418 4.3 23.5 1.0 NH2 A:ARG416 4.4 20.9 1.0 C5' P:DT5 4.5 16.5 1.0 CB A:ASP332 4.5 14.1 1.0 O2 A:GOA508 4.7 24.3 1.0 O P:HOH101 4.7 43.3 1.0 CZ3 A:TRP434 4.8 19.0 1.0 O5' P:DA4 4.8 21.4 1.0 OP1 P:DA4 4.8 20.5 1.0 O A:VAL331 4.8 16.5 1.0 C2' P:DA4 4.9 20.0 1.0 O A:HOH704 5.0 21.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (270 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+ (270 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:26.8 occ:1.00 O A:VAL246 2.3 26.0 1.0 O A:THR241 2.4 27.4 1.0 O A:ILE243 2.4 26.1 1.0 O P:HOH110 2.4 29.8 1.0 O A:HOH811 2.4 29.5 1.0 OP1 P:DT3 2.5 26.5 1.0 C A:VAL246 3.4 26.9 1.0 C A:ILE243 3.4 28.6 1.0 C A:THR241 3.5 30.6 1.0 P P:DT3 3.6 26.2 1.0 N A:VAL246 3.6 26.8 1.0 O P:HOH113 3.7 50.6 1.0 OP2 P:DT3 3.7 23.3 1.0 CA A:VAL246 4.0 28.3 1.0 N A:GLY245 4.1 22.8 1.0 N A:ILE243 4.1 31.6 1.0 N A:PHE244 4.2 28.1 1.0 C A:GLN242 4.2 32.0 0.6 CA A:PHE244 4.2 26.0 1.0 CA A:THR241 4.2 29.1 1.0 C A:GLN242 4.3 32.1 0.5 CB A:VAL246 4.4 25.8 1.0 N A:GLY247 4.4 23.2 1.0 CA A:ILE243 4.4 28.4 1.0 O A:HOH840 4.4 38.7 1.0 N A:GLN242 4.5 33.1 0.5 N A:GLN242 4.5 33.1 0.6 O A:GLN242 4.5 30.3 0.6 O3' P:DG2 4.5 24.7 1.0 C A:PHE244 4.5 24.7 1.0 CA A:GLN242 4.6 34.4 0.5 CA A:GLN242 4.6 34.4 0.6 C A:GLY245 4.7 24.3 1.0 CA A:GLY247 4.7 22.1 1.0 O5' P:DT3 4.8 22.1 1.0 O A:PHE240 4.8 26.4 1.0 O A:GLN242 4.8 30.7 0.5 CB A:THR241 4.9 29.7 1.0 CA A:GLY245 4.9 21.6 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