Sodium in PDB 5tye: Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min)

All present enzymatic activity of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min):
2.7.7.7;

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min), PDB code: 5tye 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)	21.36 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.998, 68.573, 110.478, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.8

The structure of Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 Min) (pdb code 5tye). 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+ (60 Min), PDB code: 5tye:
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+ (60 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+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:19.1 occ:0.26 MG A:MG502 0.0 16.7 0.7 OD1 A:ASP332 2.1 16.6 1.0 OD2 A:ASP418 2.2 19.9 1.0 OP1 P:DT5 2.3 19.5 1.0 OD1 A:ASP330 2.6 23.2 1.0 O A:HOH627 2.7 28.1 1.0 O3' P:DA4 2.7 20.5 1.0 CG A:ASP332 3.1 20.6 1.0 P P:DT5 3.1 21.6 1.0 CG A:ASP330 3.2 30.8 1.0 CG A:ASP418 3.2 20.5 1.0 OD2 A:ASP332 3.3 19.4 1.0 MG A:MG501 3.4 19.4 1.0 OD2 A:ASP330 3.7 33.0 1.0 CB A:ASP418 3.8 19.4 1.0 C3' P:DA4 3.9 18.7 1.0 CB A:ASP330 4.0 22.8 1.0 C4' P:DA4 4.0 19.2 1.0 C5' P:DA4 4.0 21.1 1.0 OP2 P:DT5 4.1 20.8 1.0 OD1 A:ASP418 4.2 21.1 1.0 O5' P:DT5 4.3 18.7 1.0 CB A:ASP332 4.4 17.8 1.0 C5' P:DT5 4.4 17.7 1.0 NH2 A:ARG416 4.5 18.2 1.0 O A:HOH709 4.6 26.5 0.7 O A:VAL331 4.6 18.1 1.0 CZ3 A:TRP434 4.8 19.0 1.0 O5' P:DA4 4.9 21.8 1.0 C A:VAL331 4.9 20.1 1.0 N A:ASP418 4.9 16.9 1.0 CA A:ASP332 4.9 18.2 1.0 OP1 P:DA4 5.0 20.1 1.0 O A:HOH666 5.0 19.9 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu Product Complex, 10 Mm MG2+ (60 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+ (60 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:27.4 occ:1.00 O A:THR241 2.3 27.7 1.0 O A:ILE243 2.3 25.7 1.0 O P:HOH113 2.4 24.8 1.0 O A:VAL246 2.4 26.3 1.0 O A:HOH803 2.4 26.8 1.0 OP1 P:DT3 2.5 19.7 1.0 C A:ILE243 3.4 27.6 1.0 C A:VAL246 3.4 24.6 1.0 C A:THR241 3.5 28.5 1.0 P P:DT3 3.6 23.6 1.0 N A:VAL246 3.7 27.1 1.0 OP2 P:DT3 3.8 21.9 1.0 O P:HOH108 4.0 34.9 1.0 N A:ILE243 4.0 27.6 1.0 N A:GLY245 4.0 23.7 1.0 CA A:VAL246 4.1 26.2 1.0 C A:GLN242 4.1 29.9 0.4 N A:PHE244 4.2 25.4 1.0 CA A:PHE244 4.2 23.3 1.0 C A:GLN242 4.2 29.8 0.6 CA A:THR241 4.3 28.4 1.0 CA A:ILE243 4.3 28.1 1.0 N A:GLN242 4.4 29.1 0.6 O A:HOH824 4.4 36.6 1.0 N A:GLN242 4.4 29.1 0.4 CA A:GLN242 4.5 28.9 0.6 N A:GLY247 4.5 23.7 1.0 CB A:VAL246 4.5 25.5 1.0 O A:GLN242 4.5 30.4 0.4 CA A:GLN242 4.5 28.9 0.4 C A:PHE244 4.5 24.1 1.0 O3' P:DG2 4.6 21.9 1.0 C A:GLY245 4.7 27.6 1.0 O5' P:DT3 4.7 20.6 1.0 O A:GLN242 4.8 30.6 0.6 O A:PHE240 4.8 26.6 1.0 CA A:GLY247 4.8 23.7 1.0 CA A:GLY245 4.9 22.7 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