Sodium in PDB 5tws: Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp

The structure of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp, PDB code: 5tws was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.48 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.935, 68.858, 110.319, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20

The structure of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	4 atoms

The binding sites of Sodium atom in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp (pdb code 5tws). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp, PDB code: 5tws:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:12.0 occ:1.00 OD1 A:ASP332 2.1 14.0 1.0 OD2 A:ASP418 2.2 19.4 1.0 OP1 P:U5 2.3 12.8 1.0 OD1 A:ASP330 2.6 14.5 1.0 O P:HOH107 2.7 27.0 1.0 O3' P:DA4 2.9 11.1 1.0 CG A:ASP332 3.0 13.7 1.0 P P:U5 3.1 12.6 1.0 CG A:ASP330 3.2 22.2 1.0 CG A:ASP418 3.2 18.6 1.0 MG A:MG501 3.3 12.8 1.0 OD2 A:ASP332 3.3 12.6 1.0 CB A:ASP418 3.9 12.1 1.0 OD2 A:ASP330 3.9 24.2 1.0 CB A:ASP330 4.0 13.9 1.0 C3' P:DA4 4.0 11.2 1.0 C5' P:DA4 4.1 13.7 1.0 C4' P:DA4 4.1 11.9 1.0 OD1 A:ASP418 4.2 20.9 1.0 OP2 P:U5 4.2 12.2 1.0 O5' P:U5 4.3 10.9 1.0 CB A:ASP332 4.4 9.0 1.0 NH2 A:ARG416 4.5 15.5 1.0 C5' P:U5 4.5 10.1 1.0 O A:VAL331 4.5 10.6 1.0 O2 A:GOA503 4.6 17.8 0.9 C A:VAL331 4.8 11.9 1.0 O P:HOH102 4.8 32.5 1.0 N A:ASP418 4.8 10.8 1.0 CA A:ASP332 4.8 8.8 1.0 CZ3 A:TRP434 4.9 8.1 0.9 O A:HOH735 4.9 14.5 1.0 N A:ASP332 4.9 10.1 1.0 O5' P:DA4 5.0 13.8 1.0 OP1 P:DA4 5.0 15.1 1.0 CA A:ASP418 5.0 11.7 1.0 N A:VAL331 5.0 9.8 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:18.8 occ:1.00 O A:ILE243 2.3 18.8 1.0 O A:VAL246 2.3 20.1 1.0 O A:THR241 2.4 22.0 1.0 O A:HOH814 2.5 26.4 1.0 O P:HOH118 2.5 23.8 1.0 OP1 P:DT3 2.6 18.1 1.0 C A:ILE243 3.3 21.2 1.0 C A:VAL246 3.4 21.3 1.0 C A:THR241 3.4 23.4 1.0 P P:DT3 3.7 18.4 1.0 N A:VAL246 3.7 20.3 1.0 OP2 P:DT3 3.9 16.8 1.0 CA A:VAL246 4.0 21.2 1.0 O P:HOH116 4.0 39.2 1.0 N A:ILE243 4.0 22.5 1.0 N A:PHE244 4.1 19.7 1.0 N A:GLY245 4.1 17.7 1.0 C A:GLN242 4.2 24.4 1.0 CA A:PHE244 4.2 20.0 1.0 CA A:THR241 4.2 20.6 1.0 CA A:ILE243 4.3 20.6 1.0 CB A:VAL246 4.4 21.1 1.0 O A:HOH832 4.4 41.3 1.0 N A:GLN242 4.4 22.6 1.0 N A:GLY247 4.4 18.5 1.0 O A:GLN242 4.5 24.9 1.0 C A:PHE244 4.5 20.8 1.0 CA A:GLN242 4.6 25.5 1.0 O3' P:DG2 4.6 17.8 1.0 O A:PHE240 4.7 17.6 1.0 C A:GLY245 4.7 19.9 1.0 CA A:GLY247 4.7 18.5 1.0 CB A:THR241 4.9 20.2 1.0 O5' P:DT3 4.9 15.6 1.0

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Structural Accommodation of Ribonucleotide Incorporation By the Dna Repair Enzyme Polymerase Mu. Nucleic Acids Res. V. 45 9138 2017.
ISSN: ESSN 1362-4962
PubMed: 28911097
DOI: 10.1093/NAR/GKX527