Sodium in PDB 6wie: Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate:
2.7.7.7;

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wie was solved by A.M.Kaminski, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.90 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.073, 62.247, 118.318, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 18.7

The structure of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate (pdb code 6wie). 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 Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate, PDB code: 6wie:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:17.8 occ:0.40 MG A:MG501 0.1 16.6 0.6 OD2 A:ASP418 1.9 19.4 1.0 OD2 A:ASP330 1.9 22.3 1.0 OD1 A:ASP332 2.0 15.0 1.0 OP1 P:DT5 2.2 15.4 1.0 O3' P:DA4 2.5 17.2 1.0 CG A:ASP330 2.8 18.2 1.0 CG A:ASP332 2.9 13.2 1.0 P P:DT5 3.0 16.1 1.0 CG A:ASP418 3.0 16.3 1.0 OD1 A:ASP330 3.1 14.3 1.0 OD2 A:ASP332 3.2 14.6 1.0 MG A:MG503 3.5 13.6 1.0 C3' P:DA4 3.7 13.4 1.0 CB A:ASP418 3.7 12.0 1.0 C4' P:DA4 3.8 15.9 1.0 C5' P:DA4 3.9 14.4 1.0 OD1 A:ASP418 4.0 17.1 1.0 CB A:ASP330 4.0 12.9 1.0 OP2 P:DT5 4.0 13.8 1.0 O5' P:DT5 4.1 12.2 1.0 C5' P:DT5 4.2 13.0 1.0 CB A:ASP332 4.3 10.7 1.0 O32 A:PPV507 4.5 23.8 0.4 CZ3 A:TRP434 4.5 19.0 1.0 O A:HOH629 4.5 17.1 0.6 CE1 A:HIS329 4.6 28.4 1.0 NH2 A:ARG416 4.7 13.1 1.0 CA A:ASP332 4.8 10.4 1.0 C2' P:DA4 4.8 15.3 1.0 O A:VAL331 4.8 12.7 1.0 O5' P:DA4 4.9 13.2 1.0 C A:VAL331 4.9 12.7 1.0 N A:ASP332 5.0 10.5 1.0 OP1 P:DA4 5.0 15.1 1.0 N A:ASP418 5.0 11.1 1.0 CA A:ASP418 5.0 10.4 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Post-Catalytic Nicked Complex of Human Polymerase Mu on A Complementary Dna Double-Strand Break Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:12.9 occ:1.00 O A:HOH805 2.3 25.5 1.0 O P:HOH115 2.4 22.2 1.0 O A:VAL246 2.4 12.5 1.0 O A:THR241 2.4 17.3 1.0 O A:ILE243 2.6 14.8 1.0 OP1 P:DT3 2.7 12.4 1.0 C A:THR241 3.5 14.9 1.0 C A:VAL246 3.5 11.7 1.0 C A:ILE243 3.5 14.8 1.0 O P:HOH113 3.6 21.7 1.0 O A:HOH752 3.8 42.4 1.0 P P:DT3 3.8 11.8 1.0 N A:VAL246 3.8 11.9 1.0 OP2 P:DT3 4.0 13.0 1.0 N A:ILE243 4.1 14.2 1.0 C A:GLN242 4.1 16.8 1.0 CA A:VAL246 4.2 11.9 1.0 CA A:THR241 4.3 14.1 1.0 N A:GLY245 4.3 11.5 1.0 N A:PHE244 4.3 12.5 1.0 CA A:PHE244 4.3 12.8 1.0 N A:GLN242 4.4 15.8 1.0 O A:HOH839 4.4 29.8 1.0 O A:GLN242 4.5 21.9 1.0 CA A:GLN242 4.5 18.0 1.0 CA A:ILE243 4.5 13.9 1.0 CB A:VAL246 4.6 11.6 1.0 N A:GLY247 4.6 11.8 1.0 C A:PHE244 4.7 12.8 1.0 O3' P:DG2 4.7 12.4 1.0 C A:GLY245 4.9 13.2 1.0 O A:PHE240 4.9 15.3 1.0 CA A:GLY247 4.9 11.7 1.0 CB A:THR241 4.9 13.8 1.0

A.M.Kaminski, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Structural Snapshots of Human Dna Polymerase Mu Engaged on A Dna Double-Strand Break. Nat Commun V. 11 4784 2020.
ISSN: ESSN 2041-1723
PubMed: 32963245
DOI: 10.1038/S41467-020-18506-5