Sodium in PDB 6ipd: Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP

All present enzymatic activity of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP:
2.7.7.7;

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP, PDB code: 6ipd was solved by Y.K.Chang, W.J.Wu, M.D.Tsai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.680, 68.671, 109.576, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.8

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP (pdb code 6ipd). 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 Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP, PDB code: 6ipd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP


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 Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:12.5 occ:1.00 O P:HOH117 2.3 20.0 1.0 O A:THR241 2.4 18.1 1.0 O A:VAL246 2.4 16.0 1.0 O A:HOH866 2.4 21.2 1.0 O A:ILE243 2.4 14.8 1.0 OP1 P:DT3 2.6 11.7 1.0 C A:ILE243 3.4 15.9 1.0 C A:VAL246 3.4 15.9 1.0 C A:THR241 3.4 18.5 1.0 P P:DT3 3.6 12.2 1.0 O P:HOH115 3.8 24.1 1.0 N A:VAL246 3.8 15.2 1.0 OP2 P:DT3 3.8 10.9 1.0 O A:HOH826 4.1 34.4 1.0 N A:ILE243 4.1 17.2 1.0 CA A:VAL246 4.1 15.6 1.0 C A:GLN242 4.2 19.2 1.0 N A:PHE244 4.2 15.3 1.0 CA A:THR241 4.2 17.3 1.0 CA A:PHE244 4.3 15.6 1.0 N A:GLY245 4.3 15.1 1.0 N A:GLN242 4.4 19.1 1.0 CA A:ILE243 4.4 16.6 1.0 O A:HOH892 4.4 38.9 1.0 CB A:VAL246 4.5 15.6 1.0 N A:GLY247 4.5 15.8 1.0 CA A:GLN242 4.5 20.6 1.0 O A:GLN242 4.6 20.2 1.0 O3' P:DG2 4.6 12.2 1.0 C A:PHE244 4.7 15.6 1.0 CA A:GLY247 4.8 16.9 1.0 O A:PHE240 4.8 16.4 1.0 O5' P:DT3 4.9 10.9 1.0 C A:GLY245 4.9 15.7 1.0 CB A:THR241 5.0 17.0 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP


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 Dna Polymerase Mu with Templating Adenine and Mn-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:13.5 occ:1.00 O A:HOH899 2.2 33.8 1.0 OE2 A:GLU386 2.2 22.6 1.0 O A:HOH805 2.3 23.1 1.0 O T:HOH102 2.4 27.5 1.0 OE1 A:GLU386 2.5 27.6 1.0 CD A:GLU386 2.7 23.5 1.0 NE2 A:HIS459 2.8 19.2 1.0 CD2 A:HIS459 3.3 19.3 1.0 CE1 A:HIS459 3.9 19.6 1.0 O A:HOH799 4.1 28.7 1.0 CG A:GLU386 4.2 22.2 1.0 OP1 T:DC8 4.3 17.2 1.0 O A:HOH758 4.3 50.5 1.0 O A:HOH888 4.4 34.3 1.0 O A:HOH620 4.4 13.9 1.0 CG A:HIS459 4.5 16.5 1.0 C5' T:DC8 4.5 13.5 1.0 OE1 A:GLN426 4.6 14.6 1.0 ND1 A:HIS459 4.8 19.3 1.0 CB A:GLU386 5.0 21.2 1.0

Y.K.Chang, Y.P.Huang, X.X.Liu, T.P.Ko, Y.Bessho, Y.Kawano, M.Maestre-Reyna, W.J.Wu, M.D.Tsai. Human Dna Polymerase Mu Can Use A Noncanonical Mechanism For Multiple MN2+-Mediated Functions. J.Am.Chem.Soc. V. 141 8489 2019.
ISSN: ESSN 1520-5126
PubMed: 31067051
DOI: 10.1021/JACS.9B01741