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

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

The structure of Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP, PDB code: 6ipf 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 / 1.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.778, 68.792, 109.620, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 21.8

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

Manganese	(Mn)	4 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine and Mn-8OXODGMP (pdb code 6ipf). 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 Cytosine and Mn-8OXODGMP, PDB code: 6ipf:
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 Cytosine 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 Cytosine and Mn-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:32.6 occ:1.00 O A:HOH783 2.3 37.5 1.0 O P:HOH216 2.3 37.8 1.0 O A:VAL246 2.4 34.6 1.0 O A:THR241 2.4 36.0 1.0 O A:ILE243 2.4 30.4 1.0 OP1 P:DT3 2.5 28.4 1.0 C A:VAL246 3.4 34.1 1.0 C A:THR241 3.5 36.1 1.0 C A:ILE243 3.5 31.9 1.0 P P:DT3 3.6 29.9 1.0 N A:VAL246 3.8 33.9 1.0 OP2 P:DT3 3.8 26.5 1.0 CA A:VAL246 4.1 34.5 1.0 N A:ILE243 4.1 33.1 1.0 C A:GLN242 4.2 36.6 1.0 N A:PHE244 4.2 32.5 1.0 N A:GLY245 4.2 33.4 1.0 CA A:THR241 4.3 35.0 1.0 CA A:PHE244 4.3 33.3 1.0 N A:GLN242 4.4 37.4 1.0 CA A:ILE243 4.4 33.8 1.0 N A:GLY247 4.4 32.6 1.0 CA A:GLN242 4.5 38.5 1.0 CB A:VAL246 4.5 35.2 1.0 O A:GLN242 4.5 37.3 1.0 O3' P:DG2 4.6 29.5 1.0 C A:PHE244 4.7 34.0 1.0 CA A:GLY247 4.8 34.6 1.0 O5' P:DT3 4.8 27.4 1.0 O A:PHE240 4.8 33.0 1.0 C A:GLY245 4.8 35.7 1.0

Sodium binding site 2 out of 2 in the Post-Catalytic Complex of Human Dna Polymerase Mu with Templating Cytosine 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 Cytosine and Mn-8OXODGMP within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:33.5 occ:1.00 O A:HOH770 2.2 42.4 1.0 OE2 A:GLU386 2.3 41.4 1.0 O A:HOH800 2.3 54.5 1.0 O T:HOH101 2.4 41.0 1.0 OE1 A:GLU386 2.6 48.6 1.0 CD A:GLU386 2.8 43.0 1.0 NE2 A:HIS459 3.1 40.1 1.0 CD2 A:HIS459 3.6 39.8 1.0 CE1 A:HIS459 4.0 41.4 1.0 O A:HOH714 4.0 44.9 1.0 CG A:GLU386 4.3 40.0 1.0 OP1 T:DC8 4.3 37.3 1.0 O A:HOH618 4.5 30.7 1.0 CG A:HIS459 4.6 35.1 1.0 C5' T:DC8 4.7 30.4 1.0 OE1 A:GLN426 4.7 32.1 1.0 ND1 A:HIS459 4.7 42.2 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