Magnesium in PDB 8v7g: Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+, PDB code: 8v7g was solved by C.Chang, Y.Gao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.59 / 1.52
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.36, 98.36, 82.047, 90, 90, 120
R / Rfree (%)	18.4 / 19.8

The structure of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ (pdb code 8v7g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+, PDB code: 8v7g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:12.6 occ:1.00 OD1 A:ASP13 2.0 14.9 1.0 OD2 A:ASP115 2.0 15.0 1.0 O1G A:DZ4503 2.1 15.1 1.0 O1B A:DZ4503 2.1 14.0 1.0 O A:MET14 2.1 14.8 1.0 O1A A:DZ4503 2.2 16.5 1.0 CG A:ASP13 3.1 16.2 1.0 CG A:ASP115 3.1 14.9 1.0 PB A:DZ4503 3.2 14.3 1.0 C A:MET14 3.3 12.9 1.0 PA A:DZ4503 3.3 15.6 1.0 PG A:DZ4503 3.4 14.8 1.0 N3A A:DZ4503 3.5 16.7 1.0 OD1 A:ASP115 3.5 15.3 1.0 OD2 A:ASP13 3.5 21.6 1.0 MG A:MG502 3.5 15.6 1.0 O3B A:DZ4503 3.6 14.7 1.0 N A:MET14 3.8 13.3 1.0 O A:HOH731 3.8 18.9 1.0 NZ A:LYS231 3.8 15.0 1.0 CA A:MET14 4.1 12.0 1.0 O2G A:DZ4503 4.1 14.9 1.0 C5' A:DZ4503 4.1 15.9 1.0 C A:ASP13 4.2 13.7 1.0 O5' A:DZ4503 4.2 15.0 1.0 CB A:ASP13 4.3 13.2 1.0 N A:ASP15 4.4 12.1 1.0 CB A:ASP115 4.4 14.0 1.0 O A:HOH773 4.5 24.7 1.0 N A:CYS16 4.5 12.9 1.0 CA A:ASP15 4.5 12.5 1.0 CB A:MET14 4.6 15.4 1.0 O2B A:DZ4503 4.6 15.6 1.0 CE A:LYS231 4.6 21.9 1.0 O A:ASP13 4.6 14.4 1.0 O3G A:DZ4503 4.6 15.2 1.0 O2A A:DZ4503 4.6 17.2 1.0 C A:ASP15 4.7 13.2 1.0 CA A:ASP13 4.7 14.2 1.0 N A:PHE17 4.7 13.3 1.0 CB A:PHE17 4.8 11.8 1.0 O A:ASP115 4.9 15.6 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta-Dna-Gemc-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:15.6 occ:1.00 OD2 A:ASP13 2.1 21.6 1.0 OE2 A:GLU116 2.2 21.9 1.0 O3' P:U7B8 2.2 19.8 0.7 OD1 A:ASP115 2.2 15.3 1.0 O A:HOH773 2.2 24.7 1.0 O1A A:DZ4503 2.2 16.5 1.0 O3' P:U7B8 2.4 20.1 0.3 CG A:ASP13 3.1 16.2 1.0 CG A:ASP115 3.2 14.9 1.0 CD A:GLU116 3.2 24.7 1.0 C3' P:U7B8 3.3 24.6 0.3 PA A:DZ4503 3.3 15.6 1.0 C3' P:U7B8 3.3 25.2 0.7 OD1 A:ASP13 3.4 14.9 1.0 OD2 A:ASP115 3.5 15.0 1.0 MG A:MG501 3.5 12.6 1.0 OG A:SER113 3.7 20.7 1.0 O2A A:DZ4503 3.8 17.2 1.0 O5' A:DZ4503 3.8 15.0 1.0 OE1 A:GLU116 3.9 23.8 1.0 CG A:GLU116 3.9 18.8 1.0 O A:HOH731 4.0 18.9 1.0 C4' P:U7B8 4.0 20.4 0.3 C4' P:U7B8 4.1 20.1 0.7 C5' A:DZ4503 4.1 15.9 1.0 C5' P:U7B8 4.1 25.0 0.7 C5' P:U7B8 4.2 24.9 0.3 CB A:GLU116 4.2 18.4 1.0 NZ A:LYS224 4.4 25.1 1.0 CB A:ASP13 4.4 13.2 1.0 CB A:ASP115 4.5 14.0 1.0 C2' P:U7B8 4.6 22.5 0.7 C A:ASP115 4.6 16.9 1.0 C2' P:U7B8 4.6 22.2 0.3 F1 P:U7B8 4.6 22.2 0.7 O A:ASP115 4.7 15.6 1.0 O5' P:U7B8 4.7 30.4 1.0 O1G A:DZ4503 4.7 15.1 1.0 N3A A:DZ4503 4.8 16.7 1.0 N A:GLU116 4.8 14.7 1.0 F1 P:U7B8 4.8 21.9 0.3 CB A:SER113 4.8 17.9 1.0 O1B A:DZ4503 4.9 14.0 1.0 CA A:ASP115 5.0 15.6 1.0

C.Chang, Y.Gao. Human Dna Polymerase Eta-Dna-Arac-Ended Primer-Dampnpp Ternary Complex with MN2+ To Be Published.