Magnesium in PDB 8v7e: Human Dna Polymerase Eta-Dna-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+

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

The structure of Human Dna Polymerase Eta-Dna-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+, PDB code: 8v7e 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)	42.30 / 1.82
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.759, 98.759, 81.97, 90, 90, 120
R / Rfree (%)	17.2 / 20.4

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+ (pdb code 8v7e). 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-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+, PDB code: 8v7e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Arac-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-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:22.8 occ:1.00 OD1 A:ASP13 2.0 28.9 1.0 OD2 A:ASP115 2.1 27.6 1.0 O1G A:DZ4503 2.1 23.4 1.0 O1B A:DZ4503 2.1 23.9 1.0 O A:MET14 2.1 21.9 1.0 O1A A:DZ4503 2.2 26.5 1.0 CG A:ASP13 3.1 31.3 1.0 CG A:ASP115 3.2 28.7 1.0 PB A:DZ4503 3.2 24.4 1.0 C A:MET14 3.3 21.2 1.0 PG A:DZ4503 3.3 25.3 1.0 PA A:DZ4503 3.3 26.8 1.0 MG A:MG502 3.5 27.8 0.5 OD2 A:ASP13 3.6 45.7 1.0 O3B A:DZ4503 3.6 21.8 1.0 N3A A:DZ4503 3.6 26.8 1.0 OD1 A:ASP115 3.6 25.9 1.0 NZ A:LYS231 3.9 23.8 1.0 N A:MET14 4.0 23.2 1.0 C5' A:DZ4503 4.0 25.2 1.0 O A:HOH769 4.0 38.7 1.0 CA A:MET14 4.1 21.2 1.0 O2G A:DZ4503 4.1 24.4 1.0 O5' A:DZ4503 4.2 24.4 1.0 C A:ASP13 4.2 22.4 1.0 O A:HOH625 4.3 35.2 1.0 CB A:ASP13 4.3 23.6 1.0 N A:ASP15 4.4 24.2 1.0 CB A:ASP115 4.4 24.3 1.0 O3G A:DZ4503 4.5 24.4 1.0 CE A:LYS231 4.5 33.5 1.0 O2A A:DZ4503 4.5 31.0 1.0 CA A:ASP15 4.5 22.6 1.0 N A:CYS16 4.6 21.6 1.0 O2B A:DZ4503 4.6 24.3 1.0 CB A:MET14 4.6 24.5 1.0 O A:ASP13 4.6 23.5 1.0 C A:ASP15 4.7 24.9 1.0 CA A:ASP13 4.7 24.0 1.0 N A:PHE17 4.7 20.4 1.0 CB A:PHE17 4.8 21.4 1.0 O A:ASP115 4.9 25.4 1.0 O P:HOH105 5.0 34.6 0.4

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Arac-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-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:27.8 occ:0.50 O A:HOH625 2.1 35.2 1.0 OE2 A:GLU116 2.2 47.2 1.0 OD1 A:ASP115 2.2 25.9 1.0 O P:HOH105 2.2 34.6 0.4 OD2 A:ASP13 2.3 45.7 1.0 O1A A:DZ4503 2.4 26.5 1.0 O3' P:CAR8 2.6 34.7 0.6 CG A:ASP13 3.1 31.3 1.0 CD A:GLU116 3.1 41.5 1.0 CG A:ASP115 3.1 28.7 1.0 OD1 A:ASP13 3.2 28.9 1.0 C3' P:CAR8 3.3 34.5 0.6 OD2 A:ASP115 3.4 27.6 1.0 PA A:DZ4503 3.4 26.8 1.0 MG A:MG501 3.5 22.8 1.0 O2A A:DZ4503 3.8 31.0 1.0 CG A:GLU116 3.8 33.2 1.0 O5' A:DZ4503 3.8 24.4 1.0 OE1 A:GLU116 3.9 36.7 1.0 OG A:SER113 3.9 30.8 1.0 C4' P:CAR8 4.1 33.7 0.6 CB A:GLU116 4.1 31.7 1.0 O3' P:CAR8 4.1 37.7 0.4 C5' A:DZ4503 4.2 25.2 1.0 O A:HOH769 4.3 38.7 1.0 CB A:ASP13 4.4 23.6 1.0 C5' P:CAR8 4.5 38.4 0.6 NZ A:LYS224 4.5 45.2 1.0 CB A:ASP115 4.5 24.3 1.0 C A:ASP115 4.6 26.1 1.0 O P:HOH103 4.6 49.6 1.0 C2' P:CAR8 4.6 34.6 0.6 O A:ASP115 4.6 25.4 1.0 O1G A:DZ4503 4.6 23.4 1.0 N A:GLU116 4.7 25.7 1.0 O1B A:DZ4503 4.9 23.9 1.0 N3A A:DZ4503 4.9 26.8 1.0 O5' P:CAR8 5.0 36.7 0.6

C.Chang, Y.Gao. Human Dna Polymerase Eta-Dna-Arac-Ended Primer-Dampnpp Ternary Complex with MG2+ To Be Published.