Magnesium in PDB 8e87: Human Dna Polymerase Eta-Dna-Ra-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+

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

The structure of Human Dna Polymerase Eta-Dna-Ra-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+, PDB code: 8e87 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)	42.32 / 2.19
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.728, 97.728, 81.881, 90, 90, 120
R / Rfree (%)	20 / 24.9

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Ra-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+ (pdb code 8e87). 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-Ra-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+, PDB code: 8e87:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Ra-Ended Primer-Dgmpnpp Ternary Mismatch 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-Ra-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:29.4 occ:1.00 O2G A:XG4503 1.9 22.4 1.0 OD1 A:ASP13 2.0 27.4 1.0 O1B A:XG4503 2.1 26.1 1.0 OD2 A:ASP115 2.1 24.4 1.0 O1A A:XG4503 2.2 27.1 1.0 O A:MET14 2.2 24.8 1.0 CG A:ASP13 3.0 27.7 1.0 PB A:XG4503 3.1 27.4 1.0 PG A:XG4503 3.2 29.5 1.0 CG A:ASP115 3.2 30.5 1.0 PA A:XG4503 3.3 31.2 1.0 C A:MET14 3.4 24.2 1.0 O3B A:XG4503 3.4 30.8 1.0 N3A A:XG4503 3.4 26.4 1.0 OD2 A:ASP13 3.4 32.0 1.0 MG A:MG502 3.5 25.4 1.0 OD1 A:ASP115 3.7 28.5 1.0 O3G A:XG4503 3.8 31.9 1.0 NZ A:LYS231 3.9 22.7 1.0 N A:MET14 4.0 32.8 1.0 C5' A:XG4503 4.1 26.5 1.0 CA A:MET14 4.2 27.1 1.0 O5' A:XG4503 4.2 30.4 1.0 C A:ASP13 4.3 27.8 1.0 CB A:ASP13 4.3 34.8 1.0 O A:HOH604 4.3 28.5 1.0 N A:ASP15 4.4 22.1 1.0 O1G A:XG4503 4.4 26.8 1.0 CB A:ASP115 4.5 22.1 1.0 O2B A:XG4503 4.5 27.8 1.0 N A:CYS16 4.5 28.3 1.0 O2A A:XG4503 4.5 28.6 1.0 CE A:LYS231 4.5 32.1 1.0 CA A:ASP15 4.6 30.6 1.0 O A:ASP13 4.6 24.3 1.0 N A:PHE17 4.7 25.8 1.0 C A:ASP15 4.7 30.2 1.0 CB A:MET14 4.8 30.9 1.0 CA A:ASP13 4.8 29.7 1.0 CB A:PHE17 4.8 21.1 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Ra-Ended Primer-Dgmpnpp Ternary Mismatch 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-Ra-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:25.4 occ:1.00 OD2 A:ASP13 2.1 32.0 1.0 O A:HOH604 2.1 28.5 1.0 O3' P:A9 2.2 30.4 1.0 O1A A:XG4503 2.2 27.1 1.0 OD1 A:ASP115 2.2 28.5 1.0 OE1 A:GLU116 2.3 33.2 1.0 CG A:ASP115 3.1 30.5 1.0 CG A:ASP13 3.1 27.7 1.0 PA A:XG4503 3.2 31.2 1.0 C3' P:A9 3.2 35.0 1.0 CD A:GLU116 3.3 36.8 1.0 OD2 A:ASP115 3.3 24.4 1.0 OD1 A:ASP13 3.4 27.4 1.0 MG A:MG501 3.5 29.4 1.0 O2A A:XG4503 3.6 28.6 1.0 O5' A:XG4503 3.7 30.4 1.0 OG A:SER113 3.8 33.6 1.0 C5' A:XG4503 3.9 26.5 1.0 OE2 A:GLU116 3.9 35.7 1.0 C4' P:A9 3.9 38.5 1.0 C5' P:A9 4.1 30.5 1.0 CB A:GLU116 4.2 25.2 1.0 CG A:GLU116 4.3 35.5 1.0 NZ A:LYS224 4.3 31.5 1.0 CB A:ASP13 4.4 34.8 1.0 O2G A:XG4503 4.5 22.4 1.0 CB A:ASP115 4.5 22.1 1.0 C2' P:A9 4.5 40.6 1.0 N3A A:XG4503 4.6 26.4 1.0 C A:ASP115 4.7 31.0 1.0 O2' P:A9 4.7 36.3 1.0 O1B A:XG4503 4.8 26.1 1.0 O5' P:A9 4.8 41.6 1.0 O A:ASP115 4.8 31.6 1.0 N A:GLU116 4.9 28.9 1.0 CB A:SER113 5.0 28.7 1.0

C.Chang, C.Lee Luo, S.Eleraky, A.Lin, G.Zhou, Y.Gao. Primer Terminal Ribonucleotide Alters the Active Site Dynamics of Dna Polymerase Eta and Reduce Dna Synthesis Fidelity J.Biol.Chem. 02938 2023.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2023.102938