Magnesium in PDB 8e8k: Human Dna Polymerase Eta-Dna-Rc-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+

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

The structure of Human Dna Polymerase Eta-Dna-Rc-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+, PDB code: 8e8k 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)	42.47 / 2.40
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.077, 98.077, 81.89, 90, 90, 120
R / Rfree (%)	18.2 / 23.7

The binding sites of Magnesium atom in the Human Dna Polymerase Eta-Dna-Rc-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+ (pdb code 8e8k). 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-Rc-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+, PDB code: 8e8k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Rc-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-Rc-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:25.6 occ:1.00 O1B A:XG4503 1.9 32.0 1.0 O2G A:XG4503 2.0 24.6 1.0 OD1 A:ASP13 2.1 27.6 1.0 OD2 A:ASP115 2.2 25.9 1.0 O1A A:XG4503 2.2 29.1 1.0 O A:MET14 2.2 23.6 1.0 PB A:XG4503 2.9 28.3 1.0 CG A:ASP13 3.0 28.1 1.0 PG A:XG4503 3.2 29.4 1.0 CG A:ASP115 3.2 28.6 1.0 PA A:XG4503 3.2 31.8 1.0 N3A A:XG4503 3.3 27.0 1.0 O3B A:XG4503 3.3 25.3 1.0 OD2 A:ASP13 3.4 34.7 1.0 C A:MET14 3.4 30.1 1.0 OD1 A:ASP115 3.6 26.9 1.0 MG A:MG502 3.7 29.0 1.0 O3G A:XG4503 3.8 32.2 1.0 N A:MET14 4.0 31.6 1.0 C5' A:XG4503 4.1 19.4 1.0 NZ A:LYS231 4.1 22.7 1.0 O5' A:XG4503 4.2 34.4 1.0 O A:HOH604 4.2 34.4 1.0 CA A:MET14 4.2 29.2 1.0 O2B A:XG4503 4.3 30.4 1.0 O1G A:XG4503 4.4 27.8 1.0 CB A:ASP13 4.4 26.7 1.0 C A:ASP13 4.4 27.9 1.0 O2A A:XG4503 4.4 28.4 1.0 N A:ASP15 4.4 26.9 1.0 N A:CYS16 4.4 30.7 1.0 CB A:ASP115 4.5 23.3 1.0 CE A:LYS231 4.6 30.5 1.0 CA A:ASP15 4.6 29.2 1.0 N A:PHE17 4.6 25.4 1.0 C A:ASP15 4.7 29.5 1.0 CB A:PHE17 4.7 21.2 1.0 CB A:MET14 4.8 31.3 1.0 CA A:ASP13 4.9 28.1 1.0 O A:ASP13 5.0 29.7 1.0 O A:HOH601 5.0 32.9 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Rc-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-Rc-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:29.0 occ:1.00 O A:HOH601 1.9 32.9 1.0 OD2 A:ASP13 2.0 34.7 1.0 OE1 A:GLU116 2.0 38.4 1.0 OD1 A:ASP115 2.1 26.9 1.0 O A:HOH604 2.2 34.4 1.0 O1A A:XG4503 2.3 29.1 1.0 CD A:GLU116 3.0 41.4 1.0 CG A:ASP115 3.1 28.6 1.0 CG A:ASP13 3.1 28.1 1.0 PA A:XG4503 3.4 31.8 1.0 OD2 A:ASP115 3.5 25.9 1.0 OE2 A:GLU116 3.6 34.7 1.0 OD1 A:ASP13 3.6 27.6 1.0 OG A:SER113 3.7 35.7 1.0 O2A A:XG4503 3.7 28.4 1.0 MG A:MG501 3.7 25.6 1.0 O5' A:XG4503 3.9 34.4 1.0 CG A:GLU116 4.0 33.1 1.0 CB A:GLU116 4.1 30.8 1.0 C5' A:XG4503 4.1 19.4 1.0 NZ A:LYS224 4.2 30.3 1.0 CB A:ASP13 4.4 26.7 1.0 CB A:ASP115 4.5 23.3 1.0 C A:ASP115 4.6 26.4 1.0 O A:ASP115 4.7 30.1 1.0 O2G A:XG4503 4.7 24.6 1.0 N A:GLU116 4.8 33.0 1.0 N3A A:XG4503 4.8 27.0 1.0 CB A:SER113 4.9 29.2 1.0 CA A:ASP115 5.0 29.6 1.0 O2' P:C9 5.0 51.7 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