Manganese in PDB 8e85: Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+, PDB code: 8e85 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)	32.14 / 1.72
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.199, 98.199, 81.798, 90, 90, 120
R / Rfree (%)	20.3 / 23.4

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+ (pdb code 8e85). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+, PDB code: 8e85:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:17.7 occ:1.00 OD2 A:ASP13 2.1 18.9 1.0 O1B A:XG4503 2.1 17.4 1.0 OD2 A:ASP115 2.1 19.4 1.0 O1G A:XG4503 2.2 18.5 1.0 O A:MET14 2.2 17.2 1.0 O1A A:XG4503 2.3 18.5 1.0 CG A:ASP13 3.1 21.0 1.0 PB A:XG4503 3.1 18.5 1.0 CG A:ASP115 3.2 19.4 1.0 PG A:XG4503 3.4 19.5 1.0 C A:MET14 3.4 15.6 1.0 PA A:XG4503 3.4 18.9 1.0 OD1 A:ASP13 3.4 20.0 1.0 N3A A:XG4503 3.5 21.6 1.0 O3B A:XG4503 3.6 17.6 1.0 MN A:MN502 3.6 18.5 1.0 OD1 A:ASP115 3.6 18.9 1.0 NZ A:LYS231 3.7 18.7 1.0 N A:MET14 3.8 18.1 1.0 O A:HOH639 3.9 26.9 1.0 O2G A:XG4503 4.0 18.4 1.0 CA A:MET14 4.1 16.4 1.0 C5' A:XG4503 4.2 19.2 1.0 C A:ASP13 4.2 14.2 1.0 CB A:ASP13 4.2 20.3 1.0 O5' A:XG4503 4.3 21.2 1.0 N A:ASP15 4.4 16.8 1.0 CB A:ASP115 4.5 17.1 1.0 O P:HOH102 4.5 22.9 1.0 O2B A:XG4503 4.5 17.0 1.0 O3G A:XG4503 4.6 20.3 1.0 O2A A:XG4503 4.6 20.5 1.0 CB A:MET14 4.6 17.1 1.0 N A:CYS16 4.6 16.3 1.0 O A:ASP13 4.6 17.5 1.0 CA A:ASP15 4.7 16.1 1.0 N A:PHE17 4.7 15.8 1.0 CA A:ASP13 4.7 15.8 1.0 CB A:PHE17 4.8 15.9 1.0 CE A:LYS231 4.8 31.9 1.0 C A:ASP15 4.8 17.7 1.0 O A:ASP115 4.9 19.3 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Dna Polymerase Eta-Dna-Rg-Ended Primer-Dgmpnpp Ternary Mismatch Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:18.5 occ:1.00 O3' P:G9 2.1 12.2 0.5 OD1 A:ASP115 2.1 18.9 1.0 OD1 A:ASP13 2.1 20.0 1.0 O1A A:XG4503 2.3 18.5 1.0 OE2 A:GLU116 2.3 23.2 1.0 O P:HOH102 2.3 22.9 1.0 CG A:ASP115 3.1 19.4 1.0 C3' P:G9 3.1 23.9 0.5 CG A:ASP13 3.2 21.0 1.0 CD A:GLU116 3.3 24.5 1.0 PA A:XG4503 3.4 18.9 1.0 OD2 A:ASP115 3.4 19.4 1.0 OD2 A:ASP13 3.5 18.9 1.0 MN A:MN501 3.6 17.7 1.0 OG A:SER113 3.7 23.6 1.0 O2A A:XG4503 3.7 20.5 1.0 O5' A:XG4503 3.9 21.2 1.0 OE1 A:GLU116 3.9 29.5 1.0 C4' P:G9 3.9 28.7 0.5 O A:HOH639 4.0 26.9 1.0 CB A:GLU116 4.1 23.0 1.0 C5' P:G9 4.1 31.8 0.5 C5' A:XG4503 4.1 19.2 1.0 CG A:GLU116 4.1 19.8 1.0 NZ A:LYS224 4.3 25.1 1.0 C2' P:G9 4.4 32.5 0.5 CB A:ASP115 4.5 17.1 1.0 CB A:ASP13 4.6 20.3 1.0 O5' P:G9 4.6 42.2 0.5 O2' P:G9 4.6 24.4 0.5 C A:ASP115 4.6 17.7 1.0 O A:ASP115 4.7 19.3 1.0 OP1 P:G9 4.7 40.1 0.5 O1G A:XG4503 4.7 18.5 1.0 CB A:SER113 4.8 23.1 1.0 N3A A:XG4503 4.8 21.6 1.0 O2' P:G9 4.8 28.2 0.5 N A:GLU116 4.9 16.9 1.0 O1B A:XG4503 4.9 17.4 1.0 CA A:ASP115 5.0 16.6 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