Manganese in PDB 8e8d: Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S, PDB code: 8e8d 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)	31.43 / 2.09
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.48, 98.48, 81.68, 90, 90, 120
R / Rfree (%)	20 / 23.5

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S (pdb code 8e8d). 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-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S, PDB code: 8e8d:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S


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-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:54.7 occ:1.00 O2G A:DGT503 1.8 39.9 0.8 O2B A:DGT503 2.0 31.8 0.8 OD2 A:ASP115 2.1 47.3 1.0 OD2 A:ASP13 2.2 44.6 1.0 O1A A:DGT503 2.4 36.0 0.8 O A:MET14 2.4 32.3 1.0 PB A:DGT503 2.9 43.9 0.8 PG A:DGT503 3.1 40.6 0.8 CG A:ASP13 3.1 41.2 1.0 O3A A:DGT503 3.2 48.0 0.8 O3B A:DGT503 3.3 40.4 0.8 CG A:ASP115 3.3 48.7 1.0 MN A:MN502 3.4 53.8 0.8 PA A:DGT503 3.4 48.3 0.8 OD1 A:ASP13 3.5 57.5 1.0 C A:MET14 3.6 31.4 1.0 O1G A:DGT503 3.8 43.6 0.8 OD1 A:ASP115 3.9 50.0 1.0 C5' A:DGT503 4.0 43.8 0.8 O A:HOH608 4.0 54.6 1.0 O5' A:DGT503 4.1 53.2 0.8 N A:MET14 4.2 37.5 1.0 O3G A:DGT503 4.2 40.7 0.8 N A:CYS16 4.3 37.5 1.0 O1B A:DGT503 4.3 32.9 0.8 NZ A:LYS231 4.3 44.4 1.0 CB A:ASP13 4.4 49.4 1.0 CA A:MET14 4.4 34.5 1.0 C A:ASP13 4.4 37.3 1.0 CB A:ASP115 4.4 32.1 1.0 N A:ASP15 4.5 28.7 1.0 CA A:ASP15 4.6 32.0 1.0 C A:ASP15 4.6 37.6 1.0 O2A A:DGT503 4.7 39.4 0.8 N A:PHE17 4.7 29.7 1.0 CA A:ASP13 4.8 32.4 1.0 O A:ASP115 4.9 41.1 1.0 O A:ASP13 4.9 25.4 1.0 CB A:MET14 5.0 33.5 1.0 CB A:PHE17 5.0 24.6 1.0 CA A:CYS16 5.0 35.3 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S


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-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 60S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:53.8 occ:0.85 O1A A:DGT503 2.0 36.0 0.8 OD1 A:ASP115 2.3 50.0 1.0 OD1 A:ASP13 2.3 57.5 1.0 O A:HOH608 2.3 54.6 1.0 O3' P:U9 2.8 39.2 0.7 OE2 A:GLU116 2.8 65.8 1.0 CG A:ASP115 3.0 48.7 1.0 OD2 A:ASP115 3.1 47.3 1.0 CG A:ASP13 3.2 41.2 1.0 PA A:DGT503 3.3 48.3 0.8 CD A:GLU116 3.3 57.0 1.0 MN A:MN501 3.4 54.7 1.0 OD2 A:ASP13 3.5 44.6 1.0 C3' P:U9 3.6 51.2 0.7 C5' A:DGT503 3.8 43.8 0.8 OE1 A:GLU116 3.8 55.0 1.0 CB A:GLU116 3.8 42.2 1.0 O5' A:DGT503 3.9 53.2 0.8 O2A A:DGT503 3.9 39.4 0.8 OG A:SER113 4.0 37.6 1.0 CG A:GLU116 4.1 48.0 1.0 O2G A:DGT503 4.4 39.9 0.8 C4' P:U9 4.4 47.0 0.7 CB A:ASP115 4.5 32.1 1.0 O A:ASP115 4.5 41.1 1.0 C A:ASP115 4.5 44.1 1.0 O3A A:DGT503 4.5 48.0 0.8 CB A:ASP13 4.5 49.4 1.0 O2B A:DGT503 4.6 31.8 0.8 C5' P:U9 4.6 48.0 0.7 N A:GLU116 4.7 37.2 1.0 NZ A:LYS224 4.7 46.6 1.0 CA A:GLU116 4.9 41.4 1.0 C2' P:U9 4.9 47.5 0.7 CA A:ASP115 5.0 33.6 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