Manganese in PDB 8e8g: Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S, PDB code: 8e8g 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)	32.10 / 2.13
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.06, 98.06, 81.26, 90, 90, 120
R / Rfree (%)	20.1 / 24.1

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 180S (pdb code 8e8g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 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 180S, PDB code: 8e8g:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:60.8 occ:1.00 O2G A:DGT503 1.8 49.0 0.3 O1 A:DPO504 1.9 48.3 0.5 OD2 A:ASP115 2.0 54.0 1.0 O2B A:DGT503 2.1 43.3 0.3 O5 A:DPO504 2.1 43.4 0.5 OD1 A:ASP13 2.2 58.6 1.0 O A:MET14 2.4 44.4 1.0 O1A A:DGT503 2.5 47.9 0.3 OP1 P:DG10 2.5 47.8 0.5 PB A:DGT503 2.9 53.0 0.3 PG A:DGT503 3.1 53.9 0.3 CG A:ASP13 3.1 48.6 1.0 P2 A:DPO504 3.1 53.5 0.5 P1 A:DPO504 3.1 54.0 0.5 CG A:ASP115 3.2 58.3 1.0 MN A:MN502 3.2 52.4 0.7 O3B A:DGT503 3.2 52.9 0.3 O3A A:DGT503 3.3 52.4 0.3 O4 A:DPO504 3.4 52.8 0.5 OD2 A:ASP13 3.4 61.8 1.0 O6 A:DPO504 3.5 53.6 0.5 PA A:DGT503 3.5 53.0 0.3 C A:MET14 3.5 44.9 1.0 O1G A:DGT503 3.7 54.6 0.3 O2 A:DPO504 3.7 55.7 0.5 OD1 A:ASP115 3.8 57.1 1.0 O A:HOH601 3.9 62.6 1.0 P P:DG10 4.0 65.9 0.5 C5' A:DGT503 4.1 54.5 0.3 NZ A:LYS231 4.1 52.9 1.0 C5' P:DG10 4.1 54.6 0.5 N A:MET14 4.2 51.5 1.0 O5' A:DGT503 4.2 53.4 0.3 O3G A:DGT503 4.3 49.4 0.3 O3 A:DPO504 4.4 49.4 0.5 N A:CYS16 4.4 50.0 1.0 O1B A:DGT503 4.4 51.4 0.3 CB A:ASP13 4.4 54.6 1.0 O5' P:DG10 4.4 53.1 0.5 CB A:ASP115 4.4 41.7 1.0 CA A:MET14 4.4 43.1 1.0 C A:ASP13 4.4 49.6 1.0 O7 A:DPO504 4.5 51.2 0.5 N A:ASP15 4.5 37.9 1.0 CA A:ASP15 4.6 54.1 1.0 C A:ASP15 4.7 53.5 1.0 N A:PHE17 4.7 39.5 1.0 O2A A:DGT503 4.8 55.7 0.3 O A:ASP13 4.8 39.5 1.0 OP2 P:DG10 4.8 55.6 0.5 CA A:ASP13 4.8 45.9 1.0 MN P:MN101 4.9 62.3 0.4 O A:ASP115 4.9 54.3 1.0 CB A:PHE17 5.0 34.9 1.0

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:52.4 occ:0.70 OP1 P:DG10 1.8 47.8 0.5 O1A A:DGT503 1.8 47.9 0.3 OD1 A:ASP115 2.2 57.1 1.0 OD2 A:ASP13 2.2 61.8 1.0 OE1 A:GLU116 2.3 62.3 1.0 O A:HOH601 2.3 62.6 1.0 P P:DG10 2.7 65.9 0.5 O3' P:U9 2.7 53.9 0.5 O3' P:U9 2.8 51.3 0.3 CG A:ASP115 3.0 58.3 1.0 OD2 A:ASP115 3.0 54.0 1.0 CG A:ASP13 3.2 48.6 1.0 PA A:DGT503 3.2 53.0 0.3 MN A:MN501 3.2 60.8 1.0 CD A:GLU116 3.3 68.2 1.0 OD1 A:ASP13 3.5 58.6 1.0 C3' P:U9 3.7 62.8 0.3 OP2 P:DG10 3.8 55.6 0.5 O5' P:DG10 3.8 53.1 0.5 C5' A:DGT503 3.8 54.5 0.3 O2A A:DGT503 3.8 55.7 0.3 O5' A:DGT503 3.8 53.4 0.3 C5' P:DG10 3.8 54.6 0.5 OE2 A:GLU116 3.9 67.6 1.0 C3' P:U9 4.0 63.9 0.5 CB A:GLU116 4.1 49.6 1.0 CG A:GLU116 4.1 58.4 1.0 OG A:SER113 4.2 54.4 1.0 O2G A:DGT503 4.2 49.0 0.3 O1 A:DPO504 4.2 48.3 0.5 C5' P:U9 4.3 62.1 0.3 O3A A:DGT503 4.3 52.4 0.3 C4' P:U9 4.3 60.0 0.3 O2B A:DGT503 4.4 43.3 0.3 O5 A:DPO504 4.4 43.4 0.5 CB A:ASP115 4.4 41.7 1.0 NZ A:LYS224 4.5 73.8 1.0 C4' P:U9 4.5 60.2 0.5 CB A:ASP13 4.5 54.6 1.0 O6 A:DPO504 4.6 53.6 0.5 C5' P:U9 4.7 61.2 0.5 O A:ASP115 4.7 54.3 1.0 C A:ASP115 4.7 54.0 1.0 O2' P:U9 4.9 60.2 0.5 N A:GLU116 4.9 52.6 1.0

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 180S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:62.3 occ:0.40 O A:HOH602 1.9 36.6 0.3 O A:HOH603 2.1 52.9 0.3 O2A A:DGT503 2.1 55.7 0.3 OP2 P:DG10 2.2 55.6 0.5 O3A A:DGT503 2.3 52.4 0.3 O6 A:DPO504 2.4 53.6 0.5 NH1 A:ARG61 2.6 56.3 0.3 PA A:DGT503 2.6 53.0 0.3 P P:DG10 3.3 65.9 0.5 CZ A:ARG61 3.4 57.6 0.3 NH2 A:ARG61 3.5 46.3 0.3 O3G A:DGT503 3.6 49.4 0.3 O1A A:DGT503 3.6 47.9 0.3 OP1 P:DG10 3.7 47.8 0.5 PB A:DGT503 3.7 53.0 0.3 O3 A:DPO504 3.7 49.4 0.5 P2 A:DPO504 3.7 53.5 0.5 O3B A:DGT503 3.8 52.9 0.3 O A:HOH601 3.8 62.6 1.0 O5' A:DGT503 3.9 53.4 0.3 O3' P:U9 3.9 56.2 0.2 O4 A:DPO504 3.9 52.8 0.5 O1 A:DPO504 3.9 48.3 0.5 O5' P:DG10 4.0 53.1 0.5 PG A:DGT503 4.0 53.9 0.3 O2G A:DGT503 4.1 49.0 0.3 P1 A:DPO504 4.1 54.0 0.5 O A:HOH604 4.2 59.0 0.3 C3' P:U9 4.3 61.1 0.2 O1B A:DGT503 4.3 51.4 0.3 NE A:ARG61 4.6 53.7 0.3 O7 A:DPO504 4.6 51.2 0.5 O5 A:DPO504 4.7 43.4 0.5 O3' P:U9 4.7 53.9 0.5 O2B A:DGT503 4.7 43.3 0.3 MN A:MN501 4.9 60.8 1.0 NH2 A:ARG55 4.9 53.4 1.0 C3' P:U9 5.0 63.9 0.5

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