Manganese in PDB 8e8f: Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 120S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 120S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Ru-Ended Primer Ternary Mismatch Complex:Reaction with 10 Mm MN2+ For 120S, PDB code: 8e8f 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)	32.16 / 2.14
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.236, 98.236, 81.296, 90, 90, 120
R / Rfree (%)	20 / 27.4

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 120S (pdb code 8e8f). 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 120S, PDB code: 8e8f:
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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:63.7 occ:1.00 O2G A:DGT503 1.7 53.1 0.5 O1 A:DPO504 1.9 52.5 0.3 OD2 A:ASP115 2.1 60.2 1.0 OD2 A:ASP13 2.1 55.0 1.0 O2B A:DGT503 2.2 42.0 0.5 O5 A:DPO504 2.3 43.3 0.3 O A:MET14 2.3 46.5 1.0 O1A A:DGT503 2.3 49.3 0.5 OP1 P:DG10 2.5 50.0 0.3 PB A:DGT503 3.0 54.7 0.5 PG A:DGT503 3.0 52.5 0.5 CG A:ASP13 3.1 51.5 1.0 P2 A:DPO504 3.2 55.5 0.3 P1 A:DPO504 3.2 51.6 0.3 CG A:ASP115 3.3 59.2 1.0 O3B A:DGT503 3.3 49.1 0.5 O3A A:DGT503 3.3 57.0 0.5 MN A:MN502 3.3 56.6 0.7 PA A:DGT503 3.4 55.9 0.5 C A:MET14 3.5 44.0 1.0 O4 A:DPO504 3.5 49.4 0.3 OD1 A:ASP13 3.5 54.2 1.0 O6 A:DPO504 3.6 56.0 0.3 O1G A:DGT503 3.7 53.0 0.5 OD1 A:ASP115 3.8 52.1 1.0 O2 A:DPO504 3.9 53.3 0.3 O A:HOH602 3.9 76.9 1.0 P P:DG10 4.0 62.6 0.3 N A:MET14 4.1 50.2 1.0 O3G A:DGT503 4.2 46.9 0.5 NZ A:LYS231 4.3 64.0 1.0 C5' A:DGT503 4.3 55.9 0.5 CB A:ASP13 4.3 53.5 1.0 CA A:MET14 4.3 48.6 1.0 O5' A:DGT503 4.3 54.1 0.5 C5' P:DG10 4.4 55.7 0.3 N A:CYS16 4.4 48.7 1.0 C A:ASP13 4.4 46.5 1.0 N A:ASP15 4.4 38.6 1.0 O3 A:DPO504 4.4 46.4 0.3 CB A:ASP115 4.4 43.7 1.0 O1B A:DGT503 4.5 49.0 0.5 CA A:ASP15 4.5 48.8 1.0 O5' P:DG10 4.5 54.2 0.3 O2A A:DGT503 4.6 56.8 0.5 C A:ASP15 4.6 56.0 1.0 O7 A:DPO504 4.6 48.6 0.3 OP2 P:DG10 4.7 56.9 0.3 N A:PHE17 4.8 40.5 1.0 O A:ASP13 4.8 39.2 1.0 CA A:ASP13 4.8 52.1 1.0 CB A:MET14 4.9 51.9 1.0 O3' P:U9 5.0 54.9 0.3 O A:ASP115 5.0 49.1 1.0 CB A:PHE17 5.0 33.2 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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:56.6 occ:0.70 O1A A:DGT503 2.0 49.3 0.5 OP1 P:DG10 2.0 50.0 0.3 OE1 A:GLU116 2.1 73.2 1.0 O A:HOH602 2.1 76.9 1.0 OD1 A:ASP115 2.3 52.1 1.0 OD1 A:ASP13 2.4 54.2 1.0 O3' P:U9 2.6 54.9 0.3 O3' P:U9 2.7 52.4 0.4 P P:DG10 2.7 62.6 0.3 CG A:ASP115 3.0 59.2 1.0 OD2 A:ASP115 3.1 60.2 1.0 CG A:ASP13 3.3 51.5 1.0 PA A:DGT503 3.3 55.9 0.5 CD A:GLU116 3.3 74.3 1.0 MN A:MN501 3.3 63.7 1.0 OD2 A:ASP13 3.5 55.0 1.0 C3' P:U9 3.6 63.1 0.4 C3' P:U9 3.7 63.1 0.3 OP2 P:DG10 3.7 56.9 0.3 O2A A:DGT503 3.7 56.8 0.5 CG A:GLU116 3.8 55.9 1.0 O5' A:DGT503 3.9 54.1 0.5 CB A:GLU116 4.0 45.3 1.0 O5' P:DG10 4.0 54.2 0.3 OG A:SER113 4.1 61.3 1.0 C4' P:U9 4.1 61.1 0.3 C5' P:U9 4.1 65.3 0.3 C4' P:U9 4.2 61.1 0.4 C5' A:DGT503 4.2 55.9 0.5 O2G A:DGT503 4.2 53.1 0.5 C5' P:U9 4.2 65.4 0.4 C5' P:DG10 4.2 55.7 0.3 OE2 A:GLU116 4.3 67.1 1.0 O1 A:DPO504 4.4 52.5 0.3 O3A A:DGT503 4.5 57.0 0.5 CB A:ASP115 4.5 43.7 1.0 NZ A:LYS224 4.5 68.0 1.0 CB A:ASP13 4.6 53.5 1.0 O5 A:DPO504 4.7 43.3 0.3 O2B A:DGT503 4.7 42.0 0.5 C A:ASP115 4.7 52.5 1.0 N A:GLU116 4.7 46.3 1.0 O3' P:U9 4.7 58.9 0.3 O6 A:DPO504 4.8 56.0 0.3 O A:ASP115 4.8 49.1 1.0 C2' P:U9 4.9 62.8 0.3 CA A:GLU116 4.9 48.9 1.0 O2' P:U9 5.0 63.5 0.3 C2' P:U9 5.0 62.7 0.4

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 120S


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 120S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn505 b:76.5 occ:0.30 NH1 A:ARG61 1.9 56.4 0.3 O6 A:DPO504 2.5 56.0 0.3 O2A A:DGT503 2.7 56.8 0.5 O3A A:DGT503 2.7 57.0 0.5 CZ A:ARG61 2.8 58.1 0.3 OP2 P:DG10 2.9 56.9 0.3 NH2 A:ARG61 2.9 48.0 0.3 PA A:DGT503 3.3 55.9 0.5 O A:HOH604 3.7 60.6 0.4 O3G A:DGT503 3.8 46.9 0.5 P2 A:DPO504 3.8 55.5 0.3 O3B A:DGT503 4.0 49.1 0.5 PB A:DGT503 4.0 54.7 0.5 O4 A:DPO504 4.0 49.4 0.3 NE A:ARG61 4.0 54.0 0.3 O3 A:DPO504 4.0 46.4 0.3 P P:DG10 4.1 62.6 0.3 O5' A:DGT503 4.4 54.1 0.5 O7 A:DPO504 4.4 48.6 0.3 O1B A:DGT503 4.4 49.0 0.5 PG A:DGT503 4.4 52.5 0.5 O2' P:U9 4.4 60.9 0.3 OP1 P:DG10 4.4 50.0 0.3 O5' P:DG10 4.5 54.2 0.3 O1A A:DGT503 4.5 49.3 0.5 P1 A:DPO504 4.5 51.6 0.3 NH2 A:ARG55 4.6 49.1 1.0 CD A:ARG61 4.6 61.2 0.7 O1 A:DPO504 4.6 52.5 0.3 CD A:ARG61 4.7 61.7 0.3 O A:HOH602 4.7 76.9 1.0 O2G A:DGT503 4.7 53.1 0.5 O3' P:U9 4.9 58.9 0.3 O5 A:DPO504 5.0 43.3 0.3 C3' P:U9 5.0 61.7 0.3

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