Manganese in PDB 7u7k: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S, PDB code: 7u7k 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)	41.95 / 1.67
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.782, 97.782, 81.673, 90, 90, 120
R / Rfree (%)	17.7 / 22.1

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S (pdb code 7u7k). 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 Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S, PDB code: 7u7k:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S


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 Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:24.0 occ:0.65 O P:HOH205 1.4 23.8 0.5 OD1 A:ASP13 2.0 32.5 0.3 OE1 A:GLU116 2.1 31.2 0.7 OP1 P:DG9 2.1 26.7 0.3 O P:HOH219 2.1 26.7 0.3 OD2 A:ASP13 2.1 30.1 0.7 OD1 A:ASP115 2.2 25.8 1.0 O1A A:DGT506 2.2 26.2 0.3 OE1 A:GLU116 2.3 30.1 0.3 O3' P:DT8 2.3 26.9 0.1 O P:HOH210 2.3 28.7 0.7 O3' P:DT8 2.7 27.9 0.3 P P:DG9 2.9 24.5 0.3 CG A:ASP115 3.0 30.0 1.0 CG A:ASP13 3.1 25.7 0.7 CD A:GLU116 3.1 32.2 0.7 OD2 A:ASP115 3.1 33.9 1.0 CG A:ASP13 3.2 25.5 0.3 CD A:GLU116 3.2 32.1 0.3 C3' P:DT8 3.4 30.8 0.1 OD1 A:ASP13 3.4 27.2 0.7 MN A:MN502 3.6 24.7 0.9 PA A:DGT506 3.6 22.9 0.3 O P:HOH219 3.7 26.6 0.2 C3' P:DT8 3.7 30.5 0.3 OG A:SER113 3.8 35.5 1.0 OD2 A:ASP13 3.8 26.4 0.3 OP1 P:DG9 3.8 26.4 0.2 CB A:GLU116 3.9 26.8 0.7 CB A:GLU116 3.9 26.8 0.3 O P:HOH203 3.9 44.4 1.0 OE2 A:GLU116 3.9 35.5 0.3 CG A:GLU116 3.9 27.9 0.7 C4' P:DT8 4.0 33.9 0.3 OE2 A:GLU116 4.0 35.9 0.7 C4' P:DT8 4.0 33.7 0.1 O5' P:DG9 4.0 23.8 0.3 CG A:GLU116 4.1 27.7 0.3 O5' A:DGT506 4.1 23.5 0.3 OP2 P:DG9 4.2 32.4 0.3 O2A A:DGT506 4.2 32.2 0.3 C5' P:DT8 4.2 35.5 0.3 NZ A:LYS224 4.3 33.0 0.8 C5' P:DG9 4.3 21.1 0.3 C5' A:DGT506 4.3 19.6 0.3 CB A:ASP13 4.3 23.0 0.3 C5' P:DG9 4.4 24.0 0.2 O3' P:DT8 4.4 27.6 0.2 CB A:ASP115 4.4 22.2 1.0 CB A:ASP13 4.4 22.9 0.7 C5' P:DT8 4.4 35.2 0.1 C A:ASP115 4.5 23.1 1.0 N A:GLU116 4.6 20.2 1.0 O A:ASP115 4.6 23.2 1.0 O2G A:DGT506 4.6 22.9 0.3 P P:DG9 4.6 30.7 0.2 C2' P:DT8 4.7 30.3 0.1 O5 A:DPO505 4.7 23.0 0.5 O3A A:DGT506 4.8 29.7 0.3 C5' P:DT8 4.8 35.2 0.2 C4' P:DT8 4.8 33.8 0.2 O1 A:DPO505 4.8 21.5 0.5 C2' P:DT8 4.8 30.3 0.3 CA A:GLU116 4.8 23.1 0.7 CA A:GLU116 4.8 23.1 0.3 CB A:SER113 4.9 27.4 1.0 CA A:ASP115 4.9 23.3 1.0 C3' P:DT8 4.9 32.7 0.2 O2B A:DGT506 4.9 20.2 0.3 O5' P:DT8 5.0 35.2 0.3

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S


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 Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:24.7 occ:0.90 O2G A:DGT506 2.0 22.9 0.3 OD2 A:ASP115 2.0 33.9 1.0 OD1 A:ASP13 2.0 27.2 0.7 O2B A:DGT506 2.1 20.2 0.3 O1 A:DPO505 2.1 21.5 0.5 O5 A:DPO505 2.2 23.0 0.5 O A:MET14 2.2 21.3 1.0 OD2 A:ASP13 2.3 26.4 0.3 O1A A:DGT506 2.4 26.2 0.3 OP1 P:DG9 2.6 26.7 0.3 O P:HOH205 2.6 23.8 0.5 CG A:ASP13 2.9 25.5 0.3 OD1 A:ASP13 3.0 32.5 0.3 CG A:ASP13 3.0 25.7 0.7 PB A:DGT506 3.1 24.5 0.3 CG A:ASP115 3.1 30.0 1.0 P1 A:DPO505 3.3 25.2 0.5 PG A:DGT506 3.3 28.8 0.3 P2 A:DPO505 3.3 28.6 0.5 O3A A:DGT506 3.4 29.7 0.3 C A:MET14 3.4 20.2 1.0 OD2 A:ASP13 3.5 30.1 0.7 PA A:DGT506 3.5 22.9 0.3 O3B A:DGT506 3.5 23.6 0.3 MN A:MN501 3.6 24.0 0.7 O4 A:DPO505 3.6 23.4 0.5 OD1 A:ASP115 3.7 25.8 1.0 O P:HOH203 3.8 44.4 1.0 O2 A:DPO505 3.8 32.1 0.5 P P:DG9 3.9 24.5 0.3 OP1 P:DG9 3.9 26.4 0.2 O1G A:DGT506 3.9 25.0 0.3 N A:MET14 3.9 17.5 1.0 O7 A:DPO505 3.9 25.2 0.5 C5' P:DG9 4.0 24.0 0.2 O5' P:DG9 4.1 23.8 0.3 NZ A:LYS231 4.1 27.7 1.0 CA A:MET14 4.2 18.5 1.0 C5' A:DGT506 4.2 19.6 0.3 CB A:ASP13 4.2 22.9 0.7 C A:ASP13 4.2 17.0 1.0 CB A:ASP115 4.3 22.2 1.0 CB A:ASP13 4.3 23.0 0.3 O5' A:DGT506 4.3 23.5 0.3 N A:CYS16 4.4 20.3 1.0 N A:ASP15 4.4 16.0 1.0 O3G A:DGT506 4.4 31.9 0.3 O P:HOH210 4.5 28.7 0.7 O1B A:DGT506 4.5 22.2 0.3 O3 A:DPO505 4.5 22.1 0.5 CA A:ASP15 4.5 17.4 1.0 O6 A:DPO505 4.6 31.8 0.5 C5' P:DG9 4.6 21.1 0.3 C A:ASP15 4.6 19.0 1.0 O5' P:DG9 4.6 24.7 0.2 N A:PHE17 4.6 17.5 1.0 O A:ASP13 4.6 20.4 1.0 CA A:ASP13 4.7 19.7 0.7 CA A:ASP13 4.7 19.8 0.3 CB A:MET14 4.7 18.4 1.0 O2A A:DGT506 4.8 32.2 0.3 CB A:PHE17 4.8 16.3 1.0 OP2 P:DG9 4.8 32.4 0.3 O A:ASP115 4.8 23.2 1.0 O3' P:DT8 4.9 26.9 0.1 O3' P:DT8 4.9 27.9 0.3 P P:DG9 4.9 30.7 0.2 MN P:MN101 5.0 32.7 0.3

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S


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 Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:32.7 occ:0.30 OP1 P:DG9 1.6 26.4 0.2 O2 A:DPO505 2.0 32.1 0.5 OP2 P:DG9 2.1 29.3 0.2 O2A A:DGT506 2.1 32.2 0.3 P P:DG9 2.1 30.7 0.2 O3A A:DGT506 2.2 29.7 0.3 O P:HOH204 2.3 30.7 0.4 OP2 P:DG9 2.3 32.4 0.3 O P:HOH224 2.4 52.8 1.0 O A:HOH664 2.5 40.5 1.0 PA A:DGT506 2.6 22.9 0.3 O P:HOH203 2.9 44.4 1.0 O5' P:DG9 3.2 24.7 0.2 P P:DG9 3.3 24.5 0.3 P1 A:DPO505 3.4 25.2 0.5 O3' P:DT8 3.4 27.6 0.2 OP1 P:DG9 3.5 26.7 0.3 O1A A:DGT506 3.5 26.2 0.3 PB A:DGT506 3.6 24.5 0.3 O3' P:DT8 3.7 31.6 0.3 O3B A:DGT506 3.7 23.6 0.3 C3' P:DT8 3.8 32.7 0.2 O3G A:DGT506 3.8 31.9 0.3 O A:HOH901 3.8 40.2 1.0 O4 A:DPO505 3.8 23.4 0.5 O A:HOH742 3.9 22.7 0.6 O6 A:DPO505 3.9 31.8 0.5 O5' A:DGT506 3.9 23.5 0.3 O5' P:DG9 4.1 23.8 0.3 O P:HOH205 4.1 23.8 0.5 PG A:DGT506 4.1 28.8 0.3 O5 A:DPO505 4.1 23.0 0.5 O2G A:DGT506 4.2 22.9 0.3 P2 A:DPO505 4.2 28.6 0.5 C5' P:DG9 4.3 24.0 0.2 O1B A:DGT506 4.3 22.2 0.3 C3' P:DT8 4.3 34.3 0.3 O A:HOH953 4.3 51.3 1.0 O3 A:DPO505 4.4 22.1 0.5 O1 A:DPO505 4.4 21.5 0.5 C2' P:DT8 4.4 33.6 0.2 O P:HOH210 4.5 28.7 0.7 O3' P:DT8 4.6 27.9 0.3 O2B A:DGT506 4.6 20.2 0.3 C3' P:DT8 4.7 30.8 0.1 C3' P:DT8 4.8 30.5 0.3 O3' P:DT8 4.8 26.9 0.1 O A:HOH959 4.8 42.5 0.5 O A:HOH678 4.9 28.6 1.0 C2' P:DT8 4.9 30.3 0.1 MN A:MN502 5.0 24.7 0.9 O P:HOH225 5.0 58.4 1.0

C.Chang, C.Lee Luo, Y.Gao. In Crystallo Observation of Three Metal Ion Promoted Dna Polymerase Misincorporation. Nat Commun V. 13 2346 2022.
ISSN: ESSN 2041-1723
PubMed: 35487947
DOI: 10.1038/S41467-022-30005-3