Manganese in PDB 7u7e: Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S, PDB code: 7u7e 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)	42.05 / 1.58
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.997, 97.997, 81.944, 90, 90, 120
R / Rfree (%)	18.3 / 21.7

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S (pdb code 7u7e). 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 60S, PDB code: 7u7e:
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 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 Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:23.1 occ:0.70 OE1 A:GLU116 1.9 32.8 1.0 O A:HOH624 2.1 29.5 0.5 OD1 A:ASP115 2.1 26.7 1.0 O A:HOH690 2.2 26.3 0.3 OD1 A:ASP13 2.2 39.4 1.0 O P:HOH207 2.2 27.5 0.6 O1A A:DGT504 2.3 26.9 0.8 O3' P:DT8 2.3 28.0 0.2 O3' P:DT8 2.4 28.0 0.2 CG A:ASP115 3.0 23.8 1.0 CD A:GLU116 3.1 37.1 1.0 OD2 A:ASP115 3.3 29.7 1.0 C3' P:DT8 3.4 29.7 0.2 PA A:DGT504 3.4 23.1 0.8 CG A:ASP13 3.4 26.3 1.0 C3' P:DT8 3.5 29.8 0.2 MN A:MN502 3.6 22.4 0.9 OG A:SER113 3.7 28.6 1.0 O2A A:DGT504 3.8 26.8 0.8 OE2 A:GLU116 3.9 37.6 1.0 CB A:GLU116 3.9 25.1 1.0 CG A:GLU116 3.9 25.4 1.0 O5' A:DGT504 4.0 22.9 0.8 C5' A:DGT504 4.2 22.4 0.8 OD2 A:ASP13 4.2 30.6 1.0 O A:HOH748 4.2 37.8 1.0 C4' P:DT8 4.2 30.5 0.2 C4' P:DT8 4.3 31.2 0.2 NZ A:LYS224 4.3 34.2 1.0 O P:HOH208 4.3 33.0 0.7 CB A:ASP115 4.4 21.8 1.0 CB A:ASP13 4.4 18.6 1.0 C A:ASP115 4.5 22.6 1.0 O A:ASP115 4.6 23.1 1.0 C2' P:DT8 4.6 28.8 0.2 N A:GLU116 4.7 19.2 1.0 C2' P:DT8 4.7 28.5 0.2 CB A:SER113 4.7 21.2 1.0 O3G A:DGT504 4.7 21.7 0.8 O5' P:DT8 4.7 30.8 0.2 O3A A:DGT504 4.7 23.5 0.8 C5' P:DT8 4.8 32.0 0.2 CA A:ASP115 4.9 18.6 1.0 CA A:GLU116 4.9 20.8 1.0 O2B A:DGT504 4.9 18.6 0.8

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 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 Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:22.4 occ:0.90 OD2 A:ASP115 2.0 29.7 1.0 O3G A:DGT504 2.1 21.7 0.8 O2B A:DGT504 2.2 18.6 0.8 O A:MET14 2.2 21.4 1.0 O1A A:DGT504 2.3 26.9 0.8 OD2 A:ASP13 2.3 30.6 1.0 O A:HOH624 2.5 29.5 0.5 OD1 A:ASP13 2.6 39.4 1.0 CG A:ASP13 2.8 26.3 1.0 CG A:ASP115 3.1 23.8 1.0 PB A:DGT504 3.2 20.4 0.8 PG A:DGT504 3.3 21.4 0.8 C A:MET14 3.4 18.9 1.0 PA A:DGT504 3.4 23.1 0.8 O3A A:DGT504 3.5 23.5 0.8 MN A:MN501 3.6 23.1 0.7 O3B A:DGT504 3.6 18.5 0.8 OD1 A:ASP115 3.7 26.7 1.0 N A:MET14 3.9 17.7 1.0 NZ A:LYS231 3.9 24.5 1.0 O A:HOH748 4.0 37.8 1.0 O2G A:DGT504 4.0 20.1 0.8 CA A:MET14 4.1 17.1 1.0 C5' A:DGT504 4.2 22.4 0.8 CB A:ASP13 4.2 18.6 1.0 C A:ASP13 4.2 17.9 1.0 O5' A:DGT504 4.3 22.9 0.8 O P:HOH207 4.3 27.5 0.6 CB A:ASP115 4.3 21.8 1.0 N A:ASP15 4.4 18.0 1.0 N A:CYS16 4.4 16.9 1.0 CA A:ASP15 4.5 14.3 1.0 C A:ASP15 4.6 21.5 1.0 O1B A:DGT504 4.6 19.4 0.8 O1G A:DGT504 4.6 23.0 0.8 O A:ASP13 4.6 19.8 1.0 O2A A:DGT504 4.7 26.8 0.8 N A:PHE17 4.7 17.1 1.0 CB A:MET14 4.7 21.2 1.0 CA A:ASP13 4.7 19.1 1.0 CE A:LYS231 4.8 36.4 1.0 O A:ASP115 4.8 23.1 1.0 CB A:PHE17 4.9 14.2 1.0

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Mismatch Complex:Reaction with 10.0 Mm MN2+ For 60S


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 60S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:29.1 occ:0.13 O A:HOH712 1.9 21.2 0.1 O A:HOH849 2.3 25.1 0.1 O3A A:DGT504 2.3 23.5 0.8 O2A A:DGT504 2.4 26.8 0.8 O A:HOH644 2.4 33.3 1.0 NH1 A:ARG61 2.6 21.4 0.2 PA A:DGT504 2.9 23.1 0.8 O3' P:DT8 3.1 30.1 0.6 O A:HOH898 3.4 27.8 1.0 CZ A:ARG61 3.4 23.3 0.2 NH2 A:ARG61 3.4 22.8 0.2 O1G A:DGT504 3.5 23.0 0.8 O A:HOH736 3.5 21.8 0.5 O3B A:DGT504 3.6 18.5 0.8 PB A:DGT504 3.6 20.4 0.8 C3' P:DT8 3.9 29.4 0.6 PG A:DGT504 4.0 21.4 0.8 O A:HOH624 4.0 29.5 0.5 O A:HOH748 4.0 37.8 1.0 O1A A:DGT504 4.0 26.9 0.8 O5' A:DGT504 4.0 22.9 0.8 O3G A:DGT504 4.1 21.7 0.8 O A:HOH914 4.2 41.6 0.6 O1B A:DGT504 4.3 19.4 0.8 O A:HOH959 4.3 46.0 1.0 O P:HOH207 4.6 27.5 0.6 NE A:ARG61 4.6 24.9 0.2 O A:HOH605 4.7 22.8 1.0 O2B A:DGT504 4.8 18.6 0.8 C2' P:DT8 4.8 28.8 0.2 C4' P:DT8 4.8 30.6 0.6 NH2 A:ARG55 4.9 26.9 1.0 C2' P:DT8 4.9 28.5 0.2

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