Manganese in PDB 7u7z: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S, PDB code: 7u7z 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)	37.77 / 1.67
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.215, 98.215, 82.157, 90, 90, 120
R / Rfree (%)	18.6 / 21.9

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S (pdb code 7u7z). 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-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S, PDB code: 7u7z:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.12 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-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:30.4 occ:0.65 OD1 A:ASP115 2.2 29.2 0.9 OE1 A:GLU116 2.2 36.0 1.0 OD1 A:ASP13 2.3 34.1 1.0 O3' P:DT8 2.3 31.1 0.2 O A:HOH856 2.3 37.8 1.0 O1A A:XG4505 2.4 22.0 0.8 O A:HOH734 2.5 33.6 0.5 OD1 A:ASP115 2.8 26.1 0.1 CG A:ASP115 3.2 25.9 0.1 CG A:ASP115 3.2 25.6 0.9 CD A:GLU116 3.3 39.8 1.0 C3' P:DT8 3.3 30.4 0.2 CG A:ASP13 3.5 25.9 1.0 PA A:XG4505 3.5 23.6 0.8 OD2 A:ASP115 3.5 25.7 0.9 OD2 A:ASP115 3.6 22.5 0.1 MN A:MN502 3.6 26.4 0.8 OG A:SER113 3.8 32.5 1.0 O5' A:XG4505 3.9 24.4 0.8 CB A:ASP115 3.9 24.2 0.1 O2A A:XG4505 4.0 25.8 0.8 CB A:GLU116 4.0 30.3 1.0 OD2 A:ASP13 4.1 31.1 1.0 O P:HOH101 4.1 34.1 0.3 OE2 A:GLU116 4.1 38.1 1.0 CG A:GLU116 4.1 32.0 1.0 C5' A:XG4505 4.2 22.3 0.8 O A:HOH705 4.2 35.6 1.0 C4' P:DT8 4.3 34.1 0.2 C2' P:DT8 4.4 30.7 0.2 NZ A:LYS224 4.4 40.2 1.0 C A:ASP115 4.5 27.7 1.0 O P:HOH117 4.6 33.7 0.5 CB A:ASP13 4.6 22.1 1.0 CB A:ASP115 4.6 24.5 0.9 O A:ASP115 4.7 29.5 1.0 N A:GLU116 4.7 23.6 1.0 CA A:ASP115 4.7 24.6 0.1 O5' P:DT8 4.7 34.7 0.2 O2G A:XG4505 4.8 23.2 0.8 C5' P:DT8 4.8 35.1 0.2 CB A:SER113 4.9 30.3 1.0 N3A A:XG4505 4.9 25.7 0.8 CA A:ASP115 5.0 24.4 0.9 CA A:GLU116 5.0 24.1 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 0.12 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-Dgmpnpp Ternary Mismatch Complex in 0.12 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:26.4 occ:0.85 O A:MET14 2.2 23.6 1.0 OD2 A:ASP115 2.2 25.7 0.9 OD2 A:ASP13 2.2 31.1 1.0 O2G A:XG4505 2.2 23.2 0.8 O1B A:XG4505 2.3 23.2 0.8 O1A A:XG4505 2.5 22.0 0.8 CG A:ASP13 2.8 25.9 1.0 OD1 A:ASP13 2.9 34.1 1.0 CG A:ASP115 3.2 25.6 0.9 PB A:XG4505 3.3 23.4 0.8 C A:MET14 3.3 20.1 1.0 PG A:XG4505 3.5 24.1 0.8 PA A:XG4505 3.6 23.6 0.8 MN A:MN501 3.6 30.4 0.7 OD1 A:ASP115 3.7 29.2 0.9 O3B A:XG4505 3.7 21.5 0.8 N3A A:XG4505 3.8 25.7 0.8 N A:MET14 3.8 19.0 1.0 O A:HOH705 4.0 35.6 1.0 O3G A:XG4505 4.0 24.1 0.8 OD2 A:ASP115 4.0 22.5 0.1 NZ A:LYS231 4.1 26.8 1.0 CA A:MET14 4.1 19.7 1.0 CB A:ASP115 4.1 24.2 0.1 CB A:ASP13 4.2 22.1 1.0 CG A:ASP115 4.2 25.9 0.1 C A:ASP13 4.2 19.3 1.0 C5' A:XG4505 4.3 22.3 0.8 N A:ASP15 4.3 19.7 1.0 O5' A:XG4505 4.4 24.4 0.8 N A:CYS16 4.5 23.6 1.0 CA A:ASP15 4.5 20.5 1.0 CB A:ASP115 4.5 24.5 0.9 O A:HOH856 4.6 37.8 1.0 C A:ASP15 4.6 25.1 1.0 O A:ASP13 4.6 21.6 1.0 CA A:ASP13 4.6 21.0 1.0 CB A:MET14 4.6 21.1 1.0 O2B A:XG4505 4.7 24.0 0.8 CE A:LYS231 4.7 40.7 1.0 N A:PHE17 4.7 20.2 1.0 O1G A:XG4505 4.7 26.1 0.8 O A:ASP115 4.8 29.5 1.0 O2A A:XG4505 4.9 25.8 0.8 OD1 A:ASP115 4.9 26.1 0.1 CB A:PHE17 5.0 18.1 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