Manganese in PDB 7u84: Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 6.0 Mm MN2+ For 600S

All present enzymatic activity of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 6.0 Mm MN2+ For 600S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 6.0 Mm MN2+ For 600S, PDB code: 7u84 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 / 1.71
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	97.854, 97.854, 81.545, 90, 90, 120
R / Rfree (%)	18.5 / 23.6

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 6.0 Mm MN2+ For 600S (pdb code 7u84). 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 6.0 Mm MN2+ For 600S, PDB code: 7u84:
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 6.0 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-Dgmpnpp Ternary Mismatch Complex in 6.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:24.6 occ:1.00 OD1 A:ASP115 2.1 24.6 1.0 O A:HOH746 2.1 21.1 0.3 OD2 A:ASP13 2.1 24.5 1.0 OE1 A:GLU116 2.2 23.7 1.0 O1A A:XG4505 2.2 23.6 1.0 O A:HOH782 2.2 28.3 1.0 O3' P:DT8 2.3 21.8 0.4 CG A:ASP115 3.1 24.5 1.0 CD A:GLU116 3.2 27.4 1.0 CG A:ASP13 3.2 25.1 1.0 C3' P:DT8 3.3 24.9 0.4 PA A:XG4505 3.3 23.7 1.0 OD2 A:ASP115 3.5 23.5 1.0 MN A:MN502 3.6 23.2 1.0 OD1 A:ASP13 3.6 22.7 1.0 O2A A:XG4505 3.8 24.7 1.0 OG A:SER113 3.8 28.9 1.0 O5' A:XG4505 3.8 23.4 1.0 OE2 A:GLU116 3.9 29.8 1.0 O A:HOH720 4.0 27.0 1.0 C5' A:XG4505 4.1 22.0 1.0 CB A:GLU116 4.1 25.2 1.0 CG A:GLU116 4.1 25.0 1.0 NZ A:LYS224 4.2 28.3 1.0 C4' P:DT8 4.2 21.6 0.4 O P:HOH107 4.4 30.4 0.4 CB A:ASP13 4.5 22.7 1.0 C2' P:DT8 4.5 23.6 0.4 CB A:ASP115 4.5 24.8 1.0 O5' P:DT8 4.5 28.9 0.4 C5' P:DT8 4.6 31.4 0.4 C A:ASP115 4.6 24.3 1.0 O A:ASP115 4.6 23.9 1.0 O2G A:XG4505 4.7 22.5 1.0 CB A:SER113 4.7 26.9 1.0 N3A A:XG4505 4.8 28.0 1.0 N A:GLU116 4.8 21.7 1.0 CA A:ASP115 5.0 23.0 1.0 O1B A:XG4505 5.0 23.3 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna-Dgmpnpp Ternary Mismatch Complex in 6.0 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-Dgmpnpp Ternary Mismatch Complex in 6.0 Mm MN2+ For 600S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:23.2 occ:1.00 OD1 A:ASP13 2.0 22.7 1.0 OD2 A:ASP115 2.1 23.5 1.0 O2G A:XG4505 2.1 22.5 1.0 O A:MET14 2.2 22.4 1.0 O1B A:XG4505 2.2 23.3 1.0 O1A A:XG4505 2.3 23.6 1.0 CG A:ASP13 3.0 25.1 1.0 PB A:XG4505 3.1 24.2 1.0 CG A:ASP115 3.2 24.5 1.0 OD2 A:ASP13 3.3 24.5 1.0 PG A:XG4505 3.4 23.6 1.0 C A:MET14 3.4 22.6 1.0 PA A:XG4505 3.4 23.7 1.0 N3A A:XG4505 3.5 28.0 1.0 O3B A:XG4505 3.6 20.5 1.0 OD1 A:ASP115 3.6 24.6 1.0 MN A:MN501 3.6 24.6 1.0 O A:HOH720 3.8 27.0 1.0 N A:MET14 3.9 20.9 1.0 NZ A:LYS231 3.9 29.0 1.0 O3G A:XG4505 3.9 25.1 1.0 CA A:MET14 4.1 19.5 1.0 C5' A:XG4505 4.1 22.0 1.0 C A:ASP13 4.2 18.1 1.0 CB A:ASP13 4.3 22.7 1.0 O5' A:XG4505 4.3 23.4 1.0 N A:ASP15 4.4 23.2 1.0 O A:HOH782 4.4 28.3 1.0 CB A:ASP115 4.5 24.8 1.0 N A:CYS16 4.5 23.5 1.0 O2B A:XG4505 4.6 22.9 1.0 CA A:ASP15 4.6 22.4 1.0 CB A:MET14 4.6 21.1 1.0 O1G A:XG4505 4.6 24.3 1.0 C A:ASP15 4.6 20.8 1.0 O A:ASP13 4.7 20.9 1.0 O2A A:XG4505 4.7 24.7 1.0 N A:PHE17 4.7 20.7 1.0 CA A:ASP13 4.7 22.7 1.0 CB A:PHE17 4.8 19.8 1.0 CE A:LYS231 4.8 29.0 1.0 O A:ASP115 4.9 23.9 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