Manganese in PDB 5kfg: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S, PDB code: 5kfg was solved by Y.Gao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.380, 98.380, 82.160, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.4

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Manganese atom in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S (pdb code 5kfg). 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 Ternary Complex: Reaction with 10 Mm MN2+ For 30S, PDB code: 5kfg:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S


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 Complex: Reaction with 10 Mm MN2+ For 30S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:12.3 occ:0.80 OD2 A:ASP13 2.1 14.8 0.8 OE2 A:GLU116 2.1 18.3 1.0 O A:HOH728 2.2 17.6 1.0 OD1 A:ASP115 2.2 11.9 1.0 O3' P:DT8 2.3 15.7 1.0 O1A A:DTP506 2.4 12.2 1.0 OD2 A:ASP13 2.7 13.3 0.2 OD1 A:ASP13 2.9 11.3 0.2 CG A:ASP13 3.1 13.9 0.2 CG A:ASP115 3.1 11.9 1.0 CD A:GLU116 3.2 20.9 1.0 C3' P:DT8 3.3 17.0 1.0 CG A:ASP13 3.3 11.6 0.8 OD2 A:ASP115 3.4 11.4 1.0 MN A:MN503 3.6 12.5 0.3 CA A:CA502 3.6 12.6 0.7 PA A:DTP506 3.6 12.7 1.0 OG A:SER113 3.8 15.4 1.0 OD1 A:ASP13 3.8 14.3 0.8 OE1 A:GLU116 3.9 20.0 1.0 C4' P:DT8 4.0 18.1 1.0 O5' A:DTP506 4.1 11.5 1.0 CB A:GLU116 4.1 14.4 1.0 CG A:GLU116 4.1 11.3 1.0 O2A A:DTP506 4.1 14.4 1.0 C5' A:DTP506 4.2 13.5 1.0 NZ A:LYS224 4.3 14.1 0.6 O A:HOH643 4.4 20.4 1.0 O P:HOH103 4.4 13.8 0.7 C5' P:DT8 4.4 20.1 0.3 CB A:ASP13 4.5 11.9 0.8 CB A:ASP115 4.6 10.6 1.0 C2' P:DT8 4.6 18.3 1.0 C A:ASP115 4.6 12.8 1.0 CB A:ASP13 4.6 11.9 0.2 C5' P:DT8 4.6 20.8 0.7 O A:ASP115 4.6 12.9 1.0 N A:GLU116 4.8 10.1 1.0 CB A:SER113 4.8 13.2 1.0 O1G A:DTP506 4.9 11.9 1.0 O3A A:DTP506 4.9 11.0 1.0 CA A:ASP115 5.0 11.1 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 30S


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 Complex: Reaction with 10 Mm MN2+ For 30S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:12.5 occ:0.30 CA A:CA502 0.0 12.6 0.7 OD1 A:ASP13 2.2 11.3 0.2 O A:MET14 2.2 11.1 1.0 OD2 A:ASP115 2.3 11.4 1.0 OD1 A:ASP13 2.3 14.3 0.8 O1G A:DTP506 2.3 11.9 1.0 O1B A:DTP506 2.4 10.6 1.0 O1A A:DTP506 2.4 12.2 1.0 CG A:ASP13 3.0 11.6 0.8 OD2 A:ASP13 3.1 14.8 0.8 CG A:ASP115 3.4 11.9 1.0 PB A:DTP506 3.4 10.4 1.0 C A:MET14 3.4 9.0 1.0 CG A:ASP13 3.4 13.9 0.2 PG A:DTP506 3.5 11.8 1.0 PA A:DTP506 3.6 12.7 1.0 MN A:MN501 3.6 12.3 0.8 O3A A:DTP506 3.7 11.0 1.0 OD1 A:ASP115 3.8 11.9 1.0 O3B A:DTP506 3.9 9.8 1.0 N A:MET14 3.9 8.3 1.0 O A:HOH643 3.9 20.4 1.0 O2G A:DTP506 4.1 12.6 1.0 C5' A:DTP506 4.2 13.5 1.0 CA A:MET14 4.2 9.8 1.0 OD2 A:ASP13 4.2 13.3 0.2 C A:ASP13 4.2 9.9 1.0 O A:HOH728 4.3 17.6 1.0 NZ A:LYS231 4.3 16.6 0.5 CB A:ASP13 4.3 11.9 0.8 O5' A:DTP506 4.4 11.5 1.0 CB A:ASP13 4.4 11.9 0.2 N A:ASP15 4.4 8.0 1.0 N A:CYS16 4.4 8.7 1.0 CA A:ASP15 4.6 9.4 1.0 CB A:ASP115 4.6 10.6 1.0 O A:ASP13 4.6 11.2 1.0 CB A:MET14 4.7 12.8 1.0 C A:ASP15 4.7 9.2 1.0 O2B A:DTP506 4.8 10.9 1.0 N A:PHE17 4.8 8.8 1.0 CA A:ASP13 4.8 12.4 0.2 O A:HOH606 4.8 20.2 0.5 CA A:ASP13 4.8 12.5 0.8 O2A A:DTP506 4.8 14.4 1.0 O3G A:DTP506 4.8 12.8 1.0 CB A:PHE17 4.9 8.3 1.0 O A:ASP115 5.0 12.9 1.0

Y.Gao, W.Yang. Capture of A Third MG2+ Is Essential For Catalyzing Dna Synthesis. Science V. 352 1334 2016.
ISSN: ESSN 1095-9203
PubMed: 27284197
DOI: 10.1126/SCIENCE.AAD9633