Manganese in PDB 5kfb: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 90S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 90S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 90S, PDB code: 5kfb 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)	19.72 / 1.55
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.380, 98.380, 82.200, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.6

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 90S 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 1 Mm MN2+ For 90S (pdb code 5kfb). 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 1 Mm MN2+ For 90S, PDB code: 5kfb:
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 1 Mm MN2+ For 90S


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 1 Mm MN2+ For 90S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:11.4 occ:0.80 OD2 A:ASP13 2.1 11.7 0.7 OE2 A:GLU116 2.2 16.0 1.0 O A:HOH709 2.2 16.0 1.0 OD1 A:ASP115 2.2 11.4 1.0 O1A A:DTP506 2.3 9.6 1.0 O3' P:DT8 2.4 13.7 1.0 OD2 A:ASP13 2.7 12.5 0.3 OD1 A:ASP13 2.9 10.2 0.3 CG A:ASP13 3.1 12.0 0.3 CG A:ASP115 3.2 9.1 1.0 CG A:ASP13 3.2 11.1 0.7 CD A:GLU116 3.2 17.4 1.0 C3' P:DT8 3.3 13.7 1.0 OD2 A:ASP115 3.4 9.5 1.0 CA A:CA502 3.5 10.2 0.5 PA A:DTP506 3.5 10.6 1.0 MN A:MN503 3.5 10.2 0.6 OD1 A:ASP13 3.7 12.4 0.7 OG A:SER113 3.8 14.7 1.0 OE1 A:GLU116 3.9 18.8 1.0 O5' A:DTP506 4.0 10.9 1.0 O2A A:DTP506 4.0 12.5 1.0 CB A:GLU116 4.1 14.1 1.0 C4' P:DT8 4.1 15.5 1.0 CG A:GLU116 4.1 11.4 1.0 C5' A:DTP506 4.2 11.3 1.0 O A:HOH667 4.2 19.4 1.0 NZ A:LYS224 4.3 12.2 0.7 O P:HOH102 4.4 11.3 0.7 CB A:ASP13 4.4 9.9 0.7 C5' P:DT8 4.6 19.2 0.4 CB A:ASP13 4.6 9.9 0.3 C2' P:DT8 4.6 15.3 1.0 CB A:ASP115 4.6 8.8 1.0 C A:ASP115 4.6 11.2 1.0 O A:ASP115 4.6 11.5 1.0 C5' P:DT8 4.7 20.9 0.6 O1G A:DTP506 4.8 10.9 1.0 CB A:SER113 4.8 11.7 1.0 N A:GLU116 4.8 8.5 1.0 O3A A:DTP506 4.9 9.9 1.0

Manganese binding site 2 out of 2 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 1 Mm MN2+ For 90S


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 1 Mm MN2+ For 90S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:10.2 occ:0.55 CA A:CA502 0.1 10.2 0.5 OD1 A:ASP13 2.2 10.2 0.3 OD1 A:ASP13 2.2 12.4 0.7 OD2 A:ASP115 2.2 9.5 1.0 O A:MET14 2.2 10.2 1.0 O1G A:DTP506 2.3 10.9 1.0 O1B A:DTP506 2.3 9.9 1.0 O1A A:DTP506 2.5 9.6 1.0 CG A:ASP13 3.0 11.1 0.7 OD2 A:ASP13 3.2 11.7 0.7 CG A:ASP115 3.3 9.1 1.0 PB A:DTP506 3.3 9.8 1.0 C A:MET14 3.4 8.0 1.0 CG A:ASP13 3.4 12.0 0.3 PG A:DTP506 3.5 10.0 1.0 MN A:MN501 3.5 11.4 0.8 PA A:DTP506 3.5 10.6 1.0 O3A A:DTP506 3.7 9.9 1.0 OD1 A:ASP115 3.7 11.4 1.0 NZ A:LYS231 3.8 9.1 0.6 O3B A:DTP506 3.8 8.4 1.0 N A:MET14 3.8 7.6 1.0 O A:HOH667 3.9 19.4 1.0 O2G A:DTP506 4.0 10.6 1.0 CA A:MET14 4.1 8.1 1.0 OD2 A:ASP13 4.1 12.5 0.3 C5' A:DTP506 4.1 11.3 1.0 C A:ASP13 4.2 8.5 1.0 CB A:ASP13 4.3 9.9 0.7 O5' A:DTP506 4.3 10.9 1.0 O A:HOH709 4.4 16.0 1.0 N A:ASP15 4.4 6.5 1.0 CB A:ASP13 4.4 9.9 0.3 N A:CYS16 4.5 7.8 1.0 CB A:ASP115 4.5 8.8 1.0 CA A:ASP15 4.6 8.0 1.0 O A:ASP13 4.6 10.0 1.0 CB A:MET14 4.6 12.0 1.0 CE A:LYS231 4.6 14.3 0.6 O2B A:DTP506 4.7 9.7 1.0 CA A:ASP13 4.7 11.0 0.3 CA A:ASP13 4.7 11.1 0.7 C A:ASP15 4.8 8.7 1.0 O3G A:DTP506 4.8 11.3 1.0 N A:PHE17 4.8 7.7 1.0 O2A A:DTP506 4.8 12.5 1.0 O A:ASP115 4.9 11.5 1.0 CB A:PHE17 4.9 7.0 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