Manganese in PDB 5kfk: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S, PDB code: 5kfk 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)	19.93 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.270, 98.270, 82.010, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 21

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S 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 300S (pdb code 5kfk). 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 Complex: Reaction with 10 Mm MN2+ For 300S, PDB code: 5kfk:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:12.6 occ:1.00 OP1 P:DA9 2.1 13.7 0.5 OD1 A:ASP115 2.1 10.0 1.0 OE2 A:GLU116 2.2 14.6 1.0 O P:HOH210 2.2 14.1 1.0 OD2 A:ASP13 2.2 13.6 1.0 O1A A:DTP507 2.3 13.7 0.5 O3' P:DT8 2.4 13.3 0.5 O3' P:DT8 2.5 14.2 0.5 P P:DA9 2.8 13.4 0.5 CG A:ASP115 3.1 12.7 1.0 CD A:GLU116 3.2 14.4 1.0 CG A:ASP13 3.2 13.2 1.0 C3' P:DT8 3.3 18.5 0.5 OD2 A:ASP115 3.4 9.6 1.0 PA A:DTP507 3.5 9.9 0.5 OD1 A:ASP13 3.6 12.2 1.0 MN A:MN503 3.6 12.0 0.9 CA A:CA502 3.6 12.0 0.1 C3' P:DT8 3.7 18.9 0.5 OG A:SER113 3.8 14.4 1.0 OP2 P:DA9 3.8 14.4 0.5 OE1 A:GLU116 3.8 19.4 1.0 O2A A:DTP507 4.0 13.8 0.5 O5' P:DA9 4.0 13.3 0.5 C4' P:DT8 4.0 18.2 0.5 C4' P:DT8 4.0 18.0 0.5 O5' A:DTP507 4.0 12.2 0.5 CB A:GLU116 4.1 13.0 1.0 CG A:GLU116 4.1 12.4 1.0 O A:HOH690 4.2 28.6 1.0 NZ A:LYS224 4.2 10.8 0.7 C5' A:DTP507 4.2 12.7 0.5 C5' P:DT8 4.2 22.1 0.5 C5' P:DA9 4.2 12.4 0.5 O P:HOH201 4.3 14.4 0.5 CB A:ASP13 4.5 11.1 1.0 C5' P:DT8 4.5 21.8 0.5 CB A:ASP115 4.5 9.7 1.0 O A:ASP115 4.6 10.1 1.0 C A:ASP115 4.6 10.8 1.0 C2' P:DT8 4.6 16.2 0.5 O5 A:DPO508 4.7 12.6 0.5 C2' P:DT8 4.8 16.5 0.5 N A:GLU116 4.8 8.7 1.0 O1G A:DTP507 4.8 13.0 0.5 CB A:SER113 4.8 13.9 1.0 O3A A:DTP507 4.8 13.2 0.5 O1 A:DPO508 4.9 10.6 0.5 CA A:ASP115 5.0 11.6 1.0

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:12.0 occ:0.95 CA A:CA502 0.0 12.0 0.1 O5 A:DPO508 2.0 12.6 0.5 O1 A:DPO508 2.0 10.6 0.5 O1B A:DTP507 2.1 10.5 0.5 OD2 A:ASP115 2.2 9.6 1.0 O1G A:DTP507 2.3 13.0 0.5 O1A A:DTP507 2.3 13.7 0.5 OD1 A:ASP13 2.3 12.2 1.0 O A:MET14 2.3 10.6 1.0 OP1 P:DA9 2.4 13.7 0.5 PB A:DTP507 3.1 11.8 0.5 CG A:ASP13 3.1 13.2 1.0 P1 A:DPO508 3.2 11.8 0.5 CG A:ASP115 3.2 12.7 1.0 PA A:DTP507 3.3 9.9 0.5 P2 A:DPO508 3.3 13.8 0.5 O3A A:DTP507 3.4 13.2 0.5 PG A:DTP507 3.4 13.7 0.5 OD2 A:ASP13 3.4 13.6 1.0 C A:MET14 3.5 12.9 1.0 O2 A:DPO508 3.6 13.2 0.5 MN A:MN501 3.6 12.6 1.0 O4 A:DPO508 3.6 11.1 0.5 O3B A:DTP507 3.6 11.1 0.5 OD1 A:ASP115 3.7 10.0 1.0 P P:DA9 3.8 13.4 0.5 O A:HOH690 3.9 28.6 1.0 C5' A:DTP507 3.9 12.7 0.5 NZ A:LYS231 3.9 16.1 1.0 O7 A:DPO508 3.9 11.2 0.5 O2G A:DTP507 4.0 11.1 0.5 N A:MET14 4.0 9.3 1.0 O5' A:DTP507 4.1 12.2 0.5 C5' P:DA9 4.1 12.4 0.5 CA A:MET14 4.2 10.8 1.0 O5' P:DA9 4.3 13.3 0.5 C A:ASP13 4.3 10.2 1.0 N A:CYS16 4.4 10.5 1.0 CB A:ASP13 4.4 11.1 1.0 O P:HOH210 4.4 14.1 1.0 N A:ASP15 4.5 8.6 1.0 O2B A:DTP507 4.5 11.9 0.5 O3 A:DPO508 4.5 11.8 0.5 O6 A:DPO508 4.5 14.0 0.5 CB A:ASP115 4.5 9.7 1.0 O2A A:DTP507 4.5 13.8 0.5 CA A:ASP15 4.5 9.3 1.0 O3G A:DTP507 4.6 14.2 0.5 OP2 P:DA9 4.7 14.4 0.5 O A:ASP13 4.7 11.6 1.0 C A:ASP15 4.7 13.0 1.0 CB A:MET14 4.7 12.7 1.0 N A:PHE17 4.7 8.9 1.0 CE A:LYS231 4.7 23.2 1.0 O3' P:DT8 4.8 13.3 0.5 CA A:ASP13 4.9 11.4 1.0 MN P:MN101 4.9 19.4 0.5 CB A:PHE17 4.9 9.2 1.0 O A:ASP115 5.0 10.1 1.0

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 300S


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 Complex: Reaction with 10 Mm MN2+ For 300S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:19.4 occ:0.50 O2A A:DTP507 1.6 13.8 0.5 OP2 P:DA9 2.0 14.4 0.5 O3A A:DTP507 2.2 13.2 0.5 O2 A:DPO508 2.2 13.2 0.5 O A:HOH878 2.2 18.9 0.5 O A:HOH790 2.2 30.6 1.0 PA A:DTP507 2.4 9.9 0.5 NH1 A:ARG61 2.5 20.9 0.5 O A:HOH636 2.8 18.2 1.0 O A:HOH690 2.9 28.6 1.0 P P:DA9 3.1 13.4 0.5 O1A A:DTP507 3.4 13.7 0.5 OP1 P:DA9 3.5 13.7 0.5 CZ A:ARG61 3.6 17.8 0.5 O5' A:DTP507 3.6 12.2 0.5 P1 A:DPO508 3.6 11.8 0.5 PB A:DTP507 3.7 11.8 0.5 O5' P:DA9 3.8 13.3 0.5 NH2 A:ARG61 3.8 16.4 0.5 O A:HOH835 3.8 16.3 0.5 O6 A:DPO508 3.8 14.0 0.5 O5 A:DPO508 4.0 12.6 0.5 O1G A:DTP507 4.0 13.0 0.5 O3B A:DTP507 4.1 11.1 0.5 O4 A:DPO508 4.1 11.1 0.5 O3G A:DTP507 4.1 14.2 0.5 O A:HOH897 4.2 21.3 1.0 P2 A:DPO508 4.2 13.8 0.5 O P:HOH210 4.3 14.1 1.0 O A:HOH866 4.3 32.2 0.5 PG A:DTP507 4.3 13.7 0.5 O P:HOH212 4.3 31.0 1.0 O2B A:DTP507 4.4 11.9 0.5 O P:HOH214 4.4 21.3 1.0 O3' P:DT8 4.4 13.3 0.5 O1 A:DPO508 4.5 10.6 0.5 O3 A:DPO508 4.5 11.8 0.5 O1B A:DTP507 4.7 10.5 0.5 C2' P:DT8 4.7 16.2 0.5 C3' P:DT8 4.8 18.5 0.5 NE A:ARG61 4.8 22.2 0.5 C5' A:DTP507 4.8 12.7 0.5 C8 A:DTP507 4.8 14.9 0.5 C3' P:DT8 4.9 18.9 0.5 CA A:CA502 4.9 12.0 0.1 MN A:MN503 4.9 12.0 0.9 C5' P:DA9 5.0 12.4 0.5 C8 P:DA9 5.0 14.9 0.5

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