Manganese in PDB 5kfj: Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 180S

All present enzymatic activity of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 180S:
2.7.7.7;

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 180S, PDB code: 5kfj 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)	19.99 / 1.70
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.120, 98.120, 82.250, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 21

The structure of Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 180S 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 180S (pdb code 5kfj). 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 180S, PDB code: 5kfj:
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 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:12.5 occ:1.00 OD2 A:ASP13 2.1 13.7 1.0 OD1 A:ASP115 2.1 10.5 1.0 OP1 P:DA9 2.1 13.0 0.4 OE2 A:GLU116 2.2 13.8 1.0 O A:HOH747 2.2 13.5 1.0 O1A A:DTP507 2.3 13.3 0.6 O3' P:DT8 2.4 11.1 0.4 O3' P:DT8 2.4 11.9 0.6 P P:DA9 2.8 13.9 0.4 CG A:ASP115 3.1 13.6 1.0 CG A:ASP13 3.1 13.2 1.0 CD A:GLU116 3.2 17.0 1.0 C3' P:DT8 3.3 16.2 0.6 OD2 A:ASP115 3.3 11.0 1.0 MN A:MN503 3.5 12.7 0.9 OD1 A:ASP13 3.5 11.3 1.0 CA A:CA502 3.5 12.6 0.1 PA A:DTP507 3.6 11.3 0.6 C3' P:DT8 3.7 16.9 0.4 OG A:SER113 3.8 14.1 1.0 OP2 P:DA9 3.8 15.1 0.4 OE1 A:GLU116 3.8 17.7 1.0 O5' P:DA9 4.0 13.5 0.4 O2A A:DTP507 4.0 14.5 0.6 C4' P:DT8 4.0 18.2 0.4 C4' P:DT8 4.1 18.3 0.6 CB A:GLU116 4.1 10.8 1.0 O5' A:DTP507 4.1 12.5 0.6 CG A:GLU116 4.1 10.8 1.0 C5' A:DTP507 4.2 11.7 0.6 NZ A:LYS224 4.2 9.5 0.7 C5' P:DA9 4.2 11.6 0.4 O A:HOH717 4.3 17.2 0.6 O A:HOH717 4.4 16.8 0.5 O P:HOH203 4.4 13.1 0.6 CB A:ASP13 4.4 8.9 1.0 CB A:ASP115 4.5 9.8 1.0 C5' P:DT8 4.5 21.5 0.4 C2' P:DT8 4.6 14.0 0.6 C A:ASP115 4.6 11.1 1.0 O A:ASP115 4.6 12.1 1.0 C2' P:DT8 4.6 18.2 0.4 C5' P:DT8 4.6 21.4 0.6 O5 A:DPO508 4.7 11.5 0.4 N A:GLU116 4.8 8.8 1.0 CB A:SER113 4.8 13.8 1.0 O3A A:DTP507 4.8 11.0 0.6 O A:HOH657 4.9 27.4 1.0 O1G A:DTP507 4.9 11.7 0.6 O1 A:DPO508 5.0 10.8 0.4 CA A:ASP115 5.0 11.2 1.0

Manganese binding site 2 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:12.7 occ:0.90 CA A:CA502 0.0 12.6 0.1 O5 A:DPO508 2.1 11.5 0.4 OD1 A:ASP13 2.2 11.3 1.0 O1 A:DPO508 2.2 10.8 0.4 O1B A:DTP507 2.2 10.6 0.6 O1A A:DTP507 2.2 13.3 0.6 OD2 A:ASP115 2.3 11.0 1.0 O1G A:DTP507 2.3 11.7 0.6 OP1 P:DA9 2.4 13.0 0.4 O A:MET14 2.4 10.8 1.0 CG A:ASP13 3.1 13.2 1.0 PB A:DTP507 3.2 11.8 0.6 P1 A:DPO508 3.3 11.8 0.4 CG A:ASP115 3.3 13.6 1.0 PA A:DTP507 3.3 11.3 0.6 P2 A:DPO508 3.3 13.4 0.4 OD2 A:ASP13 3.4 13.7 1.0 O3A A:DTP507 3.4 11.0 0.6 PG A:DTP507 3.4 13.0 0.6 C A:MET14 3.5 11.8 1.0 MN A:MN501 3.5 12.5 1.0 O2 A:DPO508 3.6 10.6 0.4 O3B A:DTP507 3.7 10.2 0.6 O4 A:DPO508 3.7 10.2 0.4 OD1 A:ASP115 3.7 10.5 1.0 P P:DA9 3.8 13.9 0.4 O A:HOH717 3.9 17.2 0.6 NZ A:LYS231 3.9 13.2 0.7 O7 A:DPO508 3.9 12.9 0.4 C5' A:DTP507 4.0 11.7 0.6 N A:MET14 4.0 9.8 1.0 O2G A:DTP507 4.1 12.6 0.6 O A:HOH717 4.1 16.8 0.5 O5' A:DTP507 4.2 12.5 0.6 C5' P:DA9 4.2 11.6 0.4 CA A:MET14 4.3 12.0 1.0 O5' P:DA9 4.3 13.5 0.4 C A:ASP13 4.3 9.2 1.0 O A:HOH747 4.4 13.5 1.0 CB A:ASP13 4.4 8.9 1.0 N A:CYS16 4.5 9.7 1.0 N A:ASP15 4.5 9.7 1.0 O2B A:DTP507 4.5 11.6 0.6 O6 A:DPO508 4.5 12.1 0.4 O2A A:DTP507 4.6 14.5 0.6 O3 A:DPO508 4.6 11.7 0.4 CB A:ASP115 4.6 9.8 1.0 CA A:ASP15 4.6 9.8 1.0 OP2 P:DA9 4.6 15.1 0.4 CE A:LYS231 4.6 17.2 0.7 O3G A:DTP507 4.7 12.7 0.6 CB A:MET14 4.7 15.0 1.0 O A:ASP13 4.7 11.0 1.0 C A:ASP15 4.8 10.5 1.0 N A:PHE17 4.8 8.8 1.0 O3' P:DT8 4.8 11.1 0.4 CA A:ASP13 4.8 11.8 1.0 MN P:MN101 4.9 19.1 0.4 CB A:PHE17 4.9 9.0 1.0

Manganese binding site 3 out of 3 in the Human Dna Polymerase Eta-Dna Ternary Complex: Reaction with 10 Mm MN2+ For 180S


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 180S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mn101 b:19.1 occ:0.40 O2A A:DTP507 1.8 14.5 0.6 OP2 P:DA9 2.0 15.1 0.4 O A:HOH893 2.1 16.9 0.5 O3A A:DTP507 2.2 11.0 0.6 O A:HOH725 2.2 31.1 1.0 O A:HOH717 2.2 16.8 0.5 O2 A:DPO508 2.2 10.6 0.4 PA A:DTP507 2.4 11.3 0.6 O A:HOH626 2.7 18.4 1.0 NH1 A:ARG61 2.7 22.1 0.6 P P:DA9 3.2 13.9 0.4 O A:HOH717 3.4 17.2 0.6 O1A A:DTP507 3.5 13.3 0.6 OP1 P:DA9 3.6 13.0 0.4 PB A:DTP507 3.6 11.8 0.6 O5' A:DTP507 3.6 12.5 0.6 P1 A:DPO508 3.6 11.8 0.4 CZ A:ARG61 3.7 18.2 0.6 NH2 A:ARG61 3.7 14.4 0.6 O6 A:DPO508 3.8 12.1 0.4 O5' P:DA9 3.9 13.5 0.4 O A:HOH624 3.9 35.9 0.7 O A:HOH781 3.9 14.3 0.4 O5 A:DPO508 3.9 11.5 0.4 O3B A:DTP507 4.0 10.2 0.6 O4 A:DPO508 4.0 10.2 0.4 O3G A:DTP507 4.1 12.7 0.6 O1G A:DTP507 4.1 11.7 0.6 P2 A:DPO508 4.1 13.4 0.4 O A:HOH919 4.2 21.1 1.0 PG A:DTP507 4.3 13.0 0.6 O A:HOH792 4.3 22.6 0.6 O2B A:DTP507 4.4 11.6 0.6 O A:HOH878 4.4 29.9 0.5 O P:HOH219 4.4 21.4 1.0 O A:HOH747 4.4 13.5 1.0 O3' P:DT8 4.5 11.1 0.4 O3 A:DPO508 4.5 11.7 0.4 O1 A:DPO508 4.5 10.8 0.4 C3' P:DT8 4.6 16.9 0.4 C2' P:DT8 4.7 14.0 0.6 O1B A:DTP507 4.7 10.6 0.6 C3' P:DT8 4.9 16.2 0.6 C5' A:DTP507 4.9 11.7 0.6 NE A:ARG61 4.9 19.9 0.6 CA A:CA502 4.9 12.6 0.1 C8 A:DTP507 4.9 13.6 0.6 MN A:MN503 4.9 12.7 0.9

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