Magnesium in PDB 5kfw: Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S

All present enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S:
2.7.7.7;

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S, PDB code: 5kfw 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)	19.92 / 1.62
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.290, 98.290, 81.960, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S also contains other interesting chemical elements:

Potassium	(K)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S (pdb code 5kfw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S, PDB code: 5kfw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:12.7 occ:0.75 K A:K509 0.0 15.7 0.1 OP1 P:DA9 2.1 15.1 0.1 OD2 A:ASP13 2.1 21.5 0.8 OE2 A:GLU116 2.2 23.0 1.0 O P:HOH212 2.3 21.7 1.0 OD1 A:ASP115 2.3 15.1 1.0 O1A A:DTP507 2.3 14.9 0.8 O3' P:DT8 2.4 16.1 0.1 O3' P:DT8 2.4 15.2 0.4 O3' P:DT8 2.4 15.2 0.5 OD2 A:ASP13 2.5 14.0 0.1 P P:DA9 2.7 17.1 0.1 OD1 A:ASP13 3.2 12.0 0.1 CG A:ASP13 3.2 15.7 0.1 C3' P:DT8 3.2 19.8 0.5 CD A:GLU116 3.2 21.8 1.0 CG A:ASP13 3.3 16.0 0.8 CG A:ASP115 3.3 14.3 1.0 C3' P:DT8 3.3 19.8 0.4 PA A:DTP507 3.5 12.8 0.8 CA A:CA502 3.5 11.3 0.3 MG A:MG503 3.6 11.3 0.7 OD2 A:ASP115 3.6 13.7 1.0 C3' P:DT8 3.6 18.9 0.1 OP2 P:DA9 3.7 17.3 0.1 OG A:SER113 3.7 17.3 1.0 OD1 A:ASP13 3.8 19.5 0.8 O5' P:DA9 3.9 14.2 0.1 OE1 A:GLU116 3.9 24.2 1.0 O2A A:DTP507 4.0 16.1 0.8 C4' P:DT8 4.0 19.9 0.1 O5' A:DTP507 4.0 12.6 0.8 C4' P:DT8 4.1 20.5 0.5 CB A:GLU116 4.1 18.1 1.0 CG A:GLU116 4.1 13.8 1.0 C4' P:DT8 4.1 20.7 0.4 C5' P:DT8 4.2 22.3 0.1 O A:HOH605 4.2 21.4 1.0 C5' A:DTP507 4.2 13.8 0.8 C5' P:DA9 4.2 13.8 0.1 NZ A:LYS224 4.3 16.6 0.7 O P:HOH201 4.4 20.8 0.8 CB A:ASP13 4.5 12.7 0.8 C2' P:DT8 4.5 19.0 0.5 CB A:ASP13 4.6 13.0 0.1 C2' P:DT8 4.6 19.1 0.4 C5' P:DT8 4.6 22.3 0.5 C A:ASP115 4.6 14.4 1.0 O A:ASP115 4.7 12.2 1.0 CB A:ASP115 4.7 11.7 1.0 C2' P:DT8 4.7 17.4 0.1 O5 A:DPO508 4.8 14.1 0.1 CB A:SER113 4.8 15.1 1.0 O1G A:DTP507 4.8 14.1 0.8 C5' P:DT8 4.8 24.6 0.4 O3A A:DTP507 4.9 13.3 0.8 N A:GLU116 4.9 11.9 1.0 O5' P:DT8 5.0 20.0 0.4 O2 A:DPO508 5.0 13.4 0.1

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:11.3 occ:0.70 CA A:CA502 0.0 11.3 0.3 OD1 A:ASP13 2.1 12.0 0.1 O5 A:DPO508 2.2 14.1 0.1 O1G A:DTP507 2.2 14.1 0.8 O1B A:DTP507 2.2 11.5 0.8 OD1 A:ASP13 2.2 19.5 0.8 O1 A:DPO508 2.2 11.6 0.1 OD2 A:ASP115 2.2 13.7 1.0 O A:MET14 2.3 12.5 1.0 O1A A:DTP507 2.3 14.9 0.8 OP1 P:DA9 2.6 15.1 0.1 CG A:ASP13 2.9 16.0 0.8 OD2 A:ASP13 3.0 21.5 0.8 PB A:DTP507 3.2 12.4 0.8 CG A:ASP115 3.3 14.3 1.0 CG A:ASP13 3.3 15.7 0.1 P1 A:DPO508 3.3 12.6 0.1 PA A:DTP507 3.4 12.8 0.8 PG A:DTP507 3.4 14.1 0.8 C A:MET14 3.4 12.0 1.0 P2 A:DPO508 3.4 14.1 0.1 O3A A:DTP507 3.5 13.3 0.8 MG A:MG501 3.6 12.7 0.8 K A:K509 3.6 15.7 0.1 O2 A:DPO508 3.6 13.4 0.1 OD1 A:ASP115 3.7 15.1 1.0 O3B A:DTP507 3.7 11.4 0.8 NZ A:LYS231 3.7 14.1 0.8 O4 A:DPO508 3.8 11.6 0.1 P P:DA9 3.9 17.1 0.1 O A:HOH605 3.9 21.4 1.0 N A:MET14 3.9 11.4 1.0 OD2 A:ASP13 3.9 14.0 0.1 C5' A:DTP507 4.1 13.8 0.8 O7 A:DPO508 4.1 13.1 0.1 C5' P:DA9 4.1 13.8 0.1 O2G A:DTP507 4.1 12.9 0.8 NZ A:LYS231 4.1 18.8 0.2 CA A:MET14 4.2 13.2 1.0 O5' A:DTP507 4.2 12.6 0.8 C A:ASP13 4.2 9.9 1.0 O P:HOH212 4.3 21.7 1.0 CB A:ASP13 4.3 12.7 0.8 CB A:ASP13 4.4 13.0 0.1 O5' P:DA9 4.4 14.2 0.1 N A:ASP15 4.4 10.9 1.0 N A:CYS16 4.5 9.7 1.0 CB A:ASP115 4.6 11.7 1.0 CA A:ASP15 4.6 9.6 1.0 O2B A:DTP507 4.6 11.5 0.8 O6 A:DPO508 4.6 14.3 0.1 O2A A:DTP507 4.6 16.1 0.8 O3 A:DPO508 4.6 11.6 0.1 O3G A:DTP507 4.6 14.2 0.8 O A:ASP13 4.6 11.7 1.0 CB A:MET14 4.7 14.4 1.0 OP2 P:DA9 4.7 17.3 0.1 C A:ASP15 4.7 11.8 1.0 CE A:LYS231 4.7 23.9 0.8 CA A:ASP13 4.8 12.7 0.1 CA A:ASP13 4.8 12.7 0.8 N A:PHE17 4.8 10.9 1.0 O A:ASP115 4.9 12.2 1.0 O3' P:DT8 4.9 16.1 0.1 CB A:PHE17 4.9 10.2 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 200S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:19.2 occ:0.15 O2A A:DTP507 1.8 16.1 0.8 O A:HOH645 1.8 39.9 1.0 O P:HOH225 1.9 23.6 0.6 OP2 P:DA9 2.2 17.3 0.1 O3A A:DTP507 2.4 13.3 0.8 O2 A:DPO508 2.4 13.4 0.1 PA A:DTP507 2.6 12.8 0.8 O A:HOH668 2.7 17.0 1.0 P P:DA9 3.5 17.1 0.1 O A:HOH951 3.6 19.1 1.0 O A:HOH810 3.6 21.9 0.5 O1A A:DTP507 3.7 14.9 0.8 O5' A:DTP507 3.7 12.6 0.8 P1 A:DPO508 3.8 12.6 0.1 OP1 P:DA9 3.8 15.1 0.1 PB A:DTP507 3.8 12.4 0.8 O5' P:DA9 3.9 14.2 0.1 O A:HOH1001 4.0 32.4 0.5 O6 A:DPO508 4.0 14.3 0.1 O3B A:DTP507 4.1 11.4 0.8 O3G A:DTP507 4.1 14.2 0.8 O4 A:DPO508 4.2 11.6 0.1 O5 A:DPO508 4.3 14.1 0.1 O A:HOH605 4.3 21.4 1.0 O P:HOH224 4.4 31.3 1.0 P2 A:DPO508 4.4 14.1 0.1 O1G A:DTP507 4.4 14.1 0.8 PG A:DTP507 4.5 14.1 0.8 O3 A:DPO508 4.5 11.6 0.1 O2B A:DTP507 4.5 11.5 0.8 O P:HOH212 4.5 21.7 1.0 C2' P:DT8 4.7 19.0 0.5 C2' P:DT8 4.7 19.1 0.4 O3' P:DT8 4.7 16.1 0.1 C8 A:DTP507 4.8 16.1 0.8 O1 A:DPO508 4.8 11.6 0.1 O1B A:DTP507 4.9 11.5 0.8 C8 P:DA9 4.9 16.2 0.1 C3' P:DT8 4.9 19.8 0.4 O P:HOH215 5.0 31.0 1.0 C5' P:DA9 5.0 13.8 0.1

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