Magnesium in PDB 5kfx: Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S

All present enzymatic activity of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S:
2.7.7.7;

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S, PDB code: 5kfx 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)	19.98 / 1.52
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.480, 98.480, 82.200, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.2

The structure of Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S 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 300S (pdb code 5kfx). 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 300S, PDB code: 5kfx:
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 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:8.8 occ:0.65 K A:K509 0.0 11.6 0.1 OP1 P:DA9 2.1 12.5 0.3 OD2 A:ASP13 2.1 12.8 0.6 OE2 A:GLU116 2.2 18.3 1.0 OD1 A:ASP115 2.3 11.5 1.0 O3' P:DT8 2.3 13.2 0.3 O3' P:DT8 2.3 11.6 0.3 O A:HOH712 2.4 17.5 1.0 O3' P:DT8 2.4 11.6 0.3 O1A A:DTP507 2.4 12.5 0.7 OD2 A:ASP13 2.6 13.6 0.4 P P:DA9 2.7 15.3 0.3 OD1 A:ASP13 3.2 11.5 0.4 CD A:GLU116 3.2 17.5 1.0 CG A:ASP13 3.2 12.7 0.4 C3' P:DT8 3.3 14.4 0.3 CG A:ASP115 3.3 10.5 1.0 CG A:ASP13 3.3 12.2 0.6 C3' P:DT8 3.3 14.6 0.3 PA A:DTP507 3.5 7.8 0.7 C3' P:DT8 3.5 14.2 0.3 OD2 A:ASP115 3.6 10.4 1.0 MG A:MG503 3.6 7.7 0.8 CA A:CA502 3.6 7.9 0.2 OP2 P:DA9 3.7 13.3 0.3 OG A:SER113 3.7 13.8 1.0 C4' P:DT8 3.8 14.6 0.3 OD1 A:ASP13 3.8 13.4 0.6 OE1 A:GLU116 3.9 20.1 1.0 O2A A:DTP507 3.9 11.5 0.7 O5' A:DTP507 3.9 10.5 0.7 O5' P:DA9 3.9 10.9 0.3 C5' P:DT8 4.0 18.1 0.3 CG A:GLU116 4.1 12.1 1.0 CB A:GLU116 4.1 13.7 1.0 C4' P:DT8 4.1 15.4 0.3 C4' P:DT8 4.1 15.3 0.3 C5' A:DTP507 4.2 11.0 0.7 C5' P:DA9 4.2 9.2 0.3 NZ A:LYS224 4.3 12.1 0.7 O A:HOH611 4.3 21.3 1.0 O P:HOH201 4.3 13.8 0.7 CB A:ASP13 4.5 9.7 0.6 C2' P:DT8 4.5 13.2 0.3 CB A:ASP13 4.6 9.7 0.4 CB A:ASP115 4.6 9.1 1.0 C2' P:DT8 4.6 13.4 0.3 C A:ASP115 4.6 11.9 1.0 C2' P:DT8 4.7 13.2 0.3 O A:ASP115 4.7 10.6 1.0 C5' P:DT8 4.7 17.6 0.3 CB A:SER113 4.8 12.5 1.0 C5' P:DT8 4.8 19.8 0.3 O5 A:DPO508 4.8 10.8 0.3 N A:GLU116 4.8 9.4 1.0 O3A A:DTP507 4.9 9.8 0.7 O1G A:DTP507 4.9 11.0 0.7 O5' P:DT8 4.9 16.5 0.3 O2 A:DPO508 5.0 9.8 0.3

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Eta R61A-Dna Ternary Complex: Reaction with 1 Mm MG2+ For 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:7.7 occ:0.80 CA A:CA502 0.0 7.9 0.2 OD1 A:ASP13 2.1 11.5 0.4 O5 A:DPO508 2.1 10.8 0.3 O1 A:DPO508 2.1 8.8 0.3 OD1 A:ASP13 2.2 13.4 0.6 OD2 A:ASP115 2.2 10.4 1.0 O1A A:DTP507 2.2 12.5 0.7 O1G A:DTP507 2.2 11.0 0.7 O1B A:DTP507 2.3 9.5 0.7 O A:MET14 2.3 9.3 1.0 OP1 P:DA9 2.3 12.5 0.3 CG A:ASP13 2.9 12.2 0.6 OD2 A:ASP13 3.1 12.8 0.6 P1 A:DPO508 3.2 9.4 0.3 PB A:DTP507 3.2 9.6 0.7 CG A:ASP115 3.2 10.5 1.0 CG A:ASP13 3.3 12.7 0.4 PA A:DTP507 3.3 7.8 0.7 P2 A:DPO508 3.4 10.6 0.3 PG A:DTP507 3.4 10.7 0.7 C A:MET14 3.4 9.3 1.0 O2 A:DPO508 3.5 9.8 0.3 O3A A:DTP507 3.5 9.8 0.7 MG A:MG501 3.6 8.8 0.7 K A:K509 3.6 11.6 0.1 OD1 A:ASP115 3.6 11.5 1.0 O3B A:DTP507 3.7 9.3 0.7 O4 A:DPO508 3.7 9.4 0.3 P P:DA9 3.7 15.3 0.3 NZ A:LYS231 3.8 11.1 0.8 O A:HOH611 3.9 21.3 1.0 OD2 A:ASP13 3.9 13.6 0.4 N A:MET14 3.9 8.5 1.0 C5' A:DTP507 4.0 11.0 0.7 O2G A:DTP507 4.1 10.2 0.7 O7 A:DPO508 4.1 10.3 0.3 O5' A:DTP507 4.1 10.5 0.7 CA A:MET14 4.2 10.3 1.0 NZ A:LYS231 4.2 16.2 0.2 C5' P:DA9 4.3 9.2 0.3 C A:ASP13 4.3 8.0 1.0 O5' P:DA9 4.3 10.9 0.3 CB A:ASP13 4.3 9.7 0.6 O A:HOH712 4.3 17.5 1.0 CB A:ASP13 4.4 9.7 0.4 N A:ASP15 4.4 7.0 1.0 N A:CYS16 4.5 8.3 1.0 O2A A:DTP507 4.5 11.5 0.7 O3 A:DPO508 4.5 10.1 0.3 O6 A:DPO508 4.6 12.1 0.3 CB A:ASP115 4.6 9.1 1.0 CA A:ASP15 4.6 7.2 1.0 OP2 P:DA9 4.6 13.3 0.3 O2B A:DTP507 4.6 10.2 0.7 O A:ASP13 4.6 9.9 1.0 CB A:MET14 4.7 10.0 1.0 O3G A:DTP507 4.7 11.9 0.7 C A:ASP15 4.7 8.6 1.0 CE A:LYS231 4.7 18.8 0.8 MG P:MG101 4.7 16.8 0.3 CA A:ASP13 4.8 10.6 0.4 CA A:ASP13 4.8 10.6 0.6 O3' P:DT8 4.8 13.2 0.3 N A:PHE17 4.8 8.6 1.0 CB A:PHE17 4.9 8.2 1.0 O A:ASP115 4.9 10.6 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 300S


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 300S within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg101 b:16.8 occ:0.35 O2A A:DTP507 1.5 11.5 0.7 O3A A:DTP507 1.9 9.8 0.7 OP2 P:DA9 1.9 13.3 0.3 O P:HOH222 2.1 20.5 0.7 O2 A:DPO508 2.1 9.8 0.3 PA A:DTP507 2.1 7.8 0.7 O A:HOH617 2.2 33.9 1.0 O A:HOH674 2.9 16.1 1.0 P P:DA9 3.0 15.3 0.3 O1A A:DTP507 3.2 12.5 0.7 O5' A:DTP507 3.3 10.5 0.7 PB A:DTP507 3.4 9.6 0.7 P1 A:DPO508 3.5 9.4 0.3 OP1 P:DA9 3.5 12.5 0.3 O5' P:DA9 3.5 10.9 0.3 O A:HOH739 3.8 16.2 0.5 O A:HOH952 3.8 15.8 1.0 O3B A:DTP507 3.8 9.3 0.7 O4 A:DPO508 3.8 9.4 0.3 O6 A:DPO508 3.9 12.1 0.3 O A:HOH611 3.9 21.3 1.0 O3G A:DTP507 4.0 11.9 0.7 O1G A:DTP507 4.0 11.0 0.7 O5 A:DPO508 4.0 10.8 0.3 O2B A:DTP507 4.1 10.2 0.7 P2 A:DPO508 4.2 10.6 0.3 PG A:DTP507 4.2 10.7 0.7 O A:HOH1005 4.2 29.4 0.5 O3 A:DPO508 4.3 10.1 0.3 O A:HOH712 4.3 17.5 1.0 O3' P:DT8 4.4 13.2 0.3 O1B A:DTP507 4.4 9.5 0.7 O1 A:DPO508 4.4 8.8 0.3 C5' A:DTP507 4.5 11.0 0.7 C2' P:DT8 4.6 13.2 0.3 O P:HOH219 4.6 24.4 1.0 C2' P:DT8 4.7 13.4 0.3 C8 A:DTP507 4.7 11.6 0.7 MG A:MG503 4.7 7.7 0.8 CA A:CA502 4.7 7.9 0.2 C3' P:DT8 4.7 14.6 0.3 C5' P:DA9 4.8 9.2 0.3 C3' P:DT8 4.8 14.4 0.3 C3' P:DT8 4.8 14.2 0.3 C8 P:DA9 4.9 11.6 0.3 O3' P:DT8 4.9 11.6 0.3 O3' P:DT8 5.0 11.6 0.3

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