Magnesium in PDB 4ecs: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec:
2.7.7.7;

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec, PDB code: 4ecs was solved by T.Nakamura, Y.Zhao, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 1.95
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	98.786, 98.786, 82.431, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 23.5

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Magnesium atom in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec (pdb code 4ecs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec, PDB code: 4ecs:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec


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 - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:15.8 occ:0.85 OD2 A:ASP13 2.2 21.6 0.8 O3' P:DT8 2.2 15.3 0.8 OP1 P:DA9 2.2 12.9 0.1 OE2 A:GLU116 2.3 22.0 1.0 O2A P:DTP501 2.3 12.6 0.8 OD2 A:ASP115 2.3 10.7 1.0 O A:HOH603 2.3 17.9 1.0 O3' P:DT8 2.4 16.1 0.1 P P:DA9 2.8 13.9 0.1 OD1 A:ASP13 3.0 9.4 0.2 OD2 A:ASP13 3.0 16.0 0.2 C3' P:DT8 3.1 21.4 0.8 CD A:GLU116 3.2 28.5 1.0 CG A:ASP115 3.3 13.5 1.0 CG A:ASP13 3.3 9.7 0.8 CG A:ASP13 3.4 11.4 0.2 CA A:CA504 3.4 8.8 0.3 MG A:MG505 3.4 8.0 0.7 PA P:DTP501 3.4 14.9 0.8 C3' P:DT8 3.6 18.8 0.1 OD1 A:ASP115 3.6 9.0 1.0 OP2 P:DA9 3.8 15.9 0.1 C4' P:DT8 3.8 19.9 0.1 OG A:SER113 3.9 13.5 1.0 OD1 A:ASP13 3.9 14.1 0.8 O1A P:DTP501 4.0 16.5 0.8 O5' P:DTP501 4.0 11.3 0.8 O5' P:DA9 4.0 12.2 0.1 C4' P:DT8 4.0 20.4 0.8 OE1 A:GLU116 4.0 23.8 1.0 CG A:GLU116 4.0 14.9 1.0 C5' P:DT8 4.0 22.1 0.1 CB A:GLU116 4.1 16.0 1.0 C5' P:DTP501 4.1 10.9 0.8 C5' P:DA9 4.2 11.4 0.1 O P:HOH101 4.3 22.1 0.8 C2' P:DT8 4.4 18.9 0.8 CB A:ASP13 4.5 8.1 0.8 C5' P:DT8 4.6 21.7 0.8 C A:ASP115 4.6 12.2 1.0 C2' P:DT8 4.6 17.4 0.1 O A:ASP115 4.7 9.2 1.0 CB A:ASP115 4.7 6.4 1.0 O7 P:DPO502 4.7 8.6 0.1 NZ A:LYS224 4.7 17.9 0.5 O3G P:DTP501 4.7 8.1 0.8 O A:HOH714 4.8 21.3 1.0 N A:GLU116 4.8 8.9 1.0 O3A P:DTP501 4.8 12.1 0.8 CB A:ASP13 4.8 8.7 0.2 O1 P:DPO502 4.8 11.9 0.1 O1B P:DTP501 4.9 9.9 0.8 CB A:SER113 5.0 16.4 1.0 O2 P:DPO502 5.0 9.9 0.1

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec


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 - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 80 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:8.0 occ:0.70 CA A:CA504 0.0 8.8 0.3 O7 P:DPO502 2.1 8.6 0.1 O2 P:DPO502 2.1 9.9 0.1 O1B P:DTP501 2.2 9.9 0.8 O3G P:DTP501 2.2 8.1 0.8 O2A P:DTP501 2.2 12.6 0.8 OD1 A:ASP13 2.2 9.4 0.2 OD1 A:ASP13 2.3 14.1 0.8 OD1 A:ASP115 2.3 9.0 1.0 OP1 P:DA9 2.4 12.9 0.1 O A:MET14 2.4 9.4 1.0 OD2 A:ASP13 2.9 21.6 0.8 CG A:ASP13 2.9 9.7 0.8 P1 P:DPO502 3.2 10.0 0.1 PB P:DTP501 3.2 9.6 0.8 CG A:ASP115 3.3 13.5 1.0 PA P:DTP501 3.4 14.9 0.8 MG A:MG503 3.4 15.8 0.8 O1 P:DPO502 3.4 11.9 0.1 CG A:ASP13 3.4 11.4 0.2 P2 P:DPO502 3.4 11.5 0.1 PG P:DTP501 3.5 11.4 0.8 O3A P:DTP501 3.5 12.1 0.8 OD2 A:ASP115 3.5 10.7 1.0 C A:MET14 3.6 5.8 1.0 O3B P:DTP501 3.7 13.5 0.8 O4 P:DPO502 3.8 12.7 0.1 P P:DA9 3.8 13.9 0.1 C5' P:DTP501 4.0 10.9 0.8 NZ A:LYS231 4.0 11.1 1.0 O5 P:DPO502 4.0 10.6 0.1 N A:MET14 4.1 5.5 1.0 O A:HOH603 4.1 17.9 1.0 OD2 A:ASP13 4.1 16.0 0.2 O5' P:DTP501 4.2 11.3 0.8 O2G P:DTP501 4.2 10.4 0.8 O A:HOH714 4.2 21.3 1.0 C5' P:DA9 4.3 11.4 0.1 O5' P:DA9 4.3 12.2 0.1 C A:ASP13 4.4 6.7 1.0 CA A:MET14 4.4 7.5 1.0 CB A:ASP13 4.4 8.1 0.8 CB A:ASP13 4.5 8.7 0.2 O3 P:DPO502 4.6 11.0 0.1 N A:ASP15 4.6 6.9 1.0 N A:CYS16 4.6 7.4 1.0 O2B P:DTP501 4.6 11.5 0.8 CB A:ASP115 4.6 6.4 1.0 O6 P:DPO502 4.7 11.2 0.1 CA A:ASP15 4.7 10.2 1.0 O1G P:DTP501 4.7 11.1 0.8 O1A P:DTP501 4.7 16.5 0.8 O3' P:DT8 4.7 16.1 0.1 C A:ASP15 4.7 11.9 1.0 OP2 P:DA9 4.8 15.9 0.1 O A:ASP13 4.8 10.0 1.0 N A:PHE17 4.8 8.0 1.0 CA A:ASP13 4.8 9.3 0.2 CB A:MET14 4.8 7.0 1.0 CE A:LYS231 4.8 27.3 1.0 CA A:ASP13 4.9 9.3 0.8 CB A:PHE17 4.9 5.1 1.0 O3' P:DT8 4.9 15.3 0.8 O A:ASP115 5.0 9.2 1.0

T.Nakamura, Y.Zhao, Y.Yamagata, Y.J.Hua, W.Yang. Watching Dna Polymerase Eta Make A Phosphodiester Bond Nature V. 487 196 2012.
ISSN: ISSN 0028-0836
PubMed: 22785315
DOI: 10.1038/NATURE11181