Magnesium in PDB 4ed8: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation:
2.7.7.7;

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation, PDB code: 4ed8 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)	28.52 / 1.52
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 (%)	17.1 / 20

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation 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 Tg Crystal at pH 7.0, Normal Translocation (pdb code 4ed8). 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 Tg Crystal at pH 7.0, Normal Translocation, PDB code: 4ed8:
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 Tg Crystal at pH 7.0, Normal Translocation


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 Tg Crystal at pH 7.0, Normal Translocation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:13.5 occ:0.50 OE2 A:GLU116 2.1 43.3 1.0 O A:HOH601 2.2 29.6 1.0 OD2 A:ASP13 2.2 20.9 0.5 O2A P:DTP501 2.3 15.1 1.0 O3' P:DA9 2.3 29.5 1.0 OD2 A:ASP115 2.4 17.2 1.0 CD A:GLU116 3.0 38.6 1.0 OD1 A:ASP13 3.2 12.2 0.5 C3' P:DA9 3.2 31.5 1.0 OD2 A:ASP13 3.3 19.7 0.5 CG A:ASP115 3.4 14.2 1.0 CG A:ASP13 3.4 15.2 0.5 MG A:MG504 3.4 11.9 0.5 CG A:ASP13 3.4 16.0 0.5 CA A:CA503 3.5 9.6 0.5 PA P:DTP501 3.6 17.9 1.0 OD1 A:ASP115 3.6 14.7 1.0 OE1 A:GLU116 3.8 34.3 1.0 CG A:GLU116 3.9 24.7 1.0 OG A:SER113 3.9 20.9 1.0 C4' P:DA9 3.9 24.3 1.0 OD1 A:ASP13 4.0 19.1 0.5 O1A P:DTP501 4.1 17.7 1.0 CB A:GLU116 4.1 27.4 1.0 O5' P:DTP501 4.1 13.6 1.0 C5' P:DTP501 4.3 13.3 1.0 C5' P:DA9 4.3 31.6 0.5 C5' P:DA9 4.4 30.5 0.5 NZ A:LYS224 4.4 24.1 0.5 O A:HOH726 4.5 32.2 1.0 CB A:ASP13 4.5 12.5 0.5 C2' P:DA9 4.5 35.1 1.0 C A:ASP115 4.7 14.0 1.0 O A:ASP115 4.7 13.7 1.0 CB A:ASP13 4.7 14.5 0.5 O3G P:DTP501 4.8 14.3 1.0 CB A:ASP115 4.8 12.5 1.0 N A:GLU116 4.9 12.2 1.0 O3A P:DTP501 4.9 13.5 1.0

Magnesium binding site 2 out of 2 in the Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the Tg Crystal at pH 7.0, Normal Translocation


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 Tg Crystal at pH 7.0, Normal Translocation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:11.9 occ:0.50 CA A:CA503 0.0 9.6 0.5 OD1 A:ASP13 2.1 12.2 0.5 O3G P:DTP501 2.3 14.3 1.0 OD1 A:ASP115 2.3 14.7 1.0 O A:MET14 2.3 13.0 1.0 O1B P:DTP501 2.3 12.1 1.0 O2A P:DTP501 2.3 15.1 1.0 OD1 A:ASP13 2.4 19.1 0.5 CG A:ASP13 3.0 15.2 0.5 OD2 A:ASP13 3.0 20.9 0.5 CG A:ASP13 3.2 16.0 0.5 CG A:ASP115 3.3 14.2 1.0 PB P:DTP501 3.4 12.0 1.0 MG A:MG502 3.4 13.5 0.5 PA P:DTP501 3.5 17.9 1.0 C A:MET14 3.5 11.3 1.0 PG P:DTP501 3.5 12.7 1.0 O3A P:DTP501 3.6 13.5 1.0 OD2 A:ASP115 3.6 17.2 1.0 OD2 A:ASP13 3.7 19.7 0.5 O3B P:DTP501 3.8 13.2 1.0 N A:MET14 4.0 9.8 1.0 NZ A:LYS231 4.0 18.6 1.0 O A:HOH601 4.1 29.6 1.0 O A:HOH726 4.1 32.2 1.0 C5' P:DTP501 4.1 13.3 1.0 O2G P:DTP501 4.2 13.2 1.0 C A:ASP13 4.2 11.3 1.0 CA A:MET14 4.2 10.4 1.0 O5' P:DTP501 4.3 13.6 1.0 CB A:ASP13 4.3 12.5 0.5 CB A:ASP13 4.5 14.5 0.5 N A:ASP15 4.5 9.5 1.0 N A:CYS16 4.6 9.9 1.0 CB A:ASP115 4.6 12.5 1.0 O A:ASP13 4.6 14.0 1.0 CA A:ASP15 4.7 11.3 1.0 CA A:ASP13 4.7 13.0 0.5 CA A:ASP13 4.7 12.9 0.5 O1G P:DTP501 4.7 14.2 1.0 O1A P:DTP501 4.7 17.7 1.0 O2B P:DTP501 4.8 12.2 1.0 CB A:MET14 4.8 15.8 1.0 C A:ASP15 4.8 9.4 1.0 N A:PHE17 4.8 9.5 1.0 CE A:LYS231 4.8 33.5 1.0 O A:ASP115 4.9 13.7 1.0 O3' P:DA9 4.9 29.5 1.0 CB A:PHE17 4.9 11.3 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