Magnesium in PDB 4ecr: Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 40 Sec

All present enzymatic activity of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 40 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 40 Sec, PDB code: 4ecr 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 / 1.89
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 (%)	17.2 / 21.6

The structure of Human Dna Polymerase Eta - Dna Ternary Complex: Reaction in the at Crystal at pH 7.0 For 40 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 40 Sec (pdb code 4ecr). 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 40 Sec, PDB code: 4ecr:
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 40 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 40 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:15.7 occ:0.90 OD2 A:ASP13 2.1 16.5 0.8 O2A P:DTP504 2.2 13.6 1.0 O A:HOH601 2.2 20.6 1.0 OE2 A:GLU116 2.2 22.2 1.0 O3' P:DT8 2.2 19.0 1.0 OD2 A:ASP115 2.3 12.1 1.0 OD2 A:ASP13 2.9 17.4 0.2 OD1 A:ASP13 3.0 12.2 0.2 C3' P:DT8 3.2 21.3 1.0 CG A:ASP115 3.3 12.1 1.0 CD A:GLU116 3.3 23.6 1.0 CG A:ASP13 3.3 12.4 0.8 CG A:ASP13 3.3 14.0 0.2 MG A:MG503 3.4 11.2 0.5 PA P:DTP504 3.4 16.6 1.0 CA A:CA502 3.4 11.1 0.5 OD1 A:ASP115 3.6 11.8 1.0 OD1 A:ASP13 3.9 14.9 0.8 O5' P:DTP504 4.0 14.3 1.0 O1A P:DTP504 4.0 15.2 1.0 OG A:SER113 4.0 15.5 1.0 C4' P:DT8 4.0 20.5 1.0 OE1 A:GLU116 4.0 20.7 1.0 C5' P:DTP504 4.2 12.3 1.0 CG A:GLU116 4.2 17.8 1.0 CB A:GLU116 4.2 16.7 1.0 O A:HOH722 4.2 25.2 1.0 CB A:ASP13 4.4 11.2 0.8 C5' P:DT8 4.4 21.2 0.5 C2' P:DT8 4.5 20.9 1.0 C5' P:DT8 4.6 21.4 0.5 C A:ASP115 4.6 11.2 1.0 O A:ASP115 4.6 11.7 1.0 CB A:ASP115 4.6 9.7 1.0 NZ A:LYS224 4.7 20.3 0.8 O3G P:DTP504 4.7 12.6 1.0 CB A:ASP13 4.7 10.9 0.2 O3A P:DTP504 4.8 13.0 1.0 N A:GLU116 4.8 9.9 1.0 O1B P:DTP504 4.9 9.8 1.0

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 40 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 40 Sec within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:11.2 occ:0.50 CA A:CA502 0.0 11.1 0.5 OD1 A:ASP13 2.2 12.2 0.2 O1B P:DTP504 2.2 9.8 1.0 OD1 A:ASP13 2.3 14.9 0.8 O3G P:DTP504 2.3 12.6 1.0 OD1 A:ASP115 2.3 11.8 1.0 O2A P:DTP504 2.3 13.6 1.0 O A:MET14 2.3 9.5 1.0 OD2 A:ASP13 2.8 16.5 0.8 CG A:ASP13 2.9 12.4 0.8 PB P:DTP504 3.3 10.1 1.0 CG A:ASP115 3.3 12.1 1.0 MG A:MG501 3.4 15.7 0.9 PA P:DTP504 3.4 16.6 1.0 CG A:ASP13 3.4 14.0 0.2 PG P:DTP504 3.5 13.9 1.0 O3A P:DTP504 3.5 13.0 1.0 C A:MET14 3.5 9.3 1.0 OD2 A:ASP115 3.6 12.1 1.0 O3B P:DTP504 3.8 11.1 1.0 NZ A:LYS231 3.9 15.1 1.0 O A:HOH722 3.9 25.2 1.0 N A:MET14 4.0 9.6 1.0 C5' P:DTP504 4.1 12.3 1.0 O2G P:DTP504 4.1 11.2 1.0 OD2 A:ASP13 4.1 17.4 0.2 O A:HOH601 4.2 20.6 1.0 O5' P:DTP504 4.2 14.3 1.0 CA A:MET14 4.3 10.8 1.0 CB A:ASP13 4.3 11.2 0.8 C A:ASP13 4.3 9.3 1.0 CB A:ASP13 4.5 10.9 0.2 N A:ASP15 4.5 6.8 1.0 N A:CYS16 4.6 9.5 1.0 CB A:ASP115 4.6 9.7 1.0 CA A:ASP15 4.6 11.1 1.0 O2B P:DTP504 4.7 10.3 1.0 O1A P:DTP504 4.7 15.2 1.0 O1G P:DTP504 4.7 14.2 1.0 CE A:LYS231 4.7 25.0 1.0 O A:ASP13 4.7 7.6 1.0 C A:ASP15 4.7 13.3 1.0 CB A:MET14 4.8 10.0 1.0 N A:PHE17 4.8 6.3 1.0 CA A:ASP13 4.8 10.4 0.2 CA A:ASP13 4.8 10.3 0.8 CB A:PHE17 4.9 6.5 1.0 O3' P:DT8 4.9 19.0 1.0 O A:ASP115 4.9 11.7 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