Magnesium in PDB 2oh2: Ternary Complex of Human Dna Polymerase

All present enzymatic activity of Ternary Complex of Human Dna Polymerase:
2.7.7.7;

The structure of Ternary Complex of Human Dna Polymerase, PDB code: 2oh2 was solved by S.Lone, S.A.Townson, S.N.Uljon, S.Prakash, L.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	116.150, 152.472, 217.389, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 29.4

The binding sites of Magnesium atom in the Ternary Complex of Human Dna Polymerase (pdb code 2oh2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ternary Complex of Human Dna Polymerase, PDB code: 2oh2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Ternary Complex of Human Dna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Human Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg872 b:51.9 occ:1.00 O2B A:TTP873 1.8 55.6 1.0 OD2 A:ASP198 2.0 47.3 1.0 OD1 A:ASP107 2.2 51.8 1.0 O A:MET108 2.3 17.1 1.0 O1A A:TTP873 2.4 55.6 1.0 O3G A:TTP873 2.6 55.6 1.0 CG A:ASP107 2.9 51.8 1.0 OD2 A:ASP107 3.1 51.8 1.0 CG A:ASP198 3.1 47.3 1.0 PB A:TTP873 3.2 55.6 1.0 C A:MET108 3.5 17.1 1.0 PA A:TTP873 3.5 55.6 1.0 PG A:TTP873 3.8 55.6 1.0 OD1 A:ASP198 3.8 47.3 1.0 O3A A:TTP873 3.8 55.6 1.0 C5' A:TTP873 3.9 55.6 1.0 N A:MET108 3.9 17.1 1.0 O3B A:TTP873 4.0 55.6 1.0 NZ A:LYS328 4.1 44.0 1.0 O5' A:TTP873 4.1 55.6 1.0 C A:ASP107 4.1 28.0 1.0 CA A:MET108 4.2 17.1 1.0 CB A:ASP198 4.2 47.3 1.0 CB A:ASP107 4.2 51.8 1.0 O1B A:TTP873 4.3 55.6 1.0 O A:HOH882 4.4 59.5 1.0 O2G A:TTP873 4.4 55.6 1.0 CB A:MET108 4.5 38.2 1.0 N A:ASP109 4.5 20.1 1.0 CA A:ASP107 4.5 28.0 1.0 O A:ASP107 4.5 28.0 1.0 O2A A:TTP873 4.6 55.6 1.0 OE1 A:GLU199 4.6 74.2 1.0 N A:ALA110 4.6 25.0 1.0 CA A:ASP109 4.7 20.1 1.0 O A:ASP198 4.8 25.1 1.0 N A:PHE111 4.8 29.3 1.0 CB A:PHE111 4.9 24.5 1.0 CG A:GLU199 4.9 74.2 1.0 CE A:LYS328 5.0 44.0 1.0

Magnesium binding site 2 out of 2 in the Ternary Complex of Human Dna Polymerase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ternary Complex of Human Dna Polymerase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg873 b:56.5 occ:1.00 O2B B:TTP874 1.8 53.5 1.0 O1A B:TTP874 2.0 53.5 1.0 OD1 B:ASP107 2.1 69.2 1.0 O B:MET108 2.5 61.3 1.0 O3G B:TTP874 2.6 53.5 1.0 OD2 B:ASP198 2.8 67.7 1.0 O2G B:TTP874 2.9 53.5 1.0 CG B:ASP107 2.9 69.2 1.0 PB B:TTP874 3.0 53.5 1.0 PA B:TTP874 3.1 53.5 1.0 OD2 B:ASP107 3.1 69.2 1.0 PG B:TTP874 3.1 53.5 1.0 O3A B:TTP874 3.4 53.5 1.0 O3B B:TTP874 3.5 53.5 1.0 NZ B:LYS328 3.7 88.0 1.0 C B:MET108 3.7 61.3 1.0 O2A B:TTP874 3.8 53.5 1.0 O B:HOH883 3.8 45.7 1.0 CG B:ASP198 3.9 67.7 1.0 O5' B:TTP874 4.0 53.5 1.0 C5' B:TTP874 4.1 53.5 1.0 N B:ALA110 4.2 54.3 1.0 O1B B:TTP874 4.3 53.5 1.0 OD1 B:ASP198 4.4 67.7 1.0 N B:MET108 4.4 61.3 1.0 CB B:ASP107 4.4 69.2 1.0 CA B:ASP109 4.5 59.5 1.0 N B:ASP109 4.6 59.5 1.0 C B:ASP107 4.6 43.2 1.0 CE B:LYS328 4.6 88.0 1.0 O1G B:TTP874 4.6 53.5 1.0 CA B:MET108 4.6 61.3 1.0 OE1 B:GLU199 4.8 96.6 1.0 C B:ASP109 4.8 59.5 1.0 CD B:LYS328 4.9 88.0 1.0 N B:PHE111 4.9 61.9 1.0 O B:ASP107 4.9 43.2 1.0 CA B:ASP107 4.9 43.2 1.0

S.Lone, S.A.Townson, S.N.Uljon, R.E.Johnson, A.Brahma, D.T.Nair, S.Prakash, L.Prakash, A.K.Aggarwal. Ternary Complex of the Catalytic Core of Human Dna Polymerase Kappa with Dna and Dtt To Be Published.