Magnesium in PDB 9icn: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2, PDB code: 9icn was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.896, 57.689, 48.427, 90.00, 90.00, 90.00
R / Rfree (%)	15 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 (pdb code 9icn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2, PDB code: 9icn:

Magnesium binding site 1 out of 1 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg339 b:30.0 occ:0.83 O2B A:DCT338 2.1 88.8 0.5 O1G A:DCT338 2.1 83.3 0.5 O1A A:DCT338 2.5 94.8 0.5 PB A:DCT338 3.1 87.6 0.5 OD1 A:ASP190 3.1 39.5 1.0 PG A:DCT338 3.1 83.8 0.5 O3B A:DCT338 3.3 85.1 0.5 O3G A:DCT338 3.4 84.6 0.5 PA A:DCT338 3.4 95.2 0.5 O3A A:DCT338 3.4 90.2 0.5 OG A:SER180 3.6 47.5 1.0 O A:HOH502 3.6 14.5 1.0 O5' A:DCT338 3.7 94.8 0.5 N A:GLY189 3.7 19.0 1.0 O A:ASP190 3.8 40.0 1.0 CB A:SER188 3.8 31.2 1.0 N A:ASP190 4.1 32.5 1.0 CG A:ASP190 4.2 41.2 1.0 CA A:SER188 4.4 26.1 1.0 O1B A:DCT338 4.5 86.6 0.5 O2G A:DCT338 4.5 84.1 0.5 C A:SER188 4.6 21.4 1.0 CA A:GLY189 4.6 20.7 1.0 N A:SER180 4.6 37.5 1.0 C A:ASP190 4.8 29.3 1.0 CB A:SER180 4.8 35.0 1.0 C A:GLY189 4.8 26.9 1.0 O2A A:DCT338 4.8 97.4 0.5 OD2 A:ASP190 4.9 48.1 1.0 CA A:ASP190 4.9 32.1 1.0 OG A:SER188 5.0 36.6 1.0

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566