Magnesium in PDB 2bpf: Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp

The structure of Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp, PDB code: 2bpf was solved by H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	94.900, 94.900, 117.600, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp (pdb code 2bpf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp, PDB code: 2bpf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg339 b:6.0 occ:1.00 O2B A:DCT338 1.7 10.0 1.0 OD1 A:ASP190 2.1 14.9 1.0 O1G A:DCT338 2.3 21.7 1.0 OD2 A:ASP192 2.5 15.8 1.0 O A:HOH419 2.5 31.8 1.0 O1A A:DCT338 3.0 1.0 1.0 O A:ASP190 3.1 4.5 1.0 PB A:DCT338 3.2 17.0 1.0 CG A:ASP190 3.3 15.0 1.0 PG A:DCT338 3.4 22.7 1.0 CG A:ASP192 3.5 16.5 1.0 OG A:SER188 3.5 35.9 1.0 OG A:SER180 3.5 13.0 1.0 O3B A:DCT338 3.7 20.1 1.0 N A:ASP190 3.7 17.9 1.0 C A:ASP190 3.7 8.4 1.0 N A:SER180 3.8 5.8 1.0 O2G A:DCT338 4.0 17.6 1.0 PA A:DCT338 4.1 18.6 1.0 O3A A:DCT338 4.1 20.2 1.0 OD1 A:ASP192 4.1 16.8 1.0 OD2 A:ASP190 4.1 22.7 1.0 O1B A:DCT338 4.1 6.5 1.0 CA A:ASP190 4.2 9.5 1.0 CB A:SER180 4.2 13.3 1.0 CB A:ASP192 4.3 14.4 1.0 CB A:ASP190 4.3 11.3 1.0 O5' A:DCT338 4.4 19.9 1.0 CA A:GLY179 4.4 7.8 1.0 N A:ASP192 4.5 18.7 1.0 CA A:SER180 4.6 12.3 1.0 N A:MET191 4.6 11.0 1.0 C A:GLY179 4.6 4.3 1.0 N A:GLY189 4.6 20.6 1.0 O3G A:DCT338 4.6 27.7 1.0 MG A:MG340 4.7 79.1 1.0 CB A:SER188 4.7 32.9 1.0 C A:GLY189 4.8 24.4 1.0 C A:MET191 4.9 17.9 1.0 CA A:MET191 4.9 14.3 1.0 CA A:GLY189 4.9 21.4 1.0

Magnesium binding site 2 out of 2 in the Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg340 b:79.1 occ:1.00 OD2 A:ASP190 2.0 22.7 1.0 OD1 A:ASP192 2.5 16.8 1.0 O1A A:DCT338 2.6 1.0 1.0 CG A:ASP190 3.1 15.0 1.0 CG A:ASP192 3.1 16.5 1.0 OD2 A:ASP256 3.2 43.0 1.0 OD2 A:ASP192 3.2 15.8 1.0 OD1 A:ASP190 3.4 14.9 1.0 PA A:DCT338 3.4 18.6 1.0 O5' A:DCT338 3.5 19.9 1.0 O A:HOH403 3.8 41.7 1.0 OP1 P:DC7 3.8 20.2 1.0 O2A A:DCT338 3.9 19.2 1.0 C3' P:DC7 3.9 18.2 1.0 O5' P:DC7 3.9 21.4 1.0 CG A:ASP256 4.1 35.4 1.0 CB A:ASP190 4.3 11.3 1.0 P P:DC7 4.4 18.6 1.0 NH2 A:ARG254 4.4 58.5 1.0 C5' A:DCT338 4.4 14.9 1.0 C5' P:DC7 4.5 22.2 1.0 CB A:ASP256 4.5 16.7 1.0 C4' P:DC7 4.6 20.2 1.0 CB A:ASP192 4.6 14.4 1.0 O2B A:DCT338 4.6 10.0 1.0 MG A:MG339 4.7 6.0 1.0 O1G A:DCT338 4.8 21.7 1.0 OP2 P:DC7 4.9 23.5 1.0 O3A A:DCT338 4.9 20.2 1.0

H.Pelletier, M.R.Sawaya, A.Kumar, S.H.Wilson, J.Kraut. Structures of Ternary Complexes of Rat Dna Polymerase Beta, A Dna Template-Primer, and Ddctp. Science V. 264 1891 1994.
ISSN: ISSN 0036-8075
PubMed: 7516580