Magnesium in PDB 5bol: Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog

All present enzymatic activity of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog:
2.7.7.7;

The structure of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog, PDB code: 5bol was solved by B.D.Freudenthal, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.52 / 1.98
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.640, 79.114, 55.702, 90.00, 107.65, 90.00
R / Rfree (%)	19 / 24.7

The structure of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog (pdb code 5bol). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog, PDB code: 5bol:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog


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 Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg401 b:20.3 occ:1.00 OD2 A:ASP256 2.0 20.5 1.0 OD1 A:ASP192 2.1 19.9 1.0 OD2 A:ASP190 2.1 19.8 1.0 O A:HOH508 2.1 19.9 1.0 O3' P:DC10 2.1 14.6 1.0 O1A A:1GC402 2.2 16.7 1.0 CG A:ASP192 3.1 15.7 1.0 CG A:ASP190 3.1 18.4 1.0 C3' P:DC10 3.2 17.8 1.0 CG A:ASP256 3.2 21.9 1.0 PA A:1GC402 3.3 20.2 1.0 O2A A:1GC402 3.4 18.7 1.0 OD2 A:ASP192 3.5 17.4 1.0 OD1 A:ASP190 3.5 20.6 1.0 MG A:MG401 3.6 19.2 1.0 CB A:ASP256 3.9 24.9 1.0 C4' P:DC10 3.9 21.8 1.0 O5' A:1GC402 4.0 18.5 1.0 C5' A:1GC402 4.1 15.6 1.0 C5' P:DC10 4.1 23.8 1.0 OD1 A:ASP256 4.2 27.6 1.0 O A:HOH582 4.4 19.9 1.0 CB A:ASP192 4.4 20.3 1.0 C2' P:DC10 4.4 19.2 1.0 CB A:ASP190 4.5 20.7 1.0 O5' P:DC10 4.6 22.2 1.0 OP1 P:DC10 4.6 23.7 1.0 C3A A:1GC402 4.8 21.2 1.0 O A:MET191 4.9 19.9 1.0 O2B A:1GC402 4.9 14.0 1.0 NH2 A:ARG254 5.0 25.6 1.0 O1G A:1GC402 5.0 17.6 1.0

Magnesium binding site 2 out of 2 in the Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Ternary Complex with A Templating 5CLC and Incoming Dgtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.2 occ:1.00 O1A A:1GC402 2.1 16.7 1.0 O2B A:1GC402 2.1 14.0 1.0 OD2 A:ASP192 2.1 17.4 1.0 OD1 A:ASP190 2.1 20.6 1.0 O A:HOH518 2.1 19.4 1.0 O1G A:1GC402 2.3 17.6 1.0 PB A:1GC402 3.1 18.6 1.0 CG A:ASP192 3.1 15.7 1.0 CG A:ASP190 3.1 18.4 1.0 PA A:1GC402 3.2 20.2 1.0 PG A:1GC402 3.4 18.8 1.0 C3A A:1GC402 3.4 21.2 1.0 O3B A:1GC402 3.4 19.0 1.0 OD1 A:ASP192 3.4 19.9 1.0 OD2 A:ASP190 3.5 19.8 1.0 MG P:MG401 3.6 20.3 1.0 O A:HOH582 3.9 19.9 1.0 C5' A:1GC402 3.9 15.6 1.0 O5' A:1GC402 4.1 18.5 1.0 O A:ASP190 4.2 21.8 1.0 O3G A:1GC402 4.2 20.6 1.0 O2A A:1GC402 4.3 18.7 1.0 N A:SER180 4.4 23.8 1.0 O1B A:1GC402 4.4 17.9 1.0 CB A:ASP190 4.4 20.7 1.0 CB A:ASP192 4.4 20.3 1.0 C A:ASP190 4.4 20.4 1.0 CA A:GLY179 4.4 18.0 1.0 N A:ASP190 4.5 20.3 1.0 O A:HOH627 4.5 20.7 1.0 O A:HOH508 4.5 19.9 1.0 O2G A:1GC402 4.5 18.4 1.0 OG A:SER180 4.6 22.6 1.0 CA A:ASP190 4.7 16.6 1.0 N A:ASP192 4.9 20.0 1.0 O3' P:DC10 5.0 14.6 1.0 C A:GLY179 5.0 19.9 1.0

B.I.Fedeles, B.D.Freudenthal, E.Yau, V.Singh, S.C.Chang, D.Li, J.C.Delaney, S.H.Wilson, J.M.Essigmann. Intrinsic Mutagenic Properties of 5-Chlorocytosine: A Mechanistic Connection Between Chronic Inflammation and Cancer. Proc.Natl.Acad.Sci.Usa V. 112 E4571 2015.
ISSN: ESSN 1091-6490
PubMed: 26243878
DOI: 10.1073/PNAS.1507709112