Calcium in PDB 4jv2: Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp

All present enzymatic activity of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp:
2.7.7.7;

The structure of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp, PDB code: 4jv2 was solved by S.Banerjee, G.Shanmugam, M.P.Stone, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.09 / 2.74
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.580, 103.305, 52.780, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26.5

The binding sites of Calcium atom in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp (pdb code 4jv2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp, PDB code: 4jv2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:50.9 occ:1.00 O A:PHE8 2.7 55.5 1.0 OD2 A:ASP7 2.8 48.4 1.0 OD2 A:ASP105 2.8 56.8 1.0 O3G A:DTP401 2.8 64.2 1.0 CG A:ASP7 3.0 52.2 1.0 O2A A:DTP401 3.0 52.7 1.0 O2B A:DTP401 3.1 59.4 1.0 C A:PHE8 3.2 48.4 1.0 N A:PHE8 3.3 45.5 1.0 OD1 A:ASP7 3.3 59.6 1.0 O3B A:DTP401 3.5 60.3 1.0 PG A:DTP401 3.6 67.7 1.0 C A:ASP7 3.6 49.0 1.0 O A:HOH501 3.7 40.3 1.0 PB A:DTP401 3.7 58.6 1.0 CB A:ASP7 3.7 48.7 1.0 CA A:PHE8 3.8 46.4 1.0 CG A:ASP105 3.9 53.2 1.0 O3A A:DTP401 3.9 55.6 1.0 N A:ASP9 4.0 46.6 1.0 CA A:ASP7 4.0 46.9 1.0 PA A:DTP401 4.0 57.8 1.0 O1G A:DTP401 4.0 60.8 1.0 O A:ASP7 4.3 50.4 1.0 CA A:ASP9 4.3 46.8 1.0 CB A:ASP105 4.3 43.6 1.0 O A:ASP105 4.5 46.8 1.0 N A:TYR10 4.6 45.2 1.0 C A:ASP9 4.7 47.1 1.0 C5' A:DTP401 4.7 48.4 1.0 CB A:PHE8 4.7 41.9 1.0 NZ A:LYS159 4.8 55.4 1.0 O5' A:DTP401 4.9 51.7 1.0 OD1 A:ASP105 4.9 57.3 1.0 O2G A:DTP401 5.0 61.9 1.0

Calcium binding site 2 out of 2 in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna with Dna (-1 Primer) Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:63.8 occ:1.00 O A:ALA181 2.7 52.6 1.0 O A:HOH504 2.8 43.8 1.0 O A:HOH502 2.9 47.2 1.0 O A:HOH503 3.1 55.6 1.0 O A:ILE186 3.1 48.8 1.0 C A:ALA181 3.9 54.7 1.0 OP2 C:DC513 4.2 41.3 1.0 C A:ILE186 4.2 48.2 1.0 OP1 C:DC513 4.4 41.9 1.0 CA A:ASP182 4.7 50.3 1.0 CA A:GLY187 4.7 47.3 1.0 N A:ASP182 4.8 48.7 1.0 CA A:ALA181 4.8 53.7 1.0 P C:DC513 4.9 40.9 1.0 N A:GLY187 4.9 45.8 1.0 CB A:ALA181 5.0 51.0 1.0

G.Shanmugam, I.G.Minko, S.Banerjee, P.P.Christov, I.D.Kozekov, C.J.Rizzo, R.S.Lloyd, M.Egli, M.P.Stone. Ring-Opening of the Gamma-Oh-Pdg Adduct Promotes Error-Free Bypass By the Sulfolobus Solfataricus Dna Polymerase DPO4. Chem.Res.Toxicol. V. 26 1348 2013.
ISSN: ISSN 0893-228X
PubMed: 23947567
DOI: 10.1021/TX400200B