Calcium in PDB 4juz: Ternary Complex of Gamma-Ohpdg Adduct Modified Dna (Zero Primer) with Dna Polymerase IV and Incoming Dgtp

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

The structure of Ternary Complex of Gamma-Ohpdg Adduct Modified Dna (Zero Primer) with Dna Polymerase IV and Incoming Dgtp, PDB code: 4juz 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)	42.04 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.906, 104.358, 52.489, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.9

The binding sites of Calcium atom in the Ternary Complex of Gamma-Ohpdg Adduct Modified Dna (Zero Primer) with Dna Polymerase IV and Incoming Dgtp (pdb code 4juz). 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 (Zero Primer) with Dna Polymerase IV and Incoming Dgtp, PDB code: 4juz:
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 (Zero Primer) with Dna Polymerase IV and Incoming Dgtp


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 (Zero Primer) with Dna Polymerase IV and Incoming Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:58.7 occ:1.00 O A:PHE8 2.6 48.5 1.0 O A:HOH1124 2.9 65.9 1.0 O3B A:DGT1000 2.9 66.9 1.0 OD2 A:ASP105 2.9 52.2 1.0 OD1 A:ASP7 2.9 49.3 1.0 O1A A:DGT1000 2.9 57.0 1.0 O2B A:DGT1000 3.1 46.0 1.0 CG A:ASP105 3.4 48.0 1.0 PB A:DGT1000 3.4 66.2 1.0 C A:PHE8 3.5 43.1 1.0 C5' A:DGT1000 3.8 48.0 1.0 PA A:DGT1000 3.8 56.2 1.0 O2G A:DGT1000 3.8 70.6 1.0 CB A:ASP105 3.8 36.5 1.0 O A:HOH1101 3.8 46.8 1.0 PG A:DGT1000 3.9 79.0 1.0 O3A A:DGT1000 4.0 70.5 1.0 CB A:PHE11 4.0 41.1 1.0 N A:PHE11 4.1 41.0 1.0 N A:TYR10 4.1 42.0 1.0 OD1 A:ASP105 4.1 54.3 1.0 CG A:ASP7 4.1 50.2 1.0 O5' A:DGT1000 4.2 54.8 1.0 N A:PHE8 4.2 36.8 1.0 N A:ASP9 4.2 43.3 1.0 CA A:ASP9 4.3 41.6 1.0 CA A:PHE8 4.3 41.0 1.0 C A:ASP9 4.3 44.1 1.0 O3G A:DGT1000 4.4 58.6 1.0 CB A:PHE8 4.6 37.6 1.0 CA A:PHE11 4.7 37.3 1.0 C A:ASP7 4.7 44.2 1.0 O1B A:DGT1000 4.7 62.1 1.0 CA A:TYR10 4.8 42.5 1.0 OD2 A:ASP7 4.8 61.0 1.0 O A:ASP105 4.8 47.2 1.0 C4' A:DGT1000 4.9 42.7 1.0 C A:TYR10 5.0 40.6 1.0

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


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 (Zero Primer) with Dna Polymerase IV and Incoming Dgtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:77.5 occ:1.00 O A:HOH1104 2.9 44.2 1.0 O A:HOH1103 2.9 46.7 1.0 O A:ALA181 3.3 53.5 1.0 O A:HOH1102 3.5 69.9 1.0 OD1 A:ASP182 3.7 75.1 1.0 CA A:ASP182 4.3 49.8 1.0 C A:ALA181 4.3 54.9 1.0 N A:ASP182 4.8 55.2 1.0 CG A:ASP182 4.8 69.1 1.0 O A:ILE186 4.9 50.4 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