Calcium in PDB 3pvx: Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV

All present enzymatic activity of Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV:
2.7.7.7;

The structure of Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV, PDB code: 3pvx was solved by S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.96 / 3.03
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.752, 103.905, 52.890, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 29.9

The binding sites of Calcium atom in the Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV (pdb code 3pvx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV, PDB code: 3pvx:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:79.9 occ:1.00 OD2 A:ASP105 3.0 59.3 1.0 O A:PHE8 3.1 44.5 1.0 O A:HOH2024 3.1 29.0 1.0 OD2 A:ASP7 3.3 53.2 1.0 OD1 A:ASP7 3.4 56.1 1.0 CG A:ASP7 3.7 52.4 1.0 CG A:ASP105 4.1 56.3 1.0 C A:PHE8 4.3 44.2 1.0 O A:HOH2038 4.4 43.9 1.0 N A:TYR10 4.6 45.2 1.0 OD1 A:ASP105 4.8 58.0 1.0 CB A:ASP105 5.0 51.8 1.0

Calcium binding site 2 out of 3 in the Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:74.6 occ:1.00 O A:ALA181 2.9 68.8 1.0 O A:ILE186 2.9 65.8 1.0 O A:HOH2002 2.9 68.9 1.0 O A:HOH2026 3.1 68.0 1.0 O A:HOH2025 3.1 55.0 1.0 C A:ILE186 4.0 65.9 1.0 C A:ALA181 4.1 68.1 1.0 OP2 C:DC359 4.1 56.1 1.0 OP1 C:DC359 4.6 57.5 1.0 CA A:GLY187 4.6 69.8 1.0 CA A:ASP182 4.7 66.6 1.0 N A:GLY187 4.8 67.2 1.0 P C:DC359 4.9 57.5 1.0 N A:ASP182 4.9 67.2 1.0 O A:VAL183 4.9 60.4 1.0 CA A:ILE186 5.0 63.7 1.0

Calcium binding site 3 out of 3 in the Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Binary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:93.7 occ:1.00 OD2 A:ASP294 3.0 80.3 1.0 O A:HOH2027 3.2 47.1 1.0 OD1 A:ASP294 3.2 81.2 1.0 OP2 C:DA356 3.4 65.5 1.0 CG A:ASP294 3.5 80.7 1.0 OP1 C:DA356 3.5 67.1 1.0 P C:DA356 3.9 67.3 1.0 C3' C:DG355 4.9 69.1 1.0 O3' C:DG355 4.9 69.0 1.0

S.Banerjee, K.L.Brown, M.Egli, M.P.Stone. Bypass of Aflatoxin B(1) Adducts By the Sulfolobus Solfataricus Dna Polymerase IV. J.Am.Chem.Soc. V. 133 12556 2011.
ISSN: ISSN 0002-7863
PubMed: 21790157
DOI: 10.1021/JA2015668