Calcium in PDB 3pw0: Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp

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

The structure of Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp, PDB code: 3pw0 was solved by S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.91 / 2.91
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.848, 102.245, 53.027, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 27.7

The binding sites of Calcium atom in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp (pdb code 3pw0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp, PDB code: 3pw0:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna 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 Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:92.5 occ:1.00 O A:HOH2060 2.9 6.3 1.0 O1A A:DTP400 3.2 72.4 1.0 O A:HOH2023 3.4 22.2 1.0 O A:HOH2059 3.4 45.4 1.0 OE1 A:GLU106 3.5 50.5 1.0 O3' C:DC359 3.5 62.4 1.0 O2A A:DTP400 3.7 71.8 1.0 OD1 A:ASP105 3.8 40.4 1.0 PA A:DTP400 3.9 72.3 1.0 OG A:SER103 4.1 43.1 1.0 CD A:GLU106 4.1 49.8 1.0 C5' A:DTP400 4.2 69.8 1.0 O5' A:DTP400 4.3 70.3 1.0 CG A:GLU106 4.5 47.7 1.0 C3' C:DC359 4.6 58.6 1.0 OD2 A:ASP105 4.6 38.8 1.0 CG A:ASP105 4.7 39.1 1.0 C4' A:DTP400 4.7 67.1 1.0 CB A:SER103 4.8 40.6 1.0 OE2 A:GLU106 4.8 53.7 1.0 O A:HOH2067 4.9 27.9 1.0 O4' A:DTP400 5.0 66.2 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna 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 Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:41.8 occ:1.00 O A:PHE8 2.4 29.9 1.0 OD2 A:ASP105 2.5 38.8 1.0 O2B A:DTP400 2.6 74.8 1.0 OD1 A:ASP7 2.7 39.2 1.0 O1A A:DTP400 2.8 72.4 1.0 O1B A:DTP400 2.8 74.2 1.0 O A:HOH2033 2.9 44.3 1.0 PB A:DTP400 3.1 75.5 1.0 O A:HOH2060 3.1 6.3 1.0 CG A:ASP7 3.2 36.5 1.0 CG A:ASP105 3.3 39.1 1.0 OD2 A:ASP7 3.4 36.6 1.0 C A:PHE8 3.5 30.6 1.0 O A:HOH2066 3.5 47.2 1.0 O3A A:DTP400 3.5 74.1 1.0 N A:PHE8 3.6 31.0 1.0 C A:ASP7 3.8 32.9 1.0 PA A:DTP400 3.8 72.3 1.0 CB A:ASP105 3.9 39.3 1.0 CA A:PHE8 3.9 30.0 1.0 OD1 A:ASP105 4.1 40.4 1.0 O A:ASP105 4.1 40.1 1.0 O A:HOH2023 4.1 22.2 1.0 O A:ASP7 4.2 35.4 1.0 CA A:ASP7 4.3 33.1 1.0 CB A:ASP7 4.3 34.8 1.0 O5' A:DTP400 4.4 70.3 1.0 CB A:PHE8 4.4 29.7 1.0 N A:ASP9 4.6 32.2 1.0 O3B A:DTP400 4.6 77.0 1.0 O A:HOH2067 4.8 27.9 1.0 C A:ASP105 4.8 40.5 1.0 O2G A:DTP400 4.9 82.7 1.0 O A:HOH2057 4.9 9.0 1.0 CB A:PHE11 5.0 27.8 1.0 CA A:ASP9 5.0 35.1 1.0 CA A:ASP105 5.0 40.4 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna 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 3 of Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:81.2 occ:1.00 O A:ALA181 3.0 54.2 1.0 O A:HOH2019 3.0 32.8 1.0 O C:HOH2020 3.2 51.4 1.0 OD1 A:ASP182 3.6 54.0 1.0 C A:ALA181 4.0 53.7 1.0 CA A:ASP182 4.1 51.0 1.0 N A:ASP182 4.5 52.1 1.0 CG A:ASP182 4.6 53.7 1.0 C A:ASP182 4.8 50.5 1.0 CB A:ASP182 4.9 51.2 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