Calcium in PDB 3pw4: Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) with Dna Polymerase IV and Incoming Datp

All present enzymatic activity of Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) with Dna Polymerase IV and Incoming Datp:
2.7.7.7;

The structure of Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) with Dna Polymerase IV and Incoming Datp, PDB code: 3pw4 was solved by S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.987, 102.581, 52.682, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 29.4

The binding sites of Calcium atom in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) with Dna Polymerase IV and Incoming Datp (pdb code 3pw4). 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-N7-Gua) with Dna Polymerase IV and Incoming Datp, PDB code: 3pw4:
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-N7-Gua) 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-N7-Gua) with Dna Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:75.9 occ:1.00 O1A A:DTP400 2.7 75.6 1.0 O A:HOH2006 2.7 41.3 1.0 OE2 A:GLU107 3.0 60.4 1.0 CG A:GLU107 3.1 52.4 1.0 OD1 A:ASP106 3.1 50.8 1.0 OD1 A:ASP8 3.2 53.8 1.0 OD2 A:ASP106 3.2 51.9 1.0 OD2 A:ASP8 3.2 52.0 1.0 CD A:GLU107 3.3 56.8 1.0 CG A:ASP106 3.5 49.7 1.0 CA A:CA1002 3.5 56.2 1.0 CG A:ASP8 3.5 50.5 1.0 O2A A:DTP400 3.6 72.6 1.0 O A:HOH2007 3.7 41.0 1.0 PA A:DTP400 3.9 75.0 1.0 OE1 A:GLU107 4.3 58.6 1.0 O A:HOH2066 4.4 52.2 1.0 OG A:SER104 4.4 47.2 1.0 CB A:GLU107 4.4 47.0 1.0 O3A A:DTP400 4.4 78.5 1.0 O A:ASP106 4.6 43.0 1.0 C A:ASP106 4.8 44.5 1.0 O5' A:DTP400 4.8 72.7 1.0 CB A:ASP106 4.9 46.5 1.0 N A:GLU107 4.9 44.1 1.0 CB A:ASP8 4.9 47.4 1.0

Calcium binding site 2 out of 3 in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) 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-N7-Gua) with Dna Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:56.2 occ:1.00 O2B A:DTP400 2.4 82.2 1.0 OD1 A:ASP8 2.5 53.8 1.0 O A:PHE9 2.6 39.3 1.0 OD2 A:ASP106 2.7 51.9 1.0 O1A A:DTP400 2.8 75.6 1.0 CG A:ASP8 2.9 50.5 1.0 OD2 A:ASP8 3.0 52.0 1.0 O3A A:DTP400 3.1 78.5 1.0 PB A:DTP400 3.3 80.1 1.0 O A:HOH2008 3.4 58.6 1.0 CA A:CA1001 3.5 75.9 1.0 C A:PHE9 3.6 39.4 1.0 PA A:DTP400 3.7 75.0 1.0 O2G A:DTP400 3.8 84.1 1.0 O A:HOH2006 3.9 41.3 1.0 CG A:ASP106 3.9 49.7 1.0 C A:ASP8 4.0 41.4 1.0 O A:ASP8 4.1 44.0 1.0 CB A:ASP8 4.1 47.4 1.0 N A:PHE9 4.1 39.6 1.0 O1B A:DTP400 4.2 78.5 1.0 O3B A:DTP400 4.2 82.2 1.0 CA A:PHE9 4.4 39.2 1.0 N A:ASP10 4.4 39.4 1.0 O2A A:DTP400 4.5 72.6 1.0 O5' A:DTP400 4.5 72.7 1.0 PG A:DTP400 4.5 85.2 1.0 CA A:ASP8 4.6 43.4 1.0 CA A:ASP10 4.6 40.8 1.0 NZ A:LYS160 4.6 57.9 1.0 OD1 A:ASP106 4.6 50.8 1.0 O A:ASP106 4.9 43.0 1.0 CB A:ASP106 4.9 46.5 1.0 O1G A:DTP400 5.0 86.2 1.0 N A:TYR11 5.0 40.3 1.0

Calcium binding site 3 out of 3 in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) 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-N7-Gua) with Dna Polymerase IV and Incoming Datp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:75.2 occ:1.00 O A:ALA182 2.6 61.4 1.0 O A:HOH2001 2.6 40.9 1.0 O C:HOH2003 2.7 63.1 1.0 O A:HOH2002 2.8 73.7 1.0 O C:HOH2064 2.9 51.2 1.0 O A:ILE187 3.2 59.4 1.0 C A:ALA182 3.8 60.9 1.0 C A:ILE187 4.2 60.1 1.0 CA A:ASP183 4.4 56.9 1.0 OP1 C:DC359 4.5 76.3 1.0 OP2 C:DC359 4.5 73.8 1.0 N A:ASP183 4.6 58.9 1.0 O A:VAL184 4.7 51.7 1.0 C A:ASP183 4.8 56.5 1.0 N A:VAL184 4.8 54.2 1.0 CA A:ALA182 4.8 61.8 1.0 CA A:GLY188 5.0 62.5 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