Calcium in PDB 3pw5: Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) with Dna Polymerase IV and Incoming Dttp

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

The structure of Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-N7-Gua) with Dna Polymerase IV and Incoming Dttp, PDB code: 3pw5 was solved by S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.667, 104.415, 52.510, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 28.3

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 Dttp (pdb code 3pw5). 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 Dttp, PDB code: 3pw5:
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 Dttp


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:51.0 occ:1.00 OD1 A:ASP8 2.3 42.0 1.0 O2B A:TTP400 2.4 79.2 1.0 O A:PHE9 2.4 35.9 1.0 OD2 A:ASP106 2.8 42.5 1.0 O1A A:TTP400 2.9 75.3 1.0 O3A A:TTP400 3.1 77.4 1.0 CA A:CA1002 3.2 68.2 1.0 PB A:TTP400 3.2 77.9 1.0 CG A:ASP8 3.3 40.6 1.0 CG A:ASP106 3.3 39.8 1.0 C A:PHE9 3.5 34.3 1.0 PA A:TTP400 3.7 75.1 1.0 OD2 A:ASP8 3.7 44.1 1.0 O1B A:TTP400 3.7 74.5 1.0 N A:PHE9 3.8 33.5 1.0 OD1 A:ASP106 3.9 42.8 1.0 CB A:ASP106 4.1 37.1 1.0 CA A:PHE9 4.1 33.3 1.0 O2G A:TTP400 4.2 80.9 1.0 C A:ASP8 4.3 35.2 1.0 O2A A:TTP400 4.4 76.7 1.0 O3B A:TTP400 4.5 79.0 1.0 N A:ASP10 4.5 35.3 1.0 CB A:ASP8 4.6 38.1 1.0 CA A:ASP10 4.7 38.2 1.0 CB A:PHE9 4.7 32.0 1.0 CA A:ASP8 4.7 36.3 1.0 O A:ASP106 4.7 40.0 1.0 O A:ASP8 4.8 37.4 1.0 O5' A:TTP400 4.8 74.5 1.0 N A:TYR11 4.8 35.3 1.0 C A:ASP10 4.9 37.2 1.0 PG A:TTP400 5.0 82.8 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 Dttp


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:68.2 occ:1.00 OD2 A:ASP106 2.7 42.5 1.0 OE2 A:GLU107 2.8 53.9 1.0 CD A:GLU107 3.0 52.7 1.0 O1A A:TTP400 3.1 75.3 1.0 CG A:GLU107 3.1 48.5 1.0 OD2 A:ASP8 3.1 44.1 1.0 CA A:CA1001 3.2 51.0 1.0 O2A A:TTP400 3.2 76.7 1.0 OD1 A:ASP8 3.4 42.0 1.0 CG A:ASP8 3.5 40.6 1.0 OD1 A:ASP106 3.5 42.8 1.0 CG A:ASP106 3.5 39.8 1.0 PA A:TTP400 3.6 75.1 1.0 OE1 A:GLU107 3.8 54.2 1.0 O3A A:TTP400 3.9 77.4 1.0 CB A:GLU107 4.6 42.5 1.0 CB A:ASP8 4.7 38.1 1.0 O2B A:TTP400 4.9 79.2 1.0 O3' C:DC359 4.9 41.6 1.0 CB A:ASP106 4.9 37.1 1.0 NZ A:LYS160 5.0 47.8 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 Dttp


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 Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:73.1 occ:1.00 O A:HOH2001 2.7 24.9 1.0 O A:ILE187 2.8 50.9 1.0 O A:ALA182 2.8 51.9 1.0 C A:ILE187 3.6 50.6 1.0 OP2 C:DC359 4.0 40.5 1.0 OP1 C:DC359 4.0 42.0 1.0 C A:ALA182 4.0 52.6 1.0 CA A:GLY188 4.3 54.5 1.0 N A:GLY188 4.3 52.6 1.0 P C:DC359 4.5 41.4 1.0 CA A:ILE187 4.5 48.4 1.0 N A:ILE187 4.6 47.8 1.0 O A:VAL184 4.6 42.7 1.0 CB A:ILE187 4.7 46.6 1.0 C A:GLY188 4.9 56.1 1.0 CA A:ASP183 4.9 49.9 1.0 CA A:ALA182 4.9 53.6 1.0 N A:ASP183 4.9 51.1 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