Calcium in PDB 3pw2: Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Dttp

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

The structure of Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Dttp, PDB code: 3pw2 was solved by S.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.09 / 2.74
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.247, 104.407, 52.356, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 29.4

The binding sites of Calcium atom in the Ternary Complex of Aflatoxin B1 Adduct Modified Dna (AFB1-Fapy) with Dna Polymerase IV and Incoming Dttp (pdb code 3pw2). 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 Dttp, PDB code: 3pw2:
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 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-Fapy) with Dna Polymerase IV and Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:39.7 occ:1.00 O A:ALA182 2.7 37.7 1.0 O C:HOH2001 2.8 17.3 1.0 O C:HOH2002 2.8 19.4 1.0 O A:ILE187 3.0 27.5 1.0 O C:HOH2003 3.0 17.2 1.0 O A:HOH2004 3.0 39.1 1.0 C A:ALA182 3.8 36.8 1.0 C A:ILE187 4.1 27.4 1.0 OP2 C:DC359 4.4 21.5 1.0 CA A:GLY188 4.5 32.0 1.0 CA A:ALA182 4.5 36.4 1.0 CB A:ALA182 4.5 35.0 1.0 N A:ASP183 4.7 36.5 1.0 N A:GLY188 4.8 28.5 1.0 CA A:ASP183 4.8 35.1 1.0 C A:GLY188 4.9 34.3 1.0 OP1 C:DC359 4.9 21.9 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 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-Fapy) with Dna Polymerase IV and Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:15.5 occ:1.00 O2B A:TTP400 2.5 30.4 1.0 OD2 A:ASP106 2.6 24.9 1.0 O A:PHE9 2.6 17.9 1.0 OD1 A:ASP8 2.7 30.2 1.0 O3A A:TTP400 2.9 28.9 1.0 O2G A:TTP400 2.9 32.3 1.0 O A:HOH2026 3.0 24.2 1.0 OD2 A:ASP8 3.0 26.1 1.0 O1A A:TTP400 3.1 31.4 1.0 CG A:ASP8 3.2 26.2 1.0 CA A:CA1003 3.3 39.2 1.0 PB A:TTP400 3.4 26.9 1.0 PA A:TTP400 3.6 27.4 1.0 C A:PHE9 3.8 19.1 1.0 CG A:ASP106 3.8 22.0 1.0 PG A:TTP400 3.9 32.2 1.0 O2A A:TTP400 3.9 31.5 1.0 O3B A:TTP400 3.9 30.8 1.0 O1G A:TTP400 4.2 33.4 1.0 N A:PHE9 4.3 19.9 1.0 NZ A:LYS160 4.4 41.3 1.0 OD1 A:ASP106 4.4 20.8 1.0 CB A:ASP8 4.5 21.5 1.0 O1B A:TTP400 4.5 20.9 1.0 C A:ASP8 4.6 20.3 1.0 CA A:PHE9 4.6 18.6 1.0 N A:ASP10 4.7 21.1 1.0 N A:TYR11 4.7 15.3 1.0 O A:HOH2027 4.7 0.9 1.0 CA A:ASP10 4.7 21.3 1.0 O A:HOH2044 4.8 43.5 1.0 CB A:ASP106 4.8 20.6 1.0 O5' A:TTP400 4.9 36.5 1.0 CA A:ASP8 4.9 19.8 1.0 C A:ASP10 5.0 18.8 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 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-Fapy) with Dna Polymerase IV and Incoming Dttp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:39.2 occ:1.00 OD1 A:ASP106 2.9 20.8 1.0 OD2 A:ASP8 2.9 26.1 1.0 O2A A:TTP400 3.0 31.5 1.0 O A:HOH2044 3.0 43.5 1.0 OD2 A:ASP106 3.0 24.9 1.0 OE2 A:GLU107 3.0 36.2 1.0 CD A:GLU107 3.1 34.6 1.0 O1A A:TTP400 3.1 31.4 1.0 CG A:GLU107 3.1 31.3 1.0 CA A:CA1002 3.3 15.5 1.0 CG A:ASP106 3.3 22.0 1.0 O A:HOH2026 3.6 24.2 1.0 PA A:TTP400 3.6 27.4 1.0 OE1 A:GLU107 3.7 36.9 1.0 CG A:ASP8 4.0 26.2 1.0 O3A A:TTP400 4.2 28.9 1.0 OG A:SER104 4.3 31.8 1.0 O A:HOH2028 4.5 38.5 1.0 CB A:GLU107 4.6 26.5 1.0 OD1 A:ASP8 4.6 30.2 1.0 CB A:ASP106 4.8 20.6 1.0 O3' C:DC359 4.9 29.9 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