Calcium in PDB 2ibk: Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap

All present enzymatic activity of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap:
2.7.7.7;

The structure of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap, PDB code: 2ibk was solved by J.Bauer, H.Ling, J.M.Sayer, G.Xing, H.Yagi, D.M.Jerina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.20 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.714, 100.473, 52.332, 90.00, 90.00, 90.00
R / Rfree (%)	25 / 27.2

The binding sites of Calcium atom in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap (pdb code 2ibk). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap, PDB code: 2ibk:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:54.3 occ:1.00 OD1 A:ASP7 2.1 47.0 1.0 O A:PHE8 2.3 40.0 1.0 O5 A:POP405 2.3 68.2 1.0 OD2 A:ASP105 2.3 43.4 1.0 O2 A:POP405 2.3 65.6 1.0 O A:HOH492 2.7 50.7 1.0 P1 A:POP405 3.2 66.2 1.0 O1 A:POP405 3.3 69.7 1.0 CG A:ASP7 3.3 43.4 1.0 C A:PHE8 3.4 38.9 1.0 P2 A:POP405 3.4 67.1 1.0 CG A:ASP105 3.4 42.7 1.0 O A:POP405 3.7 68.0 1.0 O A:HOH420 3.8 68.0 1.0 O4 A:POP405 3.8 66.0 1.0 O A:HOH538 3.9 70.6 1.0 OD2 A:ASP7 3.9 47.4 1.0 CA A:CA402 4.0 66.5 1.0 N A:PHE8 4.0 38.6 1.0 O A:HOH500 4.2 45.9 1.0 OD1 A:ASP105 4.2 42.4 1.0 N A:ASP9 4.3 40.4 1.0 C A:ASP7 4.3 39.5 1.0 CA A:PHE8 4.3 38.2 1.0 CB A:ASP105 4.3 39.0 1.0 CA A:ASP9 4.3 38.8 1.0 N A:TYR10 4.3 36.4 1.0 O A:ASP105 4.5 38.2 1.0 NZ A:LYS159 4.5 66.7 1.0 CB A:ASP7 4.5 41.5 1.0 C A:ASP9 4.5 38.0 1.0 O A:ASP7 4.7 40.0 1.0 O3 A:POP405 4.7 67.3 1.0 CA A:ASP7 4.7 39.4 1.0 N A:PHE11 4.8 35.5 1.0 O6 A:POP405 4.8 68.7 1.0 O A:HOH513 4.9 76.7 1.0 CB A:PHE8 4.9 36.4 1.0 OE2 A:GLU106 5.0 53.1 1.0

Calcium binding site 2 out of 2 in the Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bypass of Major Benzopyrene-Dg Adduct By Y-Family Dna Polymerase with Unique Structural Gap within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:66.5 occ:1.00 OE2 A:GLU106 2.3 53.1 1.0 O A:HOH500 2.3 45.9 1.0 O A:HOH492 2.4 50.7 1.0 OP1 D:DT14 2.5 63.0 1.0 OD1 A:ASP105 2.6 42.4 1.0 O A:HOH465 2.7 65.7 1.0 OD2 A:ASP105 3.1 43.4 1.0 CG A:ASP105 3.2 42.7 1.0 CD A:GLU106 3.3 46.9 1.0 O1 A:POP405 3.5 69.7 1.0 O A:HOH538 3.5 70.6 1.0 CG A:GLU106 3.9 45.0 1.0 P D:DT14 3.9 64.0 1.0 CA A:CA401 4.0 54.3 1.0 OG A:SER103 4.1 39.6 1.0 C5' D:DT14 4.3 65.0 1.0 OE1 A:GLU106 4.4 49.1 1.0 O5' D:DT14 4.4 65.7 1.0 O3' D:DA13 4.6 63.0 1.0 OD1 A:ASP7 4.6 47.0 1.0 OD2 A:ASP7 4.7 47.4 1.0 O A:HOH513 4.7 76.7 1.0 O D:HOH26 4.7 69.3 1.0 CB A:ASP105 4.7 39.0 1.0 P1 A:POP405 4.9 66.2 1.0 O2 A:POP405 4.9 65.6 1.0 OP2 D:DT14 5.0 64.2 1.0

J.Bauer, G.Xing, H.Yagi, J.M.Sayer, D.M.Jerina, H.Ling. A Structural Gap in DPO4 Supports Mutagenic Bypass of A Major Benzo[A]Pyrene Dg Adduct in Dna Through Template Misalignment. Proc.Natl.Acad.Sci.Usa V. 104 14905 2007.
ISSN: ISSN 0027-8424
PubMed: 17848527
DOI: 10.1073/PNAS.0700717104