Calcium in PDB 2agp: Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis

All present enzymatic activity of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis:
2.7.7.7;

The structure of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2agp was solved by H.Ling, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.867, 101.463, 105.642, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 26.4

The structure of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis (pdb code 2agp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2agp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:59.2 occ:1.00 O2B A:DGT401 2.2 0.1 1.0 O A:PHE8 2.2 38.2 1.0 OD1 A:ASP7 2.4 42.5 1.0 OD2 A:ASP105 2.4 59.6 1.0 O3B A:DGT401 3.0 0.6 1.0 PB A:DGT401 3.1 0.7 1.0 C A:PHE8 3.4 38.9 1.0 CG A:ASP7 3.5 40.6 1.0 O2G A:DGT401 3.6 0.3 1.0 CG A:ASP105 3.6 56.5 1.0 MG A:MG403 3.7 49.1 1.0 O A:HOH738 3.8 47.3 1.0 O1B A:DGT401 3.9 0.6 1.0 PG A:DGT401 3.9 0.7 1.0 OD2 A:ASP7 4.0 42.7 1.0 NZ A:LYS159 4.1 61.5 1.0 N A:TYR10 4.3 36.9 1.0 N A:PHE8 4.3 38.7 1.0 O5' A:DGT401 4.3 1.0 1.0 C A:ASP7 4.3 34.8 1.0 O3A A:DGT401 4.3 1.0 1.0 N A:ASP9 4.3 44.6 1.0 CA A:PHE8 4.4 37.9 1.0 O A:ASP7 4.4 35.3 1.0 CA A:ASP9 4.4 45.4 1.0 O1G A:DGT401 4.4 0.9 1.0 OD1 A:ASP105 4.5 60.0 1.0 CB A:ASP105 4.5 53.5 1.0 C A:ASP9 4.5 45.6 1.0 C5' A:DGT401 4.6 0.4 1.0 O A:ASP105 4.7 33.4 1.0 N A:PHE11 4.7 35.5 1.0 O2A A:DGT401 4.7 0.6 1.0 CB A:ASP7 4.7 40.5 1.0 PA A:DGT401 4.8 0.8 1.0 CB A:PHE8 4.8 39.6 1.0 CA A:ASP7 4.9 34.5 1.0 CA A:TYR10 5.0 35.4 1.0 CB A:PHE11 5.0 27.8 1.0

Calcium binding site 2 out of 2 in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:47.4 occ:1.00 O2B B:DGT501 1.9 0.3 1.0 OD1 B:ASP7 2.1 43.5 1.0 O B:PHE8 2.4 30.0 1.0 OD2 B:ASP105 2.4 37.6 1.0 O2G B:DGT501 3.0 0.5 1.0 CG B:ASP7 3.2 40.4 1.0 PB B:DGT501 3.2 0.1 1.0 O B:HOH585 3.5 31.8 1.0 C B:PHE8 3.5 29.2 1.0 O B:HOH1138 3.5 33.2 1.0 OD2 B:ASP7 3.6 43.3 1.0 CG B:ASP105 3.7 37.7 1.0 C5' B:DGT501 3.7 0.9 1.0 O3B B:DGT501 3.8 0.0 1.0 PG B:DGT501 3.8 0.6 1.0 O1B B:DGT501 4.0 0.9 1.0 MG B:MG408 4.0 32.4 1.0 NZ B:LYS159 4.1 55.0 1.0 C B:ASP7 4.1 40.0 1.0 O B:ASP7 4.1 41.4 1.0 N B:PHE8 4.2 30.8 1.0 O1G B:DGT501 4.2 0.1 1.0 CA B:PHE8 4.4 28.9 1.0 N B:ASP9 4.4 35.5 1.0 O3A B:DGT501 4.4 0.8 1.0 CB B:ASP7 4.4 39.3 1.0 O5' B:DGT501 4.5 0.4 1.0 OD1 B:ASP105 4.5 39.2 1.0 N B:TYR10 4.5 31.8 1.0 CA B:ASP9 4.5 37.4 1.0 O B:ASP105 4.6 41.4 1.0 CB B:ASP105 4.6 37.5 1.0 C B:ASP9 4.7 37.8 1.0 CA B:ASP7 4.7 40.1 1.0 C4' B:DGT501 4.8 0.8 1.0 O2A B:DGT501 4.8 0.8 1.0 PA B:DGT501 4.9 1.0 1.0 CB B:PHE8 4.9 32.0 1.0 N B:PHE11 4.9 29.9 1.0 O B:HOH1051 5.0 65.2 1.0

A.Vaisman, H.Ling, R.Woodgate, W.Yang. Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis. Embo J. V. 24 2957 2005.
ISSN: ISSN 0261-4189
PubMed: 16107880
DOI: 10.1038/SJ.EMBOJ.7600786