Calcium in PDB 2agq: 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: 2agq 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)	26.79 / 2.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.101, 103.009, 52.399, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 25.4

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

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis (pdb code 2agq). 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: 2agq:
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:Ca4001 b:34.3 occ:1.00 OD2 A:ASP105 2.2 33.1 1.0 OD1 A:ASP7 2.2 35.2 1.0 O1A A:DTP1814 2.3 35.5 1.0 O A:PHE8 2.3 30.4 1.0 O2B A:DTP1814 2.6 33.7 1.0 O1G A:DTP1814 2.7 36.0 1.0 O3B A:DTP1814 2.8 40.5 1.0 CG A:ASP7 3.3 32.8 1.0 CG A:ASP105 3.4 36.1 1.0 O A:HOH4004 3.4 33.6 1.0 PB A:DTP1814 3.4 34.4 1.0 PA A:DTP1814 3.5 36.1 1.0 C A:PHE8 3.5 31.1 1.0 PG A:DTP1814 3.6 35.0 1.0 O A:HOH4039 3.7 45.1 1.0 OD2 A:ASP7 3.8 34.3 1.0 O3A A:DTP1814 4.0 35.8 1.0 OD1 A:ASP105 4.0 32.4 1.0 N A:PHE8 4.1 31.5 1.0 C5' A:DTP1814 4.1 29.2 1.0 O A:HOH4100 4.2 39.5 1.0 O5' A:DTP1814 4.2 34.0 1.0 O3G A:DTP1814 4.2 36.1 1.0 NZ A:LYS159 4.3 42.0 1.0 CA A:PHE8 4.3 31.1 1.0 C A:ASP7 4.4 32.2 1.0 N A:ASP9 4.5 31.6 1.0 CB A:ASP105 4.5 32.4 1.0 N A:TYR10 4.5 31.8 1.0 O2A A:DTP1814 4.6 35.3 1.0 CA A:ASP9 4.6 32.6 1.0 CB A:ASP7 4.6 30.6 1.0 C A:ASP9 4.7 31.5 1.0 O A:ASP7 4.8 32.0 1.0 MG A:MG4002 4.8 32.7 1.0 N A:PHE11 4.8 29.2 1.0 O2G A:DTP1814 4.8 39.1 1.0 O1B A:DTP1814 4.8 38.5 1.0 CB A:PHE8 4.9 30.7 1.0 CA A:ASP7 4.9 31.6 1.0 O A:ASP105 4.9 33.5 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 A:Ca4003 b:49.7 occ:1.00 O A:ALA181 2.3 41.4 1.0 O A:ILE186 2.5 34.7 1.0 O B:HOH28 2.6 43.9 1.0 C A:ALA181 3.5 41.2 1.0 C A:ILE186 3.7 35.3 1.0 CA A:ALA181 4.3 42.8 1.0 CA A:GLY187 4.4 39.8 1.0 N A:ASP182 4.5 40.0 1.0 OP1 B:DT12 4.5 39.6 1.0 CA A:ASP182 4.5 39.4 1.0 N A:GLY187 4.5 38.2 1.0 CB A:ALA181 4.7 41.1 1.0 O A:VAL183 4.7 31.4 1.0 CB A:ILE186 4.7 32.5 1.0 CA A:ILE186 4.8 33.8 1.0 OP2 B:DT12 4.8 40.1 1.0 C A:GLY187 4.9 42.4 1.0 C A:ASP182 4.9 37.0 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