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

Enzymatic activity of 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;

Protein crystallography data

The structure of Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2ago 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 / 2.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 99.044, 101.939, 53.017, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.3

Other elements in 2ago:

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

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis (pdb code 2ago). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Fidelity of DPO4: Effect of Metal Ions, Nucleotide Selection and Pyrophosphorolysis, PDB code: 2ago:

Calcium binding site 1 out of 1 in 2ago

Go back to Calcium Binding Sites List in 2ago
Calcium binding site 1 out of 1 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:Ca403

b:58.1
occ:1.00
 OD1 A:ASP7 2.1 52.6 1.0
O A:POP401 2.3 92.4 1.0
O A:PHE8 2.3 41.5 1.0
OD2 A:ASP105 2.4 51.4 1.0
O4 A:POP401 2.8 90.5 1.0
O1 A:POP401 2.9 91.7 1.0
P1 A:POP401 3.1 93.7 1.0
P2 A:POP401 3.1 92.6 1.0
CG A:ASP7 3.2 51.0 1.0
C A:PHE8 3.5 41.7 1.0
O6 A:POP401 3.6 88.8 1.0
CG A:ASP105 3.6 48.9 1.0
O2 A:POP401 3.8 91.5 1.0
OD2 A:ASP7 3.8 51.9 1.0
O A:HOH416 3.9 49.2 1.0
NZ A:LYS159 4.0 63.2 1.0
N A:PHE8 4.0 41.5 1.0
O A:HOH445 4.1 36.0 1.0
C A:ASP7 4.3 45.4 1.0
CA A:PHE8 4.3 42.0 1.0
CB A:ASP105 4.4 47.0 1.0
CB A:ASP7 4.4 49.4 1.0
O3 A:POP401 4.5 93.4 1.0
N A:ASP9 4.5 42.6 1.0
OD1 A:ASP105 4.5 48.3 1.0
O5 A:POP401 4.5 90.1 1.0
CA A:ASP9 4.5 42.7 1.0
N A:TYR10 4.6 38.6 1.0
MG A:MG402 4.6 46.6 1.0
CA A:ASP7 4.7 46.4 1.0
O A:ASP7 4.8 45.7 1.0
O A:ASP105 4.8 44.7 1.0
C A:ASP9 4.8 41.4 1.0
CE A:LYS159 4.8 64.6 1.0
CB A:PHE8 5.0 43.4 1.0

Reference:

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
Page generated: Tue Jul 8 04:19:25 2025

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