Calcium in PDB 1rpz: T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna

All present enzymatic activity of T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna:
2.7.1.78;

The structure of T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna, PDB code: 1rpz was solved by J.H.Eastberg, J.Pelletier, B.L.Stoddard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.16 / 2.90
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.565, 92.633, 122.665, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 30.2

The binding sites of Calcium atom in the T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna (pdb code 1rpz). 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 T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna, PDB code: 1rpz:

Calcium binding site 1 out of 1 in the T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of T4 Polynucleotide Kinase Bound to 5'-Tgcac-3' Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:70.1 occ:1.00 O A:ASP167 2.2 77.4 1.0 OD1 A:ASP278 2.3 90.2 1.0 OD1 A:ASP165 2.6 60.9 1.0 CG A:ASP278 3.2 90.2 1.0 CG A:ASP165 3.3 60.9 1.0 C A:ASP167 3.4 77.4 1.0 OD2 A:ASP165 3.5 60.9 1.0 OD2 A:ASP278 3.5 90.2 1.0 OD1 A:ASP277 3.7 66.1 1.0 CB A:ASP167 4.1 0.5 1.0 CE A:MSE173 4.2 0.4 1.0 CA A:ASP167 4.2 77.4 1.0 OG1 A:THR169 4.3 72.1 1.0 N A:ARG279 4.4 71.6 1.0 N A:GLY168 4.4 74.9 1.0 CB A:ARG279 4.5 76.2 1.0 N A:ASP167 4.5 77.4 1.0 N A:ASP278 4.6 69.6 1.0 CB A:ASP278 4.6 90.2 1.0 CB A:ASP165 4.6 60.9 1.0 CA A:GLY168 4.6 74.9 1.0 NZ A:LYS258 4.7 77.3 1.0 N A:THR169 4.7 54.4 1.0 OD2 A:ASP167 4.7 0.5 1.0 CG A:ASP277 4.8 66.1 1.0 CG A:ASP167 4.9 0.5 1.0 CA A:ASP278 4.9 69.6 1.0 C A:ASP278 5.0 69.6 1.0

J.H.Eastberg, J.Pelletier, B.L.Stoddard. Recognition of Dna Substrates By T4 Bacteriophage Polynucleotide Kinase. Nucleic Acids Res. V. 32 653 2004.
ISSN: ISSN 0305-1048
PubMed: 14754987
DOI: 10.1093/NAR/GKH212