Calcium in PDB 1rrc: T4 Polynucleotide Kinase Bound to 5'-Gtc-3' Ssdna

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

The structure of T4 Polynucleotide Kinase Bound to 5'-Gtc-3' Ssdna, PDB code: 1rrc 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)	38.36 / 2.46
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	81.132, 92.976, 124.137, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 27.4

The binding sites of Calcium atom in the T4 Polynucleotide Kinase Bound to 5'-Gtc-3' Ssdna (pdb code 1rrc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the T4 Polynucleotide Kinase Bound to 5'-Gtc-3' Ssdna, PDB code: 1rrc:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the T4 Polynucleotide Kinase Bound to 5'-Gtc-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'-Gtc-3' Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca700 b:51.9 occ:1.00 O A:ASP167 2.2 36.5 1.0 OD1 A:ASP278 2.3 42.6 1.0 OD1 A:ASP165 2.5 38.6 1.0 CG A:ASP165 3.3 36.6 1.0 C A:ASP167 3.4 36.4 1.0 CG A:ASP278 3.5 42.2 1.0 OD2 A:ASP165 3.6 37.6 1.0 OD1 A:ASP277 3.8 40.5 1.0 OD2 A:ASP278 4.0 41.8 1.0 CB A:ASP167 4.0 39.1 1.0 CA A:ASP167 4.1 37.8 1.0 OG1 A:THR169 4.3 31.0 1.0 N A:ASP167 4.3 36.4 1.0 N A:GLY168 4.4 35.5 1.0 N A:ARG279 4.5 37.4 1.0 CB A:ASP165 4.5 37.1 1.0 CB A:ARG279 4.5 40.4 1.0 CA A:GLY168 4.6 35.9 1.0 N A:ASP278 4.6 36.7 1.0 CB A:ASP278 4.7 40.3 1.0 NZ A:LYS258 4.8 44.6 1.0 N A:THR169 4.9 35.1 1.0 CG A:ASP277 4.9 37.3 1.0

Calcium binding site 2 out of 2 in the T4 Polynucleotide Kinase Bound to 5'-Gtc-3' Ssdna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of T4 Polynucleotide Kinase Bound to 5'-Gtc-3' Ssdna within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:56.2 occ:1.00 OH A:TYR140 3.0 39.4 1.0 N A:TRP116 3.9 32.1 1.0 OD1 A:ASP255 3.9 47.3 1.0 NH2 A:ARG288 4.0 39.5 1.0 CZ A:TYR140 4.0 37.4 1.0 CA A:PRO115 4.1 32.8 1.0 CB A:PRO115 4.2 32.4 1.0 CB A:TRP116 4.5 32.2 1.0 CG A:ASP255 4.5 44.6 1.0 C A:PRO115 4.5 32.9 1.0 OD2 A:ASP255 4.6 44.8 1.0 CE1 A:TYR140 4.7 35.4 1.0 CZ A:ARG288 4.8 40.3 1.0 CA A:TRP116 4.8 33.5 1.0 CE2 A:TYR140 4.9 35.7 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