Calcium in PDB 5c6c: Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp

All present enzymatic activity of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp:
2.7.11.12;

The structure of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp, PDB code: 5c6c was solved by J.C.Campbell, A.S.Reger, G.Y.Huang, B.Sankaran, J.J.Kim, C.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.23 / 2.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.710, 63.760, 99.540, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.3

The structure of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp also contains other interesting chemical elements:

Cobalt	(Co)	4 atoms
Cadmium	(Cd)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp (pdb code 5c6c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp, PDB code: 5c6c:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca308 b:52.1 occ:1.00 O A:ALA162 2.7 21.6 1.0 N A:THR230 2.9 18.2 1.0 OG1 A:THR230 3.5 30.8 1.0 CB A:THR230 3.6 25.1 1.0 CA A:THR229 3.7 20.5 1.0 C A:THR229 3.7 18.2 1.0 N A:ASN166 3.7 35.9 1.0 CA A:THR230 3.8 27.2 1.0 C A:ALA162 3.8 30.9 1.0 CG2 A:THR229 3.9 24.8 1.0 CB A:ASN166 3.9 24.6 1.0 CA A:ASN166 4.0 27.1 1.0 C A:LYS165 4.1 33.8 1.0 CB A:LYS165 4.2 29.4 1.0 O A:THR230 4.3 22.2 1.0 CB A:THR229 4.4 21.2 1.0 CA A:ALA162 4.4 29.8 1.0 O A:TRP228 4.5 22.7 1.0 O A:LYS165 4.5 43.8 1.0 C A:THR230 4.6 27.6 1.0 ND2 A:ASN166 4.6 26.9 1.0 CA A:LYS165 4.6 39.2 1.0 N A:THR229 4.8 20.2 1.0 CG A:ASN166 4.8 32.7 1.0 CB A:ALA162 4.9 26.5 1.0 N A:LEU163 4.9 23.5 1.0 N A:LYS165 4.9 31.6 1.0 O A:THR229 4.9 16.4 1.0

Calcium binding site 2 out of 2 in the Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pkg II'S Amino Terminal Cyclic Nucleotide Binding Domain (Cnb-A) in A Complex with Camp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca306 b:74.9 occ:1.00 OD1 B:ASP258 2.5 61.6 1.0 OH B:TYR185 2.7 62.3 1.0 NE2 B:HIS204 2.8 57.7 1.0 CG B:ASP258 3.1 51.9 1.0 OD2 B:ASP258 3.1 56.8 1.0 CD2 B:HIS204 3.4 47.8 1.0 CE1 B:HIS204 3.8 56.8 1.0 CZ B:TYR185 3.9 53.3 1.0 NH1 B:ARG187 4.0 67.7 1.0 CE1 B:TYR185 4.5 44.9 1.0 CB B:ASP258 4.5 44.6 1.0 CG B:HIS204 4.7 49.9 1.0 CE2 B:TYR185 4.8 50.0 1.0 ND1 B:HIS204 4.8 51.7 1.0

J.C.Campbell, J.J.Kim, K.Y.Li, G.Y.Huang, A.S.Reger, S.Matsuda, B.Sankaran, T.M.Link, K.Yuasa, J.E.Ladbury, D.E.Casteel, C.Kim. Structural Basis of Cyclic Nucleotide Selectivity in Cgmp-Dependent Protein Kinase II. J.Biol.Chem. V. 291 5623 2016.
ISSN: ESSN 1083-351X
PubMed: 26769964
DOI: 10.1074/JBC.M115.691303