Calcium in PDB 5bv6: Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp

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

The structure of Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp, PDB code: 5bv6 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)	40.77 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.344, 50.479, 69.167, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.1

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

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Pkg II'S Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp (pdb code 5bv6). 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 Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp, PDB code: 5bv6:
Jump to Calcium binding site number: 1; 2;

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


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 Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:27.6 occ:1.00 OD2 A:ASP364 2.4 29.3 1.0 O A:HOH705 2.5 39.3 1.0 O A:HOH695 2.5 29.8 1.0 CG A:ASP364 3.6 30.0 1.0 O A:HOH663 3.8 28.6 1.0 O A:HOH606 3.9 36.4 1.0 OD1 A:ASP364 4.1 21.3 1.0 O A:HOH645 4.5 24.8 1.0 O A:HOH648 4.6 27.8 1.0 CB A:ASP364 4.8 26.0 1.0 O A:HOH704 4.9 37.0 1.0 NZ A:LYS358 5.0 21.9 1.0

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


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 Carboxyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:64.6 occ:1.00 O A:HOH702 3.0 46.6 1.0 NE2 A:GLN276 4.4 64.0 1.0 CE1 A:TYR277 4.4 30.9 1.0 CZ A:TYR277 4.4 38.0 1.0 OH A:TYR277 4.6 40.8 1.0 CG A:GLN276 4.8 51.4 1.0 CD1 A:TYR277 4.8 17.9 1.0 CE2 A:TYR277 4.9 32.3 1.0 CB A:PHE280 5.0 26.6 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