Calcium in PDB 5jax: Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp

All present enzymatic activity of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp:
2.7.11.12;

The structure of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp, PDB code: 5jax was solved by J.C.Campbell, B.Sankaran, C.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.74 / 1.49
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	47.010, 47.010, 102.590, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 19.9

The structure of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Sodium	(Na)	1 atom

The binding sites of Calcium atom in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp (pdb code 5jax). 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 I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp, PDB code: 5jax:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:30.5 occ:0.75 O A:GLY342 2.2 18.0 1.0 OD1 A:ASP344 2.9 50.0 1.0 C A:GLY342 3.4 14.7 1.0 HA2 A:GLY342 3.8 16.3 1.0 O A:HOH515 4.0 34.4 1.0 HA3 A:GLY342 4.0 16.3 1.0 CA A:GLY342 4.0 13.6 1.0 CG A:ASP344 4.1 62.9 1.0 HG A:SER347 4.2 34.5 1.0 O A:HOH608 4.3 42.2 1.0 H A:ASP344 4.4 24.0 1.0 N A:ASP344 4.4 20.0 1.0 HA A:ASP344 4.4 26.9 1.0 HA A:LEU343 4.4 22.9 1.0 N A:LEU343 4.5 14.2 1.0 C A:LEU343 4.6 17.5 1.0 OD2 A:ASP344 4.7 56.6 1.0 CA A:LEU343 4.8 19.1 1.0 CA A:ASP344 4.9 22.4 1.0 OG A:SER347 4.9 28.8 1.0

Calcium binding site 2 out of 2 in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Br-Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:85.8 occ:1.00 OD2 A:ASP271 2.8 43.8 1.0 OD2 A:ASP314 2.8 40.8 1.0 HB3 A:ARG269 2.9 21.2 1.0 HH21 A:ARG269 3.2 41.4 1.0 CG A:ASP271 3.5 34.2 1.0 OD1 A:ASP271 3.5 18.5 1.0 HE A:ARG269 3.6 48.0 1.0 NH2 A:ARG269 3.6 34.5 1.0 CB A:ARG269 3.7 17.7 1.0 HB2 A:ARG269 3.8 21.2 1.0 CG A:ASP314 3.8 51.2 1.0 NE A:ARG269 3.9 40.0 1.0 HB2 A:ASP314 3.9 16.1 1.0 CZ A:ARG269 4.0 38.6 1.0 HH22 A:ARG269 4.0 41.4 1.0 C A:ARG269 4.0 13.8 1.0 O A:ARG269 4.1 18.8 1.0 O A:GLY270 4.2 15.3 1.0 N A:GLY270 4.2 14.3 1.0 CB A:ASP314 4.4 13.4 1.0 C A:GLY270 4.4 15.0 1.0 H A:GLY270 4.4 17.2 1.0 CA A:ARG269 4.5 14.5 1.0 HH21 A:ARG333 4.6 16.4 1.0 CA A:GLY270 4.7 14.1 1.0 HA2 A:GLY270 4.7 17.0 1.0 HB3 A:ASP314 4.7 16.1 1.0 OD1 A:ASP314 4.8 39.9 1.0 CG A:ARG269 4.8 20.1 1.0 HA A:ARG269 4.9 17.4 1.0 CD A:ARG269 4.9 24.1 1.0 CB A:ASP271 4.9 13.9 1.0 NH1 A:ARG269 4.9 36.2 1.0 O A:HOH621 5.0 50.6 1.0

J.C.Campbell, P.Henning, E.Franz, B.Sankaran, F.W.Herberg, C.Kim. Structural Basis of Analog Specificity in Pkg I and II. Acs Chem. Biol. V. 12 2388 2017.
ISSN: ESSN 1554-8937
PubMed: 28793191
DOI: 10.1021/ACSCHEMBIO.7B00369