Sodium in PDB 5j48: Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp

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

The structure of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp, PDB code: 5j48 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)	34.95 / 1.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	35.510, 59.240, 67.320, 90.00, 100.17, 90.00
R / Rfree (%)	16.3 / 18.9

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

Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp (pdb code 5j48). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp, PDB code: 5j48:
Jump to Sodium binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:19.6 occ:1.00 O A:GLN311 2.2 26.0 1.0 O A:GLU313 2.3 16.2 1.0 O A:LYS308 2.3 14.9 1.0 O2 A:EDO403 2.4 36.5 1.0 O A:HOH573 2.5 24.6 1.0 HO2 A:EDO403 2.9 43.9 1.0 HA A:ALA309 3.2 16.3 1.0 H11 A:EDO403 3.2 59.0 1.0 C A:GLU313 3.3 15.6 1.0 C A:LYS308 3.3 14.4 1.0 C A:GLN311 3.4 27.9 1.0 H A:GLU313 3.5 23.7 1.0 HB2 A:GLU313 3.5 20.7 1.0 N A:GLU313 3.5 19.7 1.0 H A:GLN311 3.6 27.3 1.0 C2 A:EDO403 3.6 55.5 1.0 CA A:GLU313 3.8 17.5 1.0 C1 A:EDO403 3.8 49.2 1.0 CA A:ALA309 3.9 13.6 1.0 C A:GLY312 3.9 20.8 1.0 HA3 A:GLY312 4.0 34.0 1.0 N A:ALA309 4.0 12.0 1.0 CB A:GLU313 4.1 17.2 1.0 HB3 A:LYS308 4.1 19.2 1.0 H21 A:EDO403 4.2 66.5 1.0 C A:ALA309 4.2 15.8 1.0 N A:GLN311 4.2 22.7 1.0 O1 A:EDO403 4.3 45.6 1.0 CA A:GLY312 4.3 28.4 1.0 HA A:ASP314 4.3 16.5 1.0 H22 A:EDO403 4.3 66.5 1.0 N A:GLY312 4.3 30.5 1.0 CA A:GLN311 4.4 39.4 1.0 HA A:LYS308 4.4 14.2 1.0 CA A:LYS308 4.4 11.8 1.0 O A:GLY312 4.5 24.0 1.0 N A:ASP314 4.5 14.7 1.0 HB3 A:GLU313 4.5 20.7 1.0 O A:ALA309 4.5 14.8 1.0 OE1 A:GLU313 4.6 27.6 1.0 H A:VAL315 4.6 17.1 1.0 HA A:GLU313 4.7 21.0 1.0 N A:LEU310 4.8 15.8 1.0 HO1 A:EDO403 4.8 54.8 1.0 CB A:LYS308 4.8 16.1 1.0 O A:HOH518 4.8 22.5 1.0 H12 A:EDO403 4.8 59.0 1.0 H A:ALA309 4.8 14.4 1.0 H A:LEU310 4.9 19.0 1.0 CA A:ASP314 4.9 13.7 1.0 CB A:GLN311 4.9 44.9 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Pkg I'S Carboyl Terminal Cyclic Nucleotide Binding Domain (Cnb-B) in A Complex with 8-Pcpt-Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na407 b:25.6 occ:0.82 O B:GLU313 2.3 32.1 1.0 O B:GLN311 2.4 32.1 1.0 O B:LYS308 2.4 17.2 1.0 O B:HOH571 2.5 29.7 1.0 HA B:ALA309 3.0 21.8 1.0 H B:GLU313 3.1 50.0 1.0 N B:GLU313 3.3 41.7 1.0 C B:GLU313 3.3 26.7 1.0 C B:LYS308 3.4 15.3 1.0 C B:GLN311 3.5 41.3 1.0 H B:GLN311 3.7 30.0 1.0 CA B:GLU313 3.8 48.3 1.0 CA B:ALA309 3.8 18.2 1.0 C B:GLY312 3.9 34.0 1.0 HA3 B:GLY312 3.9 45.3 1.0 N B:ALA309 4.0 16.8 1.0 H B:VAL315 4.1 22.4 1.0 CB B:GLU313 4.1 42.2 1.0 C B:ALA309 4.2 20.8 1.0 CA B:GLY312 4.2 37.7 1.0 HB3 B:LYS308 4.3 20.4 1.0 N B:GLY312 4.3 47.0 1.0 N B:GLN311 4.3 25.0 1.0 O B:ALA309 4.4 20.3 1.0 HA B:ASP314 4.4 37.2 1.0 HB2 B:GLN311 4.4 53.4 1.0 CA B:GLN311 4.5 31.2 1.0 HA B:LYS308 4.5 17.1 1.0 CA B:LYS308 4.5 14.2 1.0 N B:ASP314 4.5 33.9 1.0 O B:GLY312 4.6 41.4 1.0 HA B:GLU313 4.7 57.9 1.0 O B:VAL315 4.8 17.4 1.0 N B:LEU310 4.8 19.0 1.0 H B:ALA309 4.8 20.1 1.0 CB B:LYS308 4.9 17.0 1.0 N B:VAL315 4.9 18.7 1.0 O B:HOH537 4.9 34.8 1.0 H B:LEU310 5.0 22.8 1.0 CA B:ASP314 5.0 31.0 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