Chlorine 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
Sodium	(Na)	2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404 b:23.6 occ:1.00 CL1 A:6FW404 0.0 23.6 1.0 C22 A:6FW404 1.7 19.6 1.0 C21 A:6FW404 2.7 18.6 1.0 C23 A:6FW404 2.7 18.1 1.0 H211 A:6FW404 2.8 22.3 1.0 H231 A:6FW404 2.8 21.8 1.0 H11 A:EDO402 2.8 30.4 1.0 HD1 A:TYR351 3.4 40.2 0.5 HD1 A:TYR351 3.4 40.2 0.5 HH2 A:TRP304 3.4 21.2 1.0 CD1 A:TYR351 3.6 33.5 0.5 CD1 A:TYR351 3.6 33.5 0.5 CH2 A:TRP304 3.7 17.7 1.0 HE1 A:TYR351 3.7 39.4 0.5 HE1 A:TYR351 3.7 39.4 0.5 CE1 A:TYR351 3.8 32.8 0.5 CE1 A:TYR351 3.8 32.8 0.5 H21 A:EDO402 3.8 33.2 1.0 C1 A:EDO402 3.8 25.3 1.0 H22 A:EDO402 3.9 33.2 1.0 C20 A:6FW404 4.0 16.5 1.0 C24 A:6FW404 4.0 16.5 1.0 CB A:LYS349 4.0 33.4 1.0 CZ2 A:TRP304 4.0 19.5 1.0 C2 A:EDO402 4.1 27.7 1.0 HZ2 A:TRP304 4.1 23.4 1.0 CZ3 A:TRP304 4.2 19.3 1.0 HB3 A:TYR351 4.3 42.3 0.5 CG A:TYR351 4.3 34.4 0.5 HB3 A:TYR351 4.3 42.3 0.5 CG A:TYR351 4.3 34.3 0.5 HZ3 A:TRP304 4.4 23.1 1.0 H12 A:EDO402 4.4 30.4 1.0 C19 A:6FW404 4.5 15.0 1.0 CZ A:TYR351 4.6 33.0 0.5 CZ A:TYR351 4.6 33.0 0.5 O1 A:EDO402 4.7 18.1 1.0 O A:HOH605 4.7 47.1 1.0 H201 A:6FW404 4.8 19.8 1.0 H241 A:6FW404 4.8 19.8 1.0 CE2 A:TRP304 4.9 19.0 1.0 CB A:TYR351 4.9 35.2 0.5 CB A:TYR351 4.9 35.2 0.5 HO1 A:EDO402 4.9 21.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl405 b:25.5 occ:1.00 CL1 B:6FW405 0.0 25.5 1.0 C22 B:6FW405 1.7 20.5 1.0 C23 B:6FW405 2.7 18.5 1.0 C21 B:6FW405 2.7 19.0 1.0 H231 B:6FW405 2.8 22.2 1.0 H211 B:6FW405 2.8 22.8 1.0 H22 B:EDO404 3.2 22.2 1.0 HH2 B:TRP304 3.5 21.9 1.0 H21 B:EDO404 3.6 22.2 1.0 CH2 B:TRP304 3.8 18.3 1.0 C2 B:EDO404 3.9 18.5 1.0 C24 B:6FW405 4.0 17.4 1.0 C20 B:6FW405 4.0 16.5 1.0 CZ2 B:TRP304 4.1 22.0 1.0 HZ2 B:TRP304 4.2 26.4 1.0 CZ3 B:TRP304 4.3 20.2 1.0 HZ3 B:TRP304 4.5 24.2 1.0 C19 B:6FW405 4.5 15.4 1.0 H12 B:EDO404 4.7 55.6 1.0 HO2 B:EDO404 4.7 26.0 1.0 H241 B:6FW405 4.7 20.8 1.0 O B:HOH524 4.8 34.5 1.0 H201 B:6FW405 4.8 19.8 1.0 O2 B:EDO404 4.9 21.6 1.0 C1 B:EDO404 4.9 46.3 1.0 CE2 B:TRP304 5.0 17.7 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