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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5j48:

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

Chlorine Binding Sites:

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 5j48

Go back to Chlorine Binding Sites List in 5j48
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 5j48

Go back to Chlorine Binding Sites List in 5j48
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

Reference:

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
Page generated: Sat Dec 12 11:52:11 2020

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