Chlorine in PDB 7kyh: Botulism Neurooxin Light Chain A App Form

The structure of Botulism Neurooxin Light Chain A App Form, PDB code: 7kyh was solved by M.E.Ortega, N.T.Salzameda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.09 / 2.91
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.315, 84.05, 99.723, 103.78, 91.84, 108.67
R / Rfree (%)	13.8 / 17.3

The structure of Botulism Neurooxin Light Chain A App Form also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Chlorine atom in the Botulism Neurooxin Light Chain A App Form (pdb code 7kyh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Botulism Neurooxin Light Chain A App Form, PDB code: 7kyh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:2.9 occ:1.00 CL01 A:XBM502 0.0 2.9 1.0 C17 A:XBM502 1.8 2.7 1.0 O A:PRO69 2.4 81.9 1.0 C18 A:XBM502 2.7 3.0 1.0 C16 A:XBM502 2.8 2.9 1.0 C A:PRO69 3.1 95.0 1.0 CG A:PRO69 3.2 125.3 1.0 O A:ASP370 3.3 83.0 1.0 CD A:PRO69 3.3 126.9 1.0 CG1 A:VAL70 3.5 92.1 1.0 CB A:VAL70 3.6 88.0 1.0 N A:VAL70 3.7 87.0 1.0 CA A:VAL70 3.9 84.6 1.0 C19 A:XBM502 3.9 3.5 1.0 CA A:PRO69 3.9 104.5 1.0 CB A:PRO69 4.0 115.4 1.0 N A:PRO69 4.0 114.3 1.0 C15 A:XBM502 4.1 3.2 1.0 C A:ASP370 4.4 97.2 1.0 C20 A:XBM502 4.6 3.5 1.0 C A:PHE369 4.8 105.3 1.0 CB A:PHE369 4.8 113.3 1.0 N A:ASP370 4.8 108.5 1.0 CA A:PHE369 4.9 103.0 1.0 CG2 A:VAL70 4.9 86.2 1.0

Chlorine binding site 2 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:4.4 occ:1.00 CL02 A:XBM502 0.0 4.4 1.0 C19 A:XBM502 1.8 3.5 1.0 C20 A:XBM502 2.7 3.5 1.0 C18 A:XBM502 2.7 3.0 1.0 C12 A:XBM502 3.6 14.7 1.0 C13 A:XBM502 3.8 14.1 1.0 C17 A:XBM502 3.9 2.7 1.0 C15 A:XBM502 4.0 3.2 1.0 C11 A:XBM502 4.0 13.8 1.0 CA A:PHE369 4.2 103.0 1.0 C14 A:XBM502 4.2 13.1 1.0 C16 A:XBM502 4.3 2.9 1.0 C10 A:XBM502 4.4 12.2 1.0 CB A:PHE369 4.5 113.3 1.0 C09 A:XBM502 4.5 9.6 1.0 N A:PHE369 4.5 112.1 1.0

Chlorine binding site 3 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:4.4 occ:1.00 CL01 B:XBM502 0.0 4.4 1.0 C17 B:XBM502 1.8 4.0 1.0 C18 B:XBM502 2.7 4.2 1.0 C16 B:XBM502 2.8 4.2 1.0 CB B:VAL70 3.4 81.4 1.0 O B:ASP370 3.5 93.9 1.0 CG B:PRO69 3.5 124.7 1.0 N B:VAL70 3.6 92.7 1.0 CD B:PRO69 3.7 106.2 1.0 CA B:VAL70 3.7 78.5 1.0 C19 B:XBM502 3.9 4.8 1.0 C15 B:XBM502 4.1 4.8 1.0 C B:PRO69 4.1 106.1 1.0 CG1 B:VAL70 4.3 86.8 1.0 CG2 B:VAL70 4.4 85.0 1.0 C B:ASP370 4.4 99.0 1.0 C20 B:XBM502 4.5 5.1 1.0 N B:PRO69 4.6 107.7 1.0 O B:PRO69 4.6 82.6 1.0 CB B:PRO69 4.6 125.3 1.0 CB B:PHE369 4.7 114.8 1.0 C B:PHE369 4.7 115.1 1.0 CA B:PRO69 4.8 114.7 1.0 N B:ASP370 4.9 113.9 1.0 CA B:PHE369 4.9 111.9 1.0

Chlorine binding site 4 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:6.3 occ:1.00 CL02 B:XBM502 0.0 6.3 1.0 C19 B:XBM502 1.7 4.8 1.0 C20 B:XBM502 2.6 5.1 1.0 C18 B:XBM502 2.7 4.2 1.0 C12 B:XBM502 3.7 18.9 1.0 C17 B:XBM502 3.9 4.0 1.0 C11 B:XBM502 3.9 17.8 1.0 C13 B:XBM502 3.9 18.3 1.0 C15 B:XBM502 4.0 4.8 1.0 CA B:PHE369 4.2 111.9 1.0 C10 B:XBM502 4.2 16.7 1.0 C14 B:XBM502 4.3 16.8 1.0 C16 B:XBM502 4.4 4.2 1.0 CB B:PHE369 4.4 114.8 1.0 O B:LEU367 4.5 138.7 1.0 C09 B:XBM502 4.5 13.6 1.0 CD2 B:LEU367 4.6 131.1 1.0 CD1 B:LEU367 4.7 100.9 1.0 N B:PHE369 4.7 112.8 1.0 C B:LEU367 4.9 104.3 1.0 CA B:LEU367 4.9 96.2 1.0

Chlorine binding site 5 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl502 b:7.5 occ:1.00 CL01 C:XBM502 0.0 7.5 1.0 C17 C:XBM502 1.8 6.1 1.0 C18 C:XBM502 2.7 6.7 1.0 C16 C:XBM502 2.7 6.5 1.0 O C:ASP370 3.2 86.2 1.0 CB C:VAL70 3.3 88.1 1.0 CG C:PRO69 3.5 113.8 1.0 N C:VAL70 3.6 92.5 1.0 CD C:PRO69 3.7 115.9 1.0 CA C:VAL70 3.7 81.3 1.0 C C:PRO69 3.8 100.3 1.0 CG1 C:VAL70 3.8 91.3 1.0 C19 C:XBM502 3.9 8.6 1.0 O C:PRO69 3.9 72.8 1.0 C15 C:XBM502 4.1 8.2 1.0 C C:ASP370 4.3 94.5 1.0 CG2 C:VAL70 4.4 86.1 1.0 N C:PRO69 4.4 107.3 1.0 CB C:PRO69 4.5 107.8 1.0 CA C:PRO69 4.5 102.9 1.0 C20 C:XBM502 4.6 9.2 1.0 C C:PHE369 4.7 104.5 1.0 CB C:PHE369 4.7 121.7 1.0 N C:ASP370 4.8 97.5 1.0 CA C:PHE369 4.9 114.5 1.0

Chlorine binding site 6 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl502 b:11.4 occ:1.00 CL02 C:XBM502 0.0 11.4 1.0 C19 C:XBM502 1.7 8.6 1.0 C20 C:XBM502 2.6 9.2 1.0 C18 C:XBM502 2.7 6.7 1.0 C12 C:XBM502 3.6 22.9 1.0 C13 C:XBM502 3.8 22.3 1.0 C11 C:XBM502 3.9 20.7 1.0 C17 C:XBM502 3.9 6.1 1.0 C15 C:XBM502 4.0 8.2 1.0 C10 C:XBM502 4.2 20.1 1.0 CA C:PHE369 4.2 114.5 1.0 C14 C:XBM502 4.3 20.7 1.0 C16 C:XBM502 4.4 6.5 1.0 C09 C:XBM502 4.4 17.1 1.0 CB C:PHE369 4.5 121.7 1.0 N C:PHE369 4.7 115.9 1.0 CA C:LEU367 4.9 81.9 1.0

Chlorine binding site 7 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl502 b:34.0 occ:1.00 CL01 D:XBM502 0.0 34.0 1.0 C17 D:XBM502 1.8 25.8 1.0 O D:PRO69 2.4 111.0 1.0 C18 D:XBM502 2.8 28.0 1.0 C16 D:XBM502 2.8 27.8 1.0 C D:PRO69 3.1 127.4 1.0 O D:ASP370 3.2 115.8 1.0 CG D:PRO69 3.5 124.3 1.0 CB D:VAL70 3.6 117.5 1.0 CA D:VAL70 3.7 110.4 1.0 N D:VAL70 3.7 118.4 1.0 CD D:PRO69 3.8 126.9 1.0 C19 D:XBM502 4.0 36.0 1.0 CB D:PRO69 4.1 124.9 1.0 CA D:PRO69 4.1 126.9 1.0 C15 D:XBM502 4.2 34.0 1.0 C D:ASP370 4.3 126.4 1.0 N D:PRO69 4.4 124.4 1.0 CG2 D:VAL70 4.4 123.2 1.0 CG1 D:VAL70 4.6 121.2 1.0 C20 D:XBM502 4.6 38.3 1.0 N D:ASP370 4.8 134.2 1.0 CB D:PHE369 4.8 148.0 1.0 C D:PHE369 4.8 135.1 1.0 CA D:ASP370 5.0 130.9 1.0

Chlorine binding site 8 out of 8 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl502 b:39.0 occ:1.00 CL02 D:XBM502 0.0 39.0 1.0 C19 D:XBM502 1.8 36.0 1.0 C20 D:XBM502 2.7 38.3 1.0 C18 D:XBM502 2.7 28.0 1.0 C12 D:XBM502 3.5 48.8 1.0 C13 D:XBM502 3.7 48.7 1.0 C11 D:XBM502 3.8 49.7 1.0 C15 D:XBM502 4.0 34.0 1.0 C17 D:XBM502 4.0 25.8 1.0 C14 D:XBM502 4.1 49.8 1.0 CA D:PHE369 4.2 142.5 1.0 C10 D:XBM502 4.3 48.2 1.0 CB D:PHE369 4.4 148.0 1.0 C09 D:XBM502 4.4 44.2 1.0 C16 D:XBM502 4.5 27.8 1.0 N D:PHE369 4.8 144.3 1.0 CA D:LEU367 4.9 128.6 1.0 C D:LEU367 5.0 107.7 1.0

M.Amezcua, R.S.Cruz, A.Ku, W.Moran, M.E.Ortega, N.T.Salzameda. Discovery of Dipeptides As Potent Botulinum Neurotoxin A Light-Chain Inhibitors. Acs Med.Chem.Lett. V. 12 295 2021.
ISSN: ISSN 1948-5875
PubMed: 33603978
DOI: 10.1021/ACSMEDCHEMLETT.0C00674