Zinc 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:

Chlorine

(Cl)

8 atoms

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

Zinc binding site 1 out of 4 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:109.9 occ:1.00 OE1 A:GLU262 2.4 72.7 1.0 NE2 A:HIS223 2.4 51.1 1.0 NE2 A:HIS227 2.5 30.0 1.0 CD A:GLU262 2.5 65.7 1.0 OE2 A:GLU262 2.8 85.4 1.0 O02 A:XBM502 3.0 3.1 1.0 O03 A:XBM502 3.1 2.6 1.0 CE1 A:HIS227 3.3 36.4 1.0 CD2 A:HIS223 3.3 45.6 1.0 CB A:GLU262 3.5 61.7 1.0 CE1 A:HIS223 3.5 47.8 1.0 CG A:GLU262 3.5 72.8 1.0 OH A:TYR366 3.5 104.9 1.0 CD2 A:HIS227 3.6 29.4 1.0 C04 A:XBM502 3.8 3.2 1.0 CA A:GLU262 3.9 46.6 1.0 N02 A:XBM502 4.0 2.9 1.0 CZ A:TYR366 4.2 110.0 1.0 CE1 A:TYR366 4.3 119.6 1.0 ND1 A:HIS227 4.5 38.5 1.0 CG A:HIS223 4.5 42.6 1.0 ND1 A:HIS223 4.5 43.4 1.0 CG A:HIS227 4.7 32.5 1.0 CG2 A:THR265 4.7 58.5 1.0 OE2 A:GLU224 4.8 43.3 1.0 O A:GLU262 4.9 43.8 1.0 N A:GLU262 4.9 38.1 1.0 C A:GLU262 5.0 44.6 1.0

Zinc binding site 2 out of 4 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:120.0 occ:1.00 NE2 B:HIS227 2.3 38.4 1.0 OE1 B:GLU262 2.3 52.3 1.0 NE2 B:HIS223 2.3 51.8 1.0 CD B:GLU262 2.4 64.8 1.0 CG B:GLU262 2.4 70.1 1.0 CE1 B:HIS227 3.0 44.6 1.0 O03 B:XBM502 3.0 4.0 1.0 CB B:GLU262 3.2 57.9 1.0 OE2 B:GLU262 3.2 71.8 1.0 CD2 B:HIS223 3.3 48.8 1.0 O02 B:XBM502 3.3 5.0 1.0 CE1 B:HIS223 3.3 57.2 1.0 CD2 B:HIS227 3.5 37.3 1.0 CA B:GLU262 3.8 48.7 1.0 N02 B:XBM502 4.0 4.5 1.0 C04 B:XBM502 4.1 4.9 1.0 ND1 B:HIS227 4.2 38.4 1.0 CG2 B:THR265 4.4 55.4 1.0 ND1 B:HIS223 4.4 51.7 1.0 CG B:HIS223 4.4 47.5 1.0 CG B:HIS227 4.5 39.6 1.0 OE2 B:GLU224 4.7 47.3 1.0 O B:GLU262 4.7 48.9 1.0 CB B:THR265 4.8 47.7 1.0 C B:GLU262 4.8 48.1 1.0 N B:GLU262 4.9 44.3 1.0 CE1 B:TYR366 5.0 100.5 1.0

Zinc binding site 3 out of 4 in the Botulism Neurooxin Light Chain A App Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:117.3 occ:1.00 OE2 C:GLU262 2.1 74.0 1.0 CD C:GLU262 2.2 73.4 1.0 NE2 C:HIS223 2.3 52.8 1.0 OE1 C:GLU262 2.4 98.3 1.0 NE2 C:HIS227 2.6 38.2 1.0 O02 C:XBM502 3.1 8.8 1.0 O03 C:XBM502 3.2 6.1 1.0 CE1 C:HIS223 3.2 55.0 1.0 CE1 C:HIS227 3.3 46.9 1.0 CG C:GLU262 3.3 79.0 1.0 CD2 C:HIS223 3.3 49.5 1.0 CB C:GLU262 3.4 67.5 1.0 OH C:TYR366 3.6 120.8 1.0 CD2 C:HIS227 3.7 37.7 1.0 CA C:GLU262 3.8 56.4 1.0 C04 C:XBM502 3.9 7.9 1.0 N02 C:XBM502 4.1 7.0 1.0 CZ C:TYR366 4.1 116.0 1.0 CE1 C:TYR366 4.2 118.8 1.0 CG2 C:THR265 4.4 55.3 1.0 ND1 C:HIS223 4.4 46.0 1.0 CG C:HIS223 4.4 46.1 1.0 ND1 C:HIS227 4.5 43.9 1.0 O C:GLU262 4.5 49.9 1.0 C C:GLU262 4.7 53.3 1.0 CG C:HIS227 4.8 42.0 1.0 N C:GLU262 4.9 47.0 1.0 OE2 C:GLU224 4.9 47.0 1.0 CB C:THR265 4.9 52.8 1.0

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Botulism Neurooxin Light Chain A App Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn501 b:165.3 occ:1.00 OE1 D:GLU262 1.9 87.5 1.0 NE2 D:HIS227 2.0 75.7 1.0 NE2 D:HIS223 2.1 82.4 1.0 CD D:GLU262 2.5 96.1 1.0 OE2 D:GLU262 2.7 102.4 1.0 CD2 D:HIS223 2.9 82.8 1.0 O03 D:XBM502 2.9 29.0 1.0 CD2 D:HIS227 2.9 66.2 1.0 CE1 D:HIS227 3.0 77.6 1.0 CE1 D:HIS223 3.2 85.7 1.0 O02 D:XBM502 3.2 34.0 1.0 CG D:GLU262 3.7 100.6 1.0 N02 D:XBM502 3.8 32.5 1.0 C04 D:XBM502 3.9 34.4 1.0 ND1 D:HIS227 4.1 69.2 1.0 CG D:HIS223 4.1 82.1 1.0 CG D:HIS227 4.1 69.9 1.0 ND1 D:HIS223 4.2 76.6 1.0 CG2 D:THR265 4.2 88.6 1.0 CB D:GLU262 4.2 92.0 1.0 CA D:GLU262 4.2 77.2 1.0 OE2 D:GLU224 4.4 76.2 1.0 OH D:TYR366 4.4 114.8 1.0 CB D:THR265 4.7 80.6 1.0 CE1 D:TYR366 4.8 125.7 1.0 O D:GLU262 4.9 76.4 1.0 CZ D:TYR366 5.0 125.9 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