Zinc in PDB 7z9p: The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic

The structure of The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic, PDB code: 7z9p was solved by S.Mason, P.M.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.10 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	38.576, 40.32, 40.577, 60.78, 87.31, 61.62
R / Rfree (%)	22.4 / 24.1

The structure of The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Zinc atom in the The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic (pdb code 7z9p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic, PDB code: 7z9p:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn104 b:52.5 occ:1.00 OP1 C:DG12 2.3 24.9 1.0 O C:HOH205 2.5 40.9 1.0 P C:DG12 3.4 27.3 1.0 O3' C:DC11 3.6 24.9 1.0 OP2 C:DG12 4.2 27.3 1.0 O2 C:SO4101 4.4 35.9 1.0 O3 C:SO4101 4.7 38.3 1.0 O5' C:DG12 4.7 26.9 1.0 C3' C:DC11 4.9 28.8 1.0

Zinc binding site 2 out of 3 in the The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn105 b:49.3 occ:1.00 OP1 C:DC11 2.3 36.2 1.0 OP1 E:DG12 2.4 33.3 1.0 O6 C:DG12 2.4 32.0 1.0 O C:HOH204 2.4 40.2 1.0 O C:HOH209 2.6 25.1 1.0 P E:DG12 3.5 33.9 1.0 C6 C:DG12 3.5 31.4 1.0 P C:DC11 3.6 39.6 1.0 O3' E:DC11 3.8 34.7 1.0 OP2 C:DC11 4.1 40.5 1.0 O5' C:DC11 4.2 33.1 1.0 O4 C:SO4101 4.2 41.1 1.0 OP2 E:DG12 4.3 31.9 1.0 N1 C:DG12 4.4 33.9 1.0 C5' C:DC11 4.5 31.8 1.0 C5 C:DG12 4.5 35.0 1.0 O2 C:SO4101 4.5 35.9 1.0 O1 C:SO4102 4.7 50.1 1.0 N7 C:DG12 4.7 34.0 1.0 O5' E:DG12 4.8 28.3 1.0 O3' C:DG10 4.8 32.0 1.0 OP2 C:DG12 5.0 27.3 1.0 S C:SO4101 5.0 39.3 1.0 C3' E:DC11 5.0 35.7 1.0

Zinc binding site 3 out of 3 in the The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn101 b:46.5 occ:1.00 OP1 F:DG24 2.3 35.1 1.0 P F:DG24 3.8 38.2 1.0 O3' F:DC23 4.3 33.9 1.0 C5' F:DG24 4.5 35.0 1.0 O5' F:DG24 4.6 30.8 1.0 O F:HOH203 4.7 29.6 1.0 OP2 F:DG24 4.7 37.6 1.0

T.Avis, C.Hu, N.Nagalingam, M.Mudaliar, C.Coward, K.Gajewski, M.J.Alam, S.Moss, S.Reich, E.Duperchy, K.Fox, K.Garey, D.Powell. The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic To Be Published.