Sodium 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:

Zinc

(Zn)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the The Novel Dna Binding Mechanism of Ridinilazole, A Precision Clostridiodes Difficile Antibiotic, PDB code: 7z9p:

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 A:Na103 b:18.6 occ:1.00 OP1 A:DA5 2.0 34.3 1.0 OP1 E:DA5 2.2 33.0 1.0 O A:HOH204 2.3 23.3 1.0 O E:HOH207 2.3 34.0 1.0 P A:DA5 3.3 36.6 1.0 P E:DA5 3.5 34.6 1.0 OP2 E:DA5 3.9 36.8 1.0 O5' A:DA5 3.9 42.6 1.0 OP2 A:DA5 4.0 41.6 1.0 O5' E:DA5 4.2 33.3 1.0 C5' A:DA5 4.3 39.2 1.0 O3' A:DG4 4.5 35.1 1.0 C5' E:DA5 4.7 32.1 1.0 O3' E:DG4 4.8 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.