Zinc in PDB 7rd0: Crystal Structure of C. Difficile Penicillin-Binding Protein 3 in Apo Form

The structure of Crystal Structure of C. Difficile Penicillin-Binding Protein 3 in Apo Form, PDB code: 7rd0 was solved by M.Sacco, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.98 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	85.02, 114.22, 154.63, 90, 90, 90
R / Rfree (%)	18.9 / 24.1

The binding sites of Zinc atom in the Crystal Structure of C. Difficile Penicillin-Binding Protein 3 in Apo Form (pdb code 7rd0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of C. Difficile Penicillin-Binding Protein 3 in Apo Form, PDB code: 7rd0:

Zinc binding site 1 out of 1 in the Crystal Structure of C. Difficile Penicillin-Binding Protein 3 in Apo Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of C. Difficile Penicillin-Binding Protein 3 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn605 b:53.8 occ:1.00 ND1 A:HIS344 2.0 46.5 1.0 SG A:CYS338 2.2 52.0 1.0 SG A:CYS357 2.2 50.6 1.0 SG A:CYS323 2.3 51.8 1.0 CE1 A:HIS344 2.6 46.7 1.0 CB A:CYS357 3.1 55.7 1.0 CG A:HIS344 3.2 50.2 1.0 CB A:CYS323 3.3 43.1 1.0 CB A:CYS338 3.3 64.1 1.0 CA A:CYS357 3.7 53.4 1.0 CB A:HIS344 3.9 56.5 1.0 NE2 A:HIS344 3.9 47.4 1.0 CD A:PRO359 4.1 61.0 1.0 N A:HIS344 4.1 55.0 1.0 CD2 A:HIS344 4.2 45.6 1.0 NE2 A:GLN347 4.4 48.5 1.0 CG A:PRO359 4.4 63.8 1.0 C A:CYS357 4.5 57.9 1.0 CA A:CYS338 4.6 69.4 1.0 CA A:HIS344 4.6 52.2 1.0 CA A:CYS323 4.7 46.9 1.0 OE1 A:GLN347 4.7 56.0 1.0 N A:ASN358 4.7 55.3 1.0 CD A:GLN347 4.9 54.5 1.0 CB A:PRO359 5.0 58.2 1.0

M.D.Sacco, S.Wang, S.R.Adapa, X.Zhang, E.M.Lewandowski, M.V.Gongora, D.Keramisanou, Z.D.Atlas, J.A.Townsend, J.R.Gatdula, R.T.Morgan, L.R.Hammond, M.T.Marty, J.Wang, P.J.Eswara, I.Gelis, R.H.Y.Jiang, X.Sun, Y.Chen. A Unique Class of Zn 2+ -Binding Serine-Based Pbps Underlies Cephalosporin Resistance and Sporogenesis in Clostridioides Difficile. Nat Commun V. 13 4370 2022.
ISSN: ESSN 2041-1723
PubMed: 35902581
DOI: 10.1038/S41467-022-32086-6