Zinc in PDB 7l7b: Clostridioides Difficile Rnap with Fidaxomicin

All present enzymatic activity of Clostridioides Difficile Rnap with Fidaxomicin:
2.7.7.6;

The structure of Clostridioides Difficile Rnap with Fidaxomicin also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	1 atom

The binding sites of Zinc atom in the Clostridioides Difficile Rnap with Fidaxomicin (pdb code 7l7b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Clostridioides Difficile Rnap with Fidaxomicin, PDB code: 7l7b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Clostridioides Difficile Rnap with Fidaxomicin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Clostridioides Difficile Rnap with Fidaxomicin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1401 b:126.6 occ:1.00 SG D:CYS874 2.2 100.4 1.0 SG D:CYS864 2.2 100.1 1.0 SG D:CYS790 2.2 101.4 1.0 HB2 D:CYS874 2.2 100.4 1.0 SG D:CYS871 2.3 95.8 1.0 HA D:CYS864 2.5 100.1 1.0 CB D:CYS874 2.6 100.4 1.0 CB D:CYS864 2.9 100.1 1.0 HB3 D:CYS790 2.9 101.4 1.0 HB2 D:CYS864 3.0 100.1 1.0 HB3 D:CYS874 3.0 100.4 1.0 H D:CYS871 3.0 95.8 1.0 CA D:CYS864 3.2 100.1 1.0 CB D:CYS790 3.2 101.4 1.0 H D:LYS865 3.3 101.2 1.0 CB D:CYS871 3.5 95.8 1.0 HB3 D:CYS871 3.5 95.8 1.0 H D:CYS790 3.6 101.4 1.0 H D:CYS874 3.6 100.4 1.0 HB2 D:CYS790 3.8 101.4 1.0 HB3 D:CYS864 3.8 100.1 1.0 N D:CYS871 3.8 95.8 1.0 N D:LYS865 3.9 101.2 1.0 CA D:CYS874 3.9 100.4 1.0 HG23 D:THR866 3.9 97.7 1.0 C D:CYS864 4.1 100.1 1.0 N D:CYS874 4.1 100.4 1.0 CA D:CYS871 4.2 95.8 1.0 N D:CYS864 4.3 100.1 1.0 N D:CYS790 4.3 101.4 1.0 HA D:CYS874 4.3 100.4 1.0 HB2 D:CYS871 4.3 95.8 1.0 CA D:CYS790 4.3 101.4 1.0 HG21 D:THR792 4.4 107.6 1.0 HG22 D:THR792 4.5 107.6 1.0 HH11 D:ARG859 4.5 105.3 1.0 O D:CYS871 4.6 95.8 1.0 H D:THR866 4.6 97.7 1.0 HA D:VAL870 4.6 91.3 1.0 C D:CYS871 4.7 95.8 1.0 H D:CYS864 4.7 100.1 1.0 HB D:VAL870 4.8 91.3 1.0 O D:ASN863 4.8 103.5 1.0 CG2 D:THR866 4.8 97.7 1.0 C D:ASN863 4.9 103.5 1.0 HB D:THR792 4.9 107.6 1.0 CG2 D:THR792 4.9 107.6 1.0 HA D:VAL861 4.9 95.8 1.0 C D:VAL870 5.0 91.3 1.0

Zinc binding site 2 out of 2 in the Clostridioides Difficile Rnap with Fidaxomicin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Clostridioides Difficile Rnap with Fidaxomicin within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1402 b:151.7 occ:1.00 HB3 D:CYS75 2.2 136.1 1.0 SG D:CYS75 2.2 136.1 1.0 SG D:CYS78 2.2 132.0 1.0 SG D:CYS62 2.3 133.0 1.0 HB2 D:CYS60 2.3 130.5 1.0 SG D:CYS60 2.3 130.5 1.0 CB D:CYS75 2.4 136.1 1.0 HB2 D:CYS75 2.5 136.1 1.0 CB D:CYS60 2.8 130.5 1.0 H D:CYS78 3.1 132.0 1.0 H D:CYS62 3.2 133.0 1.0 HB3 D:CYS60 3.3 130.5 1.0 H D:GLY63 3.6 135.7 1.0 CB D:CYS78 3.7 132.0 1.0 CB D:CYS62 3.8 133.0 1.0 CA D:CYS75 3.8 136.1 1.0 HB3 D:CYS78 3.9 132.0 1.0 H D:LYS64 3.9 137.2 1.0 N D:CYS78 3.9 132.0 1.0 HB2 D:ARG77 4.0 136.2 1.0 HB3 D:CYS62 4.0 133.0 1.0 N D:CYS62 4.0 133.0 1.0 HG3 D:LYS64 4.0 137.2 1.0 CA D:CYS60 4.1 130.5 1.0 H D:HIS61 4.1 127.4 1.0 H D:ARG77 4.2 136.2 1.0 HB2 D:LYS64 4.2 137.2 1.0 C D:CYS60 4.2 130.5 1.0 HA D:CYS75 4.3 136.1 1.0 N D:HIS61 4.3 127.4 1.0 N D:GLY63 4.3 135.7 1.0 H D:VAL80 4.3 124.3 1.0 H D:GLY79 4.3 129.1 1.0 HD2 D:TYR65 4.4 139.3 1.0 CA D:CYS78 4.4 132.0 1.0 C D:CYS75 4.4 136.1 1.0 CA D:CYS62 4.4 133.0 1.0 H D:TYR65 4.4 139.3 1.0 HB2 D:CYS78 4.4 132.0 1.0 HB2 D:CYS62 4.5 133.0 1.0 H D:CYS75 4.5 136.1 1.0 HB D:VAL80 4.5 124.3 1.0 HA D:CYS60 4.5 130.5 1.0 O D:CYS75 4.5 136.1 1.0 N D:LYS64 4.6 137.2 1.0 N D:CYS75 4.7 136.1 1.0 C D:CYS62 4.8 133.0 1.0 CB D:ARG77 4.8 136.2 1.0 N D:GLY79 4.8 129.1 1.0 O D:CYS60 4.8 130.5 1.0 CG D:LYS64 4.8 137.2 1.0 N D:ARG77 4.9 136.2 1.0 CB D:LYS64 4.9 137.2 1.0 C D:CYS78 5.0 132.0 1.0 C D:ARG77 5.0 136.2 1.0

X.Cao, H.Boyaci, J.Chen, Y.Bao, R.Landick, E.A.Campbell. Basis of Narrow-Spectrum Activity of Fidaxomicin on Clostridioides Difficile. Nature V. 604 541 2022.
ISSN: ESSN 1476-4687
PubMed: 35388215
DOI: 10.1038/S41586-022-04545-Z