Zinc in PDB 8byk: The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases

The structure of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases, PDB code: 8byk was solved by C.V.Knospe, M.Kamel, O.Spitz, A.Hoeppner, S.Galle, J.Reiners, A.Kedrov, S.H.Smits, L.Schmitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.89 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.14, 66.119, 117.258, 90, 90, 90
R / Rfree (%)	19 / 22

The structure of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases (pdb code 8byk). 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 The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases, PDB code: 8byk:

Zinc binding site 1 out of 1 in the The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:17.2 occ:1.00 ND1 A:HIS345 2.1 19.8 1.0 ND1 A:HIS501 2.2 20.6 1.0 SG A:CYS298 2.3 15.3 1.0 SG A:CYS344 2.3 16.0 1.0 CE1 A:HIS345 3.0 19.1 1.0 CE1 A:HIS501 3.0 31.5 1.0 CB A:CYS298 3.1 12.8 1.0 CG A:HIS345 3.2 17.8 1.0 CB A:CYS344 3.3 16.4 1.0 CG A:HIS501 3.3 35.7 1.0 CB A:HIS345 3.6 17.4 1.0 C A:CYS344 3.7 12.8 1.0 CB A:HIS501 3.8 30.7 1.0 O A:CYS344 3.8 13.6 1.0 N A:HIS345 3.9 14.9 1.0 CA A:CYS344 4.1 14.4 1.0 NE2 A:HIS345 4.1 23.1 1.0 NE2 A:HIS501 4.2 38.1 1.0 CD2 A:HIS345 4.3 20.6 1.0 CA A:HIS501 4.3 31.4 1.0 CA A:HIS345 4.3 15.8 1.0 CD2 A:HIS501 4.4 34.2 1.0 OXT A:ACT607 4.4 37.5 1.0 O A:HOH969 4.4 36.2 1.0 CA A:CYS298 4.6 11.0 1.0 NH1 A:ARG294 4.7 35.7 0.4 N A:CYS298 4.8 11.7 1.0 O A:HIS501 4.9 37.5 1.0

C.V.Knospe, M.Kamel, O.Spitz, A.Hoeppner, S.Galle, J.Reiners, A.Kedrov, S.H.J.Smits, L.Schmitt. The Structure of Madc From Clostridium Maddingley Reveals New Insights Into Class I Lanthipeptide Cyclases. Front Microbiol V. 13 57217 2022.
ISSN: ESSN 1664-302X
PubMed: 36741885
DOI: 10.3389/FMICB.2022.1057217