Zinc in PDB 5dzt: Crystal Structure of Class II Lanthipeptide Synthetase Cylm in Complex with Amp

The structure of Crystal Structure of Class II Lanthipeptide Synthetase Cylm in Complex with Amp, PDB code: 5dzt was solved by S.H.Dong, T.Lukk, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.191, 90.699, 246.361, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 27.5

The binding sites of Zinc atom in the Crystal Structure of Class II Lanthipeptide Synthetase Cylm in Complex with Amp (pdb code 5dzt). 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 Class II Lanthipeptide Synthetase Cylm in Complex with Amp, PDB code: 5dzt:

Zinc binding site 1 out of 1 in the Crystal Structure of Class II Lanthipeptide Synthetase Cylm in Complex with Amp


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 Class II Lanthipeptide Synthetase Cylm in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:47.3 occ:1.00 ND1 A:HIS912 2.1 42.4 1.0 SG A:CYS911 2.2 35.0 1.0 SG A:CYS875 2.4 50.5 1.0 CE1 A:HIS912 3.0 40.1 1.0 CB A:CYS875 3.0 51.3 1.0 CG A:HIS912 3.2 41.5 1.0 CB A:CYS911 3.3 36.2 1.0 O A:CYS911 3.5 37.6 1.0 CB A:HIS912 3.6 39.5 1.0 C A:CYS911 3.6 36.7 1.0 OH A:TYR695 4.0 40.0 1.0 CA A:CYS911 4.1 36.6 1.0 NE2 A:HIS912 4.1 41.2 1.0 N A:HIS912 4.1 37.6 1.0 CD2 A:HIS912 4.2 40.6 1.0 CA A:HIS912 4.4 38.3 1.0 CA A:CYS875 4.4 53.5 1.0 NZ A:LYS876 4.5 70.4 1.0 N A:CYS875 4.7 53.1 1.0

S.H.Dong, W.Tang, T.Lukk, Y.Yu, S.K.Nair, W.A.Van Der Donk. The Enterococcal Cytolysin Synthetase Has An Unanticipated Lipid Kinase Fold. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26226635
DOI: 10.7554/ELIFE.07607