Zinc in PDB 7mlp: Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid

All present enzymatic activity of Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid:
3.2.2.22;

The structure of Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid, PDB code: 7mlp was solved by R.K.Harijan, X.P.Li, B.Cao, D.Augeri, J.B.Bonanno, S.C.Almo, N.E.Tumer, V.L.Schramm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.63 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.658, 77.867, 53.244, 90, 111.25, 90
R / Rfree (%)	18.1 / 21.3

The binding sites of Zinc atom in the Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid (pdb code 7mlp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid, PDB code: 7mlp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid


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 Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn308 b:19.4 occ:1.00 NE2 A:HIS65 2.0 20.1 1.0 O1 A:EDO307 2.1 33.7 1.0 C2 A:EDO307 2.9 36.8 1.0 C1 A:EDO307 2.9 36.6 1.0 CD2 A:HIS65 3.0 20.7 1.0 CE1 A:HIS65 3.0 21.7 1.0 O2 A:EDO307 4.0 45.1 1.0 ND1 A:HIS65 4.1 21.6 1.0 N A:GLY15 4.1 18.0 1.0 CG A:HIS65 4.1 20.7 1.0 CA A:ALA14 4.7 18.1 1.0 CA A:GLY15 4.7 18.5 1.0 C A:ALA14 4.8 17.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Ricin A Chain in Complex with 5-(2,6- Dimethylphenyl)Thiophene-2-Carboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn309 b:37.8 occ:1.00 ND1 A:HIS40 2.2 22.9 1.0 O A:HOH604 2.5 35.5 1.0 O A:HOH610 2.5 30.3 1.0 CE1 A:HIS40 3.1 24.0 1.0 CG A:HIS40 3.2 21.6 1.0 CB A:HIS40 3.5 22.0 1.0 CA A:HIS40 3.6 20.7 1.0 O A:HOH441 3.9 26.7 1.0 NE2 A:HIS40 4.2 24.4 1.0 C A:GLN223 4.3 33.8 1.0 CD2 A:HIS40 4.3 22.6 1.0 N A:GLY224 4.4 29.9 1.0 O A:HOH545 4.4 30.9 1.0 N A:HIS40 4.4 20.1 1.0 O A:GLN223 4.5 32.2 1.0 CA A:GLY224 4.5 27.2 1.0 CA A:GLN223 4.6 37.4 1.0 C A:HIS40 4.8 20.9 1.0 CG1 A:VAL245 5.0 27.8 1.0

X.P.Li, R.K.Harijan, B.Cao, J.N.Kahn, M.Pierce, A.M.Tsymbal, J.Y.Roberge, D.Augeri, N.E.Tumer. Synthesis and Structural Characterization of Ricin Inhibitors Targeting Ribosome Binding Using Fragment-Based Methods and Structure-Based Design. J.Med.Chem. V. 64 15334 2021.
ISSN: ISSN 0022-2623
PubMed: 34648707
DOI: 10.1021/ACS.JMEDCHEM.1C01370