Zinc in PDB 5kjl: SMYD2 in Complex with AZ378

All present enzymatic activity of SMYD2 in Complex with AZ378:
2.1.1.43;

The structure of SMYD2 in Complex with AZ378, PDB code: 5kjl was solved by A.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	109.67 / 2.70
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	155.098, 155.098, 52.553, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 23.6

The binding sites of Zinc atom in the SMYD2 in Complex with AZ378 (pdb code 5kjl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the SMYD2 in Complex with AZ378, PDB code: 5kjl:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMYD2 in Complex with AZ378


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SMYD2 in Complex with AZ378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:47.3 occ:1.00 SG A:CYS52 2.4 42.8 1.0 SG A:CYS78 2.4 46.0 1.0 SG A:CYS55 2.4 39.1 1.0 SG A:CYS74 2.4 43.5 1.0 CB A:CYS52 3.1 38.7 1.0 CB A:CYS74 3.2 41.6 1.0 CB A:CYS78 3.3 41.9 1.0 CB A:CYS55 3.7 34.2 1.0 N A:CYS74 3.8 42.6 1.0 N A:CYS55 4.0 32.4 1.0 CA A:CYS74 4.1 42.4 1.0 CA A:CYS55 4.4 32.5 1.0 CA A:CYS52 4.6 38.4 1.0 CB A:THR57 4.6 41.6 1.0 OG1 A:THR57 4.7 40.0 1.0 CA A:CYS78 4.7 41.3 1.0 CB A:TYR54 4.8 34.6 1.0 C A:TYR73 4.9 47.1 1.0 CD1 A:TYR54 5.0 39.5 1.0

Zinc binding site 2 out of 3 in the SMYD2 in Complex with AZ378


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SMYD2 in Complex with AZ378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:43.6 occ:1.00 SG A:CYS90 2.2 38.6 1.0 NE2 A:HIS86 2.3 39.2 1.0 SG A:CYS65 2.3 48.2 1.0 SG A:CYS68 2.4 43.9 1.0 CB A:CYS68 3.1 42.1 1.0 CD2 A:HIS86 3.1 39.6 1.0 CB A:CYS65 3.3 44.4 1.0 CB A:CYS90 3.3 33.7 1.0 CE1 A:HIS86 3.3 37.9 1.0 N A:CYS68 3.7 46.0 1.0 CA A:CYS90 3.8 33.0 1.0 CA A:CYS68 4.0 44.0 1.0 CG A:HIS86 4.3 37.6 1.0 C A:ARG67 4.3 51.3 1.0 CB A:ARG67 4.3 46.3 1.0 ND1 A:HIS86 4.4 38.4 1.0 CB A:ALA71 4.5 38.8 1.0 O A:HOH635 4.6 35.6 1.0 C A:CYS90 4.6 39.0 1.0 CA A:CYS65 4.6 46.4 1.0 CA A:ARG67 4.7 47.4 1.0 CZ3 A:TRP83 4.7 37.8 1.0 O A:CYS65 4.7 50.0 1.0 N A:ARG67 4.8 48.0 1.0 O A:CYS90 4.8 38.9 1.0 N A:CYS90 4.9 32.6 1.0 C A:CYS65 4.9 50.2 1.0 C A:CYS68 4.9 46.0 1.0 O A:ARG67 5.0 53.1 1.0

Zinc binding site 3 out of 3 in the SMYD2 in Complex with AZ378


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of SMYD2 in Complex with AZ378 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:40.5 occ:1.00 SG A:CYS267 2.2 34.8 1.0 SG A:CYS264 2.4 40.9 1.0 SG A:CYS262 2.4 40.8 1.0 SG A:CYS209 2.5 44.3 1.0 CB A:CYS209 3.1 40.4 1.0 CB A:CYS262 3.3 36.8 1.0 CB A:CYS267 3.4 33.5 1.0 CB A:CYS264 3.4 37.1 1.0 N A:CYS209 3.5 38.9 1.0 N A:CYS267 3.9 37.5 1.0 CA A:CYS209 3.9 38.9 1.0 N A:CYS264 3.9 36.6 1.0 CA A:CYS264 4.2 38.0 1.0 CA A:CYS267 4.2 35.8 1.0 CE1 A:HIS207 4.3 35.1 1.0 CA A:CYS262 4.5 37.2 1.0 C A:CYS262 4.5 43.3 1.0 NH2 A:ARG250 4.6 22.6 1.0 C A:SER208 4.6 40.2 1.0 C A:CYS264 4.7 44.9 1.0 ND1 A:HIS207 4.7 36.2 1.0 O A:CYS264 4.7 44.6 1.0 N A:GLU263 4.7 39.0 1.0 O A:CYS262 4.8 44.6 1.0 CB A:GLU266 4.8 40.4 1.0 NE A:ARG250 4.9 40.9 1.0 C A:GLU266 4.9 43.3 1.0 CA A:SER208 4.9 34.5 1.0

S.D.Cowen, D.Russell, L.A.Dakin, H.Chen, N.A.Larsen, R.Godin, S.Throner, X.Zheng, A.Molina, J.Wu, T.Cheung, T.Howard, R.Garcia-Arenas, N.Keen, C.S.Pendleton, J.A.Pietenpol, A.D.Ferguson. Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J. Med. Chem. V. 59 11079 2016.
ISSN: ISSN 1520-4804
PubMed: 28002961