Zinc in PDB 5kjn: SMYD2 in Complex with AZ506

All present enzymatic activity of SMYD2 in Complex with AZ506:
2.1.1.43;

The structure of SMYD2 in Complex with AZ506, PDB code: 5kjn was solved by A.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.76 / 2.72
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	154.871, 154.871, 52.286, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 22.5

The structure of SMYD2 in Complex with AZ506 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Zinc atom in the SMYD2 in Complex with AZ506 (pdb code 5kjn). 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 AZ506, PDB code: 5kjn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the SMYD2 in Complex with AZ506


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 AZ506 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn511 b:54.0 occ:1.00 SG A:CYS52 2.3 58.0 1.0 SG A:CYS78 2.3 59.3 1.0 SG A:CYS55 2.4 47.9 1.0 SG A:CYS74 2.5 48.2 1.0 CB A:CYS74 3.2 45.7 1.0 CB A:CYS52 3.2 53.6 1.0 CB A:CYS78 3.4 55.0 1.0 CB A:CYS55 3.7 43.1 1.0 N A:CYS74 3.7 44.2 1.0 N A:CYS55 4.0 43.6 1.0 CA A:CYS74 4.1 45.4 1.0 CA A:CYS55 4.4 41.6 1.0 CA A:CYS52 4.6 53.3 1.0 CB A:TYR54 4.7 44.5 1.0 CA A:CYS78 4.8 54.4 1.0 C A:TYR73 4.8 49.8 1.0 OG1 A:THR57 4.8 42.4 1.0 CD1 A:TYR54 4.9 47.1 1.0 CB A:THR57 4.9 43.7 1.0 C A:TYR54 5.0 48.4 1.0

Zinc binding site 2 out of 3 in the SMYD2 in Complex with AZ506


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 AZ506 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn512 b:50.3 occ:1.00 NE2 A:HIS86 2.2 48.8 1.0 SG A:CYS68 2.2 52.2 1.0 SG A:CYS90 2.3 50.2 1.0 SG A:CYS65 2.4 58.0 1.0 CE1 A:HIS86 3.1 47.5 1.0 CD2 A:HIS86 3.2 48.9 1.0 CB A:CYS68 3.3 50.1 1.0 CB A:CYS65 3.3 54.3 1.0 CB A:CYS90 3.5 45.3 1.0 N A:CYS68 3.5 54.1 1.0 CA A:CYS90 3.9 44.0 1.0 CA A:CYS68 4.0 52.6 1.0 ND1 A:HIS86 4.3 47.1 1.0 CB A:ARG67 4.3 55.0 1.0 CG A:HIS86 4.3 45.7 1.0 CB A:ALA71 4.5 45.6 1.0 C A:ARG67 4.6 59.9 1.0 CA A:CYS65 4.6 56.6 1.0 CA A:ARG67 4.7 56.5 1.0 O A:CYS65 4.8 58.3 1.0 N A:ARG67 4.8 58.1 1.0 N A:LYS69 4.8 54.5 1.0 NH1 A:ARG67 4.8 89.8 1.0 C A:CYS90 4.8 49.5 1.0 C A:CYS68 4.9 59.8 1.0 C A:CYS65 4.9 59.6 1.0 N A:CYS90 5.0 42.9 1.0

Zinc binding site 3 out of 3 in the SMYD2 in Complex with AZ506


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 AZ506 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn513 b:52.7 occ:1.00 SG A:CYS267 2.2 40.2 1.0 SG A:CYS264 2.3 53.7 1.0 SG A:CYS262 2.5 49.8 1.0 SG A:CYS209 2.5 49.0 1.0 CB A:CYS209 3.3 45.1 1.0 CB A:CYS262 3.3 46.0 1.0 CB A:CYS267 3.4 39.5 1.0 CB A:CYS264 3.4 50.3 1.0 N A:CYS209 3.7 46.0 1.0 N A:CYS264 4.0 49.6 1.0 N A:CYS267 4.0 44.4 1.0 CA A:CYS209 4.1 44.3 1.0 CA A:CYS264 4.1 50.8 1.0 CE1 A:HIS207 4.2 40.2 1.0 CA A:CYS267 4.3 42.2 1.0 C A:CYS262 4.4 50.7 1.0 CA A:CYS262 4.4 46.3 1.0 O A:CYS262 4.6 52.0 1.0 ND1 A:HIS207 4.6 41.8 1.0 C A:SER208 4.7 48.5 1.0 C A:CYS264 4.7 57.3 1.0 NH2 A:ARG250 4.7 44.0 1.0 CB A:GLU266 4.8 47.7 1.0 O A:CYS264 4.8 58.6 1.0 N A:GLU263 4.8 47.9 1.0 NE A:ARG250 4.9 38.5 1.0 CA A:SER208 4.9 43.2 1.0 C A:GLU266 5.0 50.2 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