Zinc in PDB 5xxj: Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3

The structure of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3, PDB code: 5xxj was solved by N.Baburajendran, A.E.Jansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.61 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.386, 66.450, 108.042, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 22.7

The binding sites of Zinc atom in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3 (pdb code 5xxj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3, PDB code: 5xxj:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3


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 SMYD3 in Complex with Covalent Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:24.2 occ:1.00 NE2 A:HIS83 2.1 22.2 1.0 SG A:CYS87 2.3 27.8 1.0 SG A:CYS65 2.3 26.5 1.0 SG A:CYS62 2.3 19.8 1.0 CE1 A:HIS83 3.0 28.2 1.0 CD2 A:HIS83 3.1 25.5 1.0 CB A:CYS65 3.2 30.4 1.0 CB A:CYS62 3.2 25.1 1.0 CB A:CYS87 3.3 27.4 1.0 N A:CYS65 3.5 27.4 1.0 CA A:CYS65 4.0 32.1 1.0 CA A:CYS87 4.0 28.9 1.0 ND1 A:HIS83 4.2 22.5 1.0 CG A:HIS83 4.2 24.6 1.0 CB A:GLN64 4.4 36.7 1.0 C A:GLN64 4.6 33.8 1.0 CA A:CYS62 4.7 26.0 1.0 CZ3 A:TRP80 4.7 27.4 1.0 CB A:ALA68 4.7 24.4 1.0 O A:HOH751 4.7 25.0 1.0 N A:ARG66 4.8 29.4 1.0 CG A:GLN64 4.8 45.0 1.0 C A:CYS65 4.8 31.9 1.0 N A:GLN64 4.9 29.9 1.0 CA A:GLN64 4.9 31.6 1.0 C A:CYS87 4.9 32.9 1.0 C A:CYS62 5.0 25.4 1.0 O A:CYS87 5.0 29.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3


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 SMYD3 in Complex with Covalent Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:18.6 occ:1.00 SG A:CYS75 2.2 20.3 1.0 SG A:CYS71 2.3 23.8 1.0 SG A:CYS52 2.3 17.8 1.0 SG A:CYS49 2.4 20.4 1.0 CB A:CYS75 3.2 15.9 1.0 CB A:CYS52 3.2 19.7 1.0 CB A:CYS49 3.3 19.2 1.0 CB A:CYS71 3.4 20.2 1.0 N A:CYS52 3.8 15.9 1.0 CA A:CYS52 4.1 17.0 1.0 N A:CYS71 4.1 22.6 1.0 CA A:CYS71 4.3 22.7 1.0 OG A:SER72 4.5 22.5 1.0 CA A:CYS75 4.6 19.8 1.0 CB A:ARG51 4.7 18.8 1.0 CA A:CYS49 4.7 18.4 1.0 C A:ARG51 4.9 17.6 1.0 C A:CYS52 4.9 19.9 1.0 C A:CYS71 4.9 27.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:15.6 occ:1.00 SG A:CYS261 2.3 18.4 1.0 SG A:CYS208 2.4 15.9 1.0 SG A:CYS266 2.4 13.5 1.0 SG A:CYS263 2.4 17.6 1.0 CB A:CYS261 3.4 15.9 1.0 CB A:CYS263 3.4 19.2 1.0 CB A:CYS266 3.4 14.1 1.0 CB A:CYS208 3.4 15.8 1.0 N A:CYS266 4.1 10.2 1.0 N A:CYS263 4.2 21.9 1.0 CA A:CYS263 4.3 19.4 1.0 CA A:CYS266 4.3 11.0 1.0 N A:CYS208 4.4 12.9 1.0 CA A:CYS208 4.5 12.5 1.0 CA A:CYS261 4.6 18.0 1.0 NH2 A:ARG249 4.6 12.3 1.0 C A:CYS261 4.6 16.8 1.0 NE A:ARG249 4.6 13.4 1.0 NE2 A:HIS206 4.8 10.4 1.0 O A:HOH750 4.8 21.3 1.0 C A:CYS263 4.8 16.2 1.0 O A:CYS261 4.8 16.4 1.0 O A:CYS263 4.9 17.0 1.0 CB A:ARG265 5.0 13.7 1.0

N.Baburajendran, A.E.Jansson. Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 3 To Be Published.