Zinc in PDB 5xxd: Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 1

The structure of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 1, PDB code: 5xxd was solved by N.Baburajendran, J.Anna E, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.37 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.458, 66.472, 107.062, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.9

The binding sites of Zinc atom in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 1 (pdb code 5xxd). 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 1, PDB code: 5xxd:
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 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:16.1 occ:1.00 SG A:CYS261 2.3 18.9 1.0 SG A:CYS208 2.3 12.5 1.0 SG A:CYS263 2.3 14.8 1.0 SG A:CYS266 2.3 13.6 1.0 CB A:CYS208 3.3 12.8 1.0 CB A:CYS261 3.5 17.5 1.0 CB A:CYS263 3.5 13.7 1.0 CB A:CYS266 3.5 10.3 1.0 N A:CYS266 4.1 11.6 1.0 N A:CYS263 4.1 22.4 1.0 N A:CYS208 4.3 14.7 1.0 CA A:CYS263 4.3 16.0 1.0 CA A:CYS266 4.4 13.8 1.0 CA A:CYS208 4.4 9.5 1.0 NH2 A:ARG249 4.5 14.1 1.0 C A:CYS261 4.6 18.1 1.0 NE A:ARG249 4.6 12.6 1.0 CA A:CYS261 4.7 13.4 1.0 NE2 A:HIS206 4.7 9.2 1.0 O A:CYS261 4.8 18.1 1.0 C A:CYS263 4.8 13.5 1.0 O A:CYS263 4.8 14.2 1.0 CB A:ARG265 4.9 10.1 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 1


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:36.4 occ:1.00 NE2 A:HIS83 2.0 29.6 1.0 SG A:CYS87 2.2 34.2 1.0 SG A:CYS62 2.3 31.4 1.0 SG A:CYS65 2.3 37.1 1.0 CE1 A:HIS83 3.0 29.3 1.0 CB A:CYS87 3.1 36.5 1.0 CD2 A:HIS83 3.1 25.3 1.0 CB A:CYS62 3.2 35.6 1.0 CB A:CYS65 3.3 35.5 1.0 N A:CYS65 3.7 31.8 1.0 CA A:CYS87 3.8 38.5 1.0 ND1 A:HIS83 4.1 26.9 1.0 CA A:CYS65 4.1 40.0 1.0 O A:CYS87 4.2 39.1 1.0 CG A:HIS83 4.2 25.9 1.0 CB A:GLN64 4.3 37.7 1.0 C A:CYS87 4.4 43.0 1.0 CB A:ALA68 4.5 33.2 1.0 CA A:CYS62 4.6 28.1 1.0 O A:HOH721 4.7 22.8 1.0 C A:GLN64 4.8 38.0 1.0 CZ3 A:TRP80 4.8 30.8 1.0 CA A:GLN64 4.9 34.1 1.0 N A:ARG66 4.9 40.9 1.0 O A:CYS62 5.0 35.1 1.0 C A:CYS62 5.0 29.9 1.0 N A:CYS87 5.0 31.6 1.0

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


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 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:24.6 occ:1.00 SG A:CYS49 2.3 23.8 1.0 SG A:CYS71 2.3 30.0 1.0 SG A:CYS75 2.3 22.4 1.0 SG A:CYS52 2.3 22.6 1.0 CB A:CYS71 2.7 20.8 1.0 CB A:CYS49 2.9 22.6 1.0 CB A:CYS75 3.1 23.3 1.0 CB A:CYS52 3.4 17.0 1.0 N A:CYS71 3.4 32.0 1.0 CA A:CYS71 3.6 28.4 1.0 N A:CYS52 4.0 17.0 1.0 CA A:CYS52 4.3 22.8 1.0 N A:SER72 4.4 32.6 1.0 C A:CYS71 4.4 37.5 1.0 CA A:CYS49 4.4 26.9 1.0 CA A:CYS75 4.6 25.3 1.0 C A:TYR70 4.6 36.1 1.0 C A:CYS52 5.0 21.6 1.0 C A:CYS49 5.0 24.1 1.0

N.Baburajendran, J.Anna E. Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 1 To Be Published.