Zinc in PDB 5xxg: Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 2

The structure of Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 2, PDB code: 5xxg was solved by N.Baburajendran, E.A.Jansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.47 / 2.14
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.288, 66.374, 107.296, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 24.3

The binding sites of Zinc atom in the Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 2 (pdb code 5xxg). 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 2, PDB code: 5xxg:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:24.9 occ:1.00 SG A:CYS261 2.3 26.0 1.0 SG A:CYS208 2.3 20.2 1.0 SG A:CYS263 2.3 22.2 1.0 SG A:CYS266 2.3 18.6 1.0 CB A:CYS208 3.2 19.8 1.0 CB A:CYS261 3.3 24.6 1.0 CB A:CYS263 3.5 27.1 1.0 CB A:CYS266 3.5 15.3 1.0 N A:CYS266 4.0 19.1 1.0 N A:CYS263 4.2 32.2 1.0 N A:CYS208 4.2 19.4 1.0 CA A:CYS263 4.3 31.9 1.0 CA A:CYS208 4.3 18.9 1.0 CA A:CYS266 4.4 21.1 1.0 NH2 A:ARG249 4.5 15.4 1.0 NE A:ARG249 4.6 21.6 1.0 NE2 A:HIS206 4.6 17.6 1.0 CA A:CYS261 4.6 21.0 1.0 C A:CYS261 4.7 25.6 1.0 O A:CYS261 4.8 19.7 1.0 C A:CYS263 4.8 24.4 1.0 O A:CYS263 4.8 22.4 1.0 O A:HOH742 4.9 22.0 1.0 CB A:ARG265 4.9 17.9 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:30.9 occ:1.00 SG A:CYS75 2.2 28.0 1.0 SG A:CYS71 2.3 30.3 1.0 SG A:CYS52 2.4 27.5 1.0 SG A:CYS49 2.4 28.4 1.0 CB A:CYS75 3.2 28.6 1.0 CB A:CYS49 3.2 29.6 1.0 CB A:CYS71 3.3 21.5 1.0 CB A:CYS52 3.4 23.0 1.0 N A:CYS52 3.8 27.2 1.0 N A:CYS71 4.0 31.8 1.0 CA A:CYS52 4.2 26.6 1.0 CA A:CYS71 4.2 25.4 1.0 OG A:SER72 4.4 26.0 1.0 CA A:CYS75 4.6 29.5 1.0 CA A:CYS49 4.7 28.4 1.0 CB A:ARG51 4.8 19.7 1.0 N A:SER72 4.8 25.9 1.0 C A:CYS71 4.8 30.8 1.0 C A:CYS52 4.9 24.6 1.0 C A:ARG51 4.9 26.1 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:29.5 occ:1.00 NE2 A:HIS83 2.1 30.2 1.0 SG A:CYS87 2.3 24.5 1.0 SG A:CYS62 2.3 26.6 1.0 SG A:CYS65 2.4 27.0 1.0 CE1 A:HIS83 3.0 26.4 1.0 CD2 A:HIS83 3.2 25.9 1.0 CB A:CYS87 3.2 27.6 1.0 CB A:CYS62 3.2 30.5 1.0 CB A:CYS65 3.3 26.7 1.0 N A:CYS65 3.4 25.9 1.0 CA A:CYS87 3.9 28.7 1.0 CA A:CYS65 4.0 34.2 1.0 ND1 A:HIS83 4.1 29.8 1.0 CG A:HIS83 4.3 25.9 1.0 CB A:GLN64 4.4 30.7 1.0 C A:GLN64 4.5 33.5 1.0 CA A:CYS62 4.6 29.7 1.0 CB A:ALA68 4.7 31.4 1.0 N A:ARG66 4.8 36.1 1.0 C A:CYS87 4.8 28.5 1.0 O A:HOH717 4.8 25.8 1.0 CA A:GLN64 4.8 32.1 1.0 C A:CYS65 4.8 29.5 1.0 N A:GLN64 4.8 28.2 1.0 O A:CYS87 4.8 27.9 1.0 O A:CYS62 4.9 30.9 1.0 C A:CYS62 4.9 34.2 1.0 CZ3 A:TRP80 4.9 25.6 1.0

N.Baburajendran, E.A.Jansson. Crystal Structure of SMYD3 in Complex with Covalent Inhibitor 2 To Be Published.