Zinc in PDB 5ccm: Crystal Structure of SMYD3 with Sam and EPZ030456

All present enzymatic activity of Crystal Structure of SMYD3 with Sam and EPZ030456:
2.1.1.43;

The structure of Crystal Structure of SMYD3 with Sam and EPZ030456, PDB code: 5ccm was solved by P.A.Boriack-Sjodin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.484, 65.852, 107.358, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.5

The structure of Crystal Structure of SMYD3 with Sam and EPZ030456 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of SMYD3 with Sam and EPZ030456 (pdb code 5ccm). 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 with Sam and EPZ030456, PDB code: 5ccm:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of SMYD3 with Sam and EPZ030456


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 with Sam and EPZ030456 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:28.1 occ:1.00 SG A:CYS49 2.3 25.5 1.0 SG A:CYS52 2.3 28.3 1.0 SG A:CYS71 2.3 27.9 1.0 SG A:CYS75 2.3 27.4 1.0 CB A:CYS75 3.1 28.7 1.0 CB A:CYS49 3.2 25.0 1.0 CB A:CYS52 3.4 28.1 1.0 CB A:CYS71 3.4 28.5 1.0 N A:CYS52 3.8 26.2 1.0 N A:CYS71 4.0 29.6 1.0 CA A:CYS52 4.2 26.8 1.0 CA A:CYS71 4.3 29.2 1.0 OG A:SER72 4.5 26.0 1.0 CA A:CYS75 4.6 30.1 1.0 CA A:CYS49 4.6 25.3 1.0 CB A:ARG51 4.8 28.8 1.0 N A:SER72 4.8 28.5 1.0 C A:ARG51 4.9 26.6 1.0 C A:CYS52 4.9 26.0 1.0 C A:CYS71 5.0 28.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of SMYD3 with Sam and EPZ030456


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 with Sam and EPZ030456 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:26.8 occ:1.00 SG A:CYS263 2.3 29.0 1.0 SG A:CYS261 2.3 27.9 1.0 SG A:CYS266 2.3 24.2 1.0 SG A:CYS208 2.3 24.1 1.0 CB A:CYS261 3.4 28.1 1.0 CB A:CYS263 3.4 29.2 1.0 CB A:CYS208 3.4 24.1 1.0 CB A:CYS266 3.4 26.0 1.0 N A:CYS266 4.1 27.3 1.0 N A:CYS208 4.2 23.6 1.0 N A:CYS263 4.2 29.0 1.0 CA A:CYS263 4.3 29.0 1.0 NE2 A:HIS206 4.3 21.2 1.0 CA A:CYS266 4.4 27.0 1.0 CA A:CYS208 4.4 23.9 1.0 NH2 A:ARG249 4.6 26.4 1.0 CA A:CYS261 4.6 28.0 1.0 NE A:ARG249 4.6 23.4 1.0 C A:CYS261 4.7 29.0 1.0 O A:CYS263 4.7 28.0 1.0 C A:CYS263 4.7 28.5 1.0 O A:CYS261 4.8 28.2 1.0 CD2 A:HIS206 4.8 21.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of SMYD3 with Sam and EPZ030456


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 with Sam and EPZ030456 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:32.0 occ:1.00 NE2 A:HIS83 2.1 29.7 1.0 SG A:CYS62 2.3 34.5 1.0 SG A:CYS87 2.3 33.6 1.0 SG A:CYS65 2.3 29.9 1.0 CE1 A:HIS83 3.0 29.2 1.0 CD2 A:HIS83 3.2 30.2 1.0 CB A:CYS62 3.3 36.1 1.0 CB A:CYS65 3.3 33.3 1.0 CB A:CYS87 3.4 34.9 1.0 N A:CYS65 3.7 35.6 1.0 CA A:CYS87 3.9 36.0 1.0 CA A:CYS65 4.1 33.9 1.0 ND1 A:HIS83 4.1 29.8 1.0 CG A:HIS83 4.2 30.6 1.0 CB A:GLN64 4.3 41.3 1.0 CB A:ALA68 4.5 29.9 1.0 O A:HOH708 4.6 32.2 1.0 CA A:CYS62 4.6 36.6 1.0 CZ3 A:TRP80 4.7 36.2 1.0 C A:GLN64 4.7 37.4 1.0 C A:CYS87 4.8 39.2 1.0 OE1 A:GLN64 4.8 50.6 1.0 O A:CYS87 4.9 38.9 1.0 C A:CYS62 4.9 38.2 1.0 O A:CYS62 4.9 37.5 1.0 N A:ARG66 4.9 35.5 1.0 CA A:GLN64 4.9 39.2 1.0 N A:GLN64 5.0 37.2 1.0

L.H.Mitchell, P.A.Boriack-Sjodin, S.Smith, M.Thomenius, N.Rioux, M.Munchhof, J.E.Mills, C.Klaus, J.Totman, T.V.Riera, A.Raimondi, S.L.Jacques, K.West, M.Foley, N.J.Waters, K.W.Kuntz, T.J.Wigle, M.P.Scott, R.A.Copeland, J.J.Smith, R.Chesworth. Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor. Acs Med.Chem.Lett. V. 7 134 2016.
ISSN: ISSN 1948-5875
PubMed: 26985287
DOI: 10.1021/ACSMEDCHEMLETT.5B00272