Zinc in PDB 3pdn: Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin

All present enzymatic activity of Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin:
2.1.1.43;

The structure of Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin, PDB code: 3pdn was solved by N.Sirinupong, J.Brunzelle, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.45 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.240, 66.246, 107.384, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 18.9

The structure of Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin (pdb code 3pdn). 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 Methyltransferase Inhibitor Sinefungin, PDB code: 3pdn:
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 Methyltransferase Inhibitor Sinefungin


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 Methyltransferase Inhibitor Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn436 b:17.3 occ:1.00 NE2 A:HIS83 2.1 16.7 1.0 SG A:CYS87 2.3 18.4 1.0 SG A:CYS62 2.3 16.1 1.0 SG A:CYS65 2.4 18.9 1.0 CE1 A:HIS83 3.0 16.3 1.0 CD2 A:HIS83 3.1 16.3 1.0 CB A:CYS62 3.2 13.3 1.0 CB A:CYS87 3.2 13.9 1.0 CB A:CYS65 3.2 15.8 1.0 N A:CYS65 3.5 18.0 1.0 CA A:CYS87 3.9 14.7 1.0 CA A:CYS65 4.0 17.6 1.0 ND1 A:HIS83 4.2 16.1 1.0 CG A:HIS83 4.2 14.1 1.0 CB A:GLN64 4.6 21.2 1.0 CA A:CYS62 4.6 14.9 1.0 C A:GLN64 4.6 24.4 1.0 CB A:ALA68 4.7 17.1 1.0 CZ3 A:TRP80 4.7 17.4 1.0 O A:HOH1009 4.7 18.2 1.0 C A:CYS87 4.8 22.2 1.0 N A:ARG66 4.8 19.1 1.0 C A:CYS65 4.9 22.7 1.0 O A:CYS87 4.9 22.3 1.0 N A:GLN64 4.9 20.5 1.0 CA A:GLN64 4.9 20.2 1.0 C A:CYS62 4.9 20.3 1.0 N A:CYS87 5.0 13.5 1.0 O A:CYS62 5.0 19.2 1.0

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


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 Methyltransferase Inhibitor Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn437 b:18.2 occ:1.00 SG A:CYS75 2.3 20.4 1.0 SG A:CYS52 2.3 18.7 1.0 SG A:CYS71 2.3 23.2 1.0 SG A:CYS49 2.4 18.5 1.0 CB A:CYS75 3.1 16.1 1.0 CB A:CYS49 3.2 16.2 1.0 CB A:CYS52 3.3 15.3 1.0 CB A:CYS71 3.4 20.4 1.0 N A:CYS52 3.7 14.6 1.0 O A:HOH466 3.9 34.5 1.0 N A:CYS71 4.0 18.2 1.0 CA A:CYS52 4.1 14.7 1.0 CA A:CYS71 4.3 19.3 1.0 O A:HOH982 4.3 35.0 1.0 OG A:SER72 4.4 18.4 1.0 CA A:CYS75 4.6 15.0 1.0 CA A:CYS49 4.6 15.6 1.0 CB A:ARG51 4.7 15.3 1.0 N A:SER72 4.8 17.6 1.0 C A:ARG51 4.8 17.4 1.0 C A:CYS52 4.9 18.4 1.0 C A:CYS71 5.0 22.0 1.0

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


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 Methyltransferase Inhibitor Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn438 b:14.4 occ:1.00 SG A:CYS208 2.3 14.1 1.0 SG A:CYS261 2.3 15.4 1.0 SG A:CYS266 2.4 12.3 1.0 SG A:CYS263 2.4 15.7 1.0 CB A:CYS208 3.3 10.4 1.0 CB A:CYS266 3.4 9.6 1.0 CB A:CYS261 3.4 12.1 1.0 O A:HOH977 3.4 32.4 1.0 CB A:CYS263 3.5 12.7 1.0 N A:CYS266 4.0 10.2 1.0 N A:CYS263 4.2 15.1 1.0 CA A:CYS266 4.3 10.1 1.0 CA A:CYS263 4.3 13.3 1.0 N A:CYS208 4.5 9.5 1.0 CA A:CYS208 4.5 8.9 1.0 NE A:ARG249 4.6 12.5 1.0 NH2 A:ARG249 4.6 10.4 1.0 CA A:CYS261 4.6 12.7 1.0 C A:CYS261 4.6 15.4 1.0 O A:HOH525 4.7 33.0 1.0 O A:CYS261 4.7 15.9 1.0 O A:CYS263 4.8 14.7 1.0 C A:CYS263 4.8 16.0 1.0 NE2 A:HIS206 4.9 8.4 1.0 O A:HOH739 4.9 14.3 1.0 CB A:ARG265 4.9 10.1 1.0 C A:ARG265 5.0 12.7 1.0

N.Sirinupong, J.Brunzelle, E.Doko, Z.Yang. Structural Insights Into the Autoinhibition and Posttranslational Activation of Histone Methyltransferase SMYD3. J.Mol.Biol. V. 406 149 2011.
ISSN: ISSN 0022-2836
PubMed: 21167177
DOI: 10.1016/J.JMB.2010.12.014