Zinc in PDB 3qww: Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin

The structure of Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin, PDB code: 3qww was solved by Y.Jiang, 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)	28.13 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.520, 75.150, 112.520, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 20.7

The binding sites of Zinc atom in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin (pdb code 3qww). 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 Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin, PDB code: 3qww:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with the 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 Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn435 b:20.2 occ:1.00 SG A:CYS78 2.2 23.4 1.0 SG A:CYS55 2.4 20.6 1.0 SG A:CYS52 2.4 16.8 1.0 SG A:CYS74 2.5 27.9 1.0 CB A:CYS52 3.1 13.6 1.0 CB A:CYS74 3.2 22.9 1.0 CB A:CYS78 3.2 18.9 1.0 CB A:CYS55 3.4 17.3 1.0 N A:CYS55 3.8 19.0 1.0 N A:CYS74 3.9 20.1 1.0 CA A:CYS74 4.1 21.0 1.0 CA A:CYS55 4.2 17.6 1.0 CB A:CYS54 4.6 16.9 1.0 CA A:CYS52 4.6 13.8 1.0 CA A:CYS78 4.6 17.6 1.0 CB A:ALA57 4.7 21.3 1.0 C A:CYS54 4.9 22.2 1.0 C A:CYS55 4.9 17.3 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with the 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 Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn436 b:26.4 occ:1.00 NE2 A:HIS86 2.0 20.3 1.0 SG A:CYS68 2.1 27.1 1.0 SG A:CYS65 2.4 26.5 1.0 SG A:CYS90 2.4 30.6 1.0 CE1 A:HIS86 2.9 20.1 1.0 CD2 A:HIS86 3.1 20.6 1.0 CB A:CYS65 3.2 23.0 1.0 CB A:CYS68 3.3 25.5 1.0 CB A:CYS90 3.3 26.0 1.0 N A:CYS68 3.6 29.5 1.0 CA A:CYS90 3.9 24.7 1.0 CA A:CYS68 4.0 27.6 1.0 ND1 A:HIS86 4.1 20.8 1.0 CG A:HIS86 4.2 19.0 1.0 CB A:ARG67 4.6 35.8 1.0 CA A:CYS65 4.7 23.8 1.0 C A:ARG67 4.7 36.1 1.0 O A:HOH499 4.7 25.6 1.0 C A:CYS90 4.8 29.2 1.0 CB A:ALA71 4.8 21.8 1.0 C A:CYS68 4.9 33.2 1.0 N A:LYS69 4.9 30.7 1.0 N A:ARG67 4.9 33.0 1.0 CA A:ARG67 4.9 32.9 1.0 O A:CYS90 4.9 27.2 1.0 C A:CYS65 5.0 29.0 1.0 CE A:MET93 5.0 31.9 1.0 N A:CYS90 5.0 24.8 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Histone Lysine Methyltransferase SMYD2 in Complex with the 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 Histone Lysine Methyltransferase SMYD2 in Complex with the Methyltransferase Inhibitor Sinefungin within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn437 b:15.2 occ:1.00 SG A:CYS264 2.3 20.6 1.0 SG A:CYS262 2.3 15.5 1.0 SG A:CYS267 2.3 15.7 1.0 SG A:CYS209 2.4 13.7 1.0 CB A:CYS209 3.2 10.8 1.0 CB A:CYS262 3.2 12.3 1.0 CB A:CYS267 3.3 14.4 1.0 CB A:CYS264 3.4 18.2 1.0 N A:CYS209 3.7 13.3 1.0 N A:CYS264 3.9 20.4 1.0 N A:CYS267 4.1 18.6 1.0 CA A:CYS209 4.1 11.4 1.0 CA A:CYS264 4.2 19.3 1.0 CA A:CYS267 4.3 16.5 1.0 NE2 A:HIS207 4.4 11.2 1.0 CA A:CYS262 4.4 13.9 1.0 C A:CYS262 4.5 19.0 1.0 NH2 A:ARG250 4.5 13.5 1.0 O A:CYS262 4.7 16.7 1.0 N A:GLU263 4.7 19.2 1.0 C A:CYS264 4.7 23.5 1.0 CD2 A:HIS207 4.8 11.4 1.0 C A:SER208 4.8 11.8 1.0 O A:CYS264 4.8 20.0 1.0 NE A:ARG250 4.8 14.0 1.0

Y.Jiang, N.Sirinupong, J.Brunzelle, Z.Yang. Crystal Structures of Histone and P53 Methyltransferase SMYD2 Reveal A Conformational Flexibility of the Autoinhibitory C-Terminal Domain. Plos One V. 6 21640 2011.
ISSN: ESSN 1932-6203
PubMed: 21738746
DOI: 10.1371/JOURNAL.PONE.0021640