Zinc in PDB 3mek: Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine

All present enzymatic activity of Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine:
2.1.1.43;

The structure of Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine, PDB code: 3mek was solved by R.Lam, L.Dombrovski, Y.Li, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, H.Wu, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.70 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.809, 65.923, 108.102, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.8

The binding sites of Zinc atom in the Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine (pdb code 3mek). 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 Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine, PDB code: 3mek:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine


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 Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:13.1 occ:1.00 NE2 A:HIS83 2.1 10.6 1.0 SG A:CYS87 2.3 15.0 1.0 SG A:CYS62 2.3 15.8 1.0 SG A:CYS65 2.3 15.4 1.0 CE1 A:HIS83 3.0 8.5 1.0 CD2 A:HIS83 3.1 10.8 1.0 CB A:CYS62 3.2 17.3 1.0 CB A:CYS65 3.3 17.8 1.0 CB A:CYS87 3.3 15.0 1.0 N A:CYS65 3.5 19.5 1.0 CA A:CYS87 3.9 15.6 1.0 CA A:CYS65 4.0 19.0 1.0 ND1 A:HIS83 4.1 9.6 1.0 CG A:HIS83 4.2 12.7 1.0 CB A:GLN64 4.3 21.5 1.0 CB A:ALA68 4.6 14.4 1.0 CA A:CYS62 4.6 17.7 1.0 C A:GLN64 4.6 20.6 1.0 O A:HOH452 4.6 12.2 1.0 C A:CYS87 4.8 16.1 1.0 O A:CYS87 4.8 16.5 1.0 N A:ARG66 4.9 19.3 1.0 CA A:GLN64 4.9 20.7 1.0 C A:CYS65 4.9 19.2 1.0 C A:CYS62 4.9 18.3 1.0 CZ3 A:TRP80 4.9 19.9 1.0 N A:GLN64 4.9 19.9 1.0 N A:CYS87 5.0 15.2 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine


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 Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:17.0 occ:1.00 SG A:CYS75 2.3 18.1 1.0 SG A:CYS49 2.3 13.3 1.0 SG A:CYS52 2.4 15.3 1.0 SG A:CYS71 2.4 17.9 1.0 CB A:CYS49 3.1 14.7 1.0 CB A:CYS75 3.2 15.6 1.0 CB A:CYS52 3.2 14.8 1.0 CB A:CYS71 3.5 15.1 1.0 N A:CYS52 3.7 14.3 1.0 N A:CYS71 4.0 15.1 1.0 CA A:CYS52 4.0 14.7 1.0 CA A:CYS71 4.3 16.0 1.0 OG A:SER72 4.6 14.4 1.0 CA A:CYS49 4.6 14.5 1.0 CA A:CYS75 4.6 16.1 1.0 CB A:ARG51 4.8 15.9 1.0 C A:ARG51 4.8 14.8 1.0 C A:CYS52 4.9 14.4 1.0 N A:SER72 4.9 15.7 1.0 C A:CYS71 4.9 16.1 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine


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 Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:17.5 occ:1.00 SG A:CYS208 2.3 15.3 1.0 SG A:CYS261 2.3 16.6 1.0 SG A:CYS263 2.3 17.9 1.0 SG A:CYS266 2.3 13.8 1.0 CB A:CYS261 3.3 16.9 1.0 CB A:CYS208 3.3 15.0 1.0 CB A:CYS263 3.5 17.6 1.0 CB A:CYS266 3.5 12.8 1.0 N A:CYS266 4.1 12.5 1.0 N A:CYS263 4.1 18.5 1.0 N A:CYS208 4.2 14.2 1.0 CA A:CYS263 4.3 18.0 1.0 CA A:CYS266 4.4 13.3 1.0 CA A:CYS208 4.4 14.5 1.0 NE2 A:HIS206 4.4 8.7 1.0 CA A:CYS261 4.5 17.1 1.0 NE A:ARG249 4.6 10.1 1.0 NH2 A:ARG249 4.6 9.8 1.0 C A:CYS261 4.6 17.9 1.0 O A:CYS261 4.7 17.8 1.0 C A:CYS263 4.8 17.4 1.0 O A:CYS263 4.8 17.8 1.0 O A:HOH548 4.9 17.6 1.0 CD2 A:HIS206 5.0 8.0 1.0

R.Lam, L.Dombrovski, Y.Li, C.Bountra, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, J.Min, H.Wu. Crystal Structure of Human Histone-Lysine N-Methyltransferase SMYD3 in Complex with S-Adenosyl-L-Methionine To Be Published.