Zinc in PDB 5ex0: Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide

All present enzymatic activity of Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide:
2.1.1.43;

The structure of Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide, PDB code: 5ex0 was solved by W.Fu, N.Liu, Q.Qiao, M.Wang, J.Min, B.Zhu, R.M.Xu, N.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.66 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.598, 104.181, 117.215, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 22.5

The binding sites of Zinc atom in the Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide (pdb code 5ex0). 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 SMYD3 in Complex with A MAP3K2 Peptide, PDB code: 5ex0:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide


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 SMYD3 in Complex with A MAP3K2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:31.0 occ:1.00 SG A:CYS75 2.2 32.9 1.0 SG A:CYS49 2.3 25.7 1.0 SG A:CYS71 2.4 31.1 1.0 SG A:CYS52 2.4 34.4 1.0 CB A:CYS49 3.1 28.2 1.0 CB A:CYS75 3.1 36.2 1.0 CB A:CYS71 3.4 35.4 1.0 CB A:CYS52 3.4 30.5 1.0 N A:CYS52 3.8 31.2 1.0 N A:CYS71 3.9 34.9 1.0 CA A:CYS52 4.2 31.4 1.0 CA A:CYS71 4.2 37.0 1.0 CB A:ARG51 4.5 31.3 1.0 CA A:CYS49 4.5 27.0 1.0 CA A:CYS75 4.6 37.5 1.0 C A:CYS71 4.8 39.2 1.0 C A:ARG51 4.9 32.1 1.0 OG A:SER72 4.9 40.8 1.0 N A:SER72 4.9 36.7 1.0 CG A:ARG51 4.9 36.6 1.0 C A:CYS52 5.0 32.0 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide


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 SMYD3 in Complex with A MAP3K2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:34.5 occ:1.00 NE2 A:HIS83 2.0 30.3 1.0 SG A:CYS87 2.2 33.6 1.0 SG A:CYS65 2.3 33.5 1.0 SG A:CYS62 2.3 36.3 1.0 CE1 A:HIS83 2.9 28.9 1.0 CD2 A:HIS83 3.1 27.9 1.0 CB A:CYS65 3.2 39.8 1.0 CB A:CYS62 3.3 36.9 1.0 CB A:CYS87 3.4 32.6 1.0 N A:CYS65 3.6 38.1 1.0 CA A:CYS87 4.0 34.4 1.0 CA A:CYS65 4.0 41.9 1.0 ND1 A:HIS83 4.0 28.0 1.0 CG A:HIS83 4.2 31.4 1.0 CB A:GLN64 4.3 46.4 1.0 C A:GLN64 4.6 41.0 1.0 CA A:CYS62 4.7 36.9 1.0 O A:HOH667 4.7 33.8 1.0 CB A:ALA68 4.7 26.8 1.0 C A:CYS87 4.8 35.3 1.0 CA A:GLN64 4.8 38.9 1.0 N A:ARG66 4.9 40.1 1.0 O A:CYS87 4.9 36.4 1.0 N A:GLN64 4.9 40.8 1.0 C A:CYS65 4.9 40.6 1.0 O A:CYS62 4.9 41.6 1.0 C A:CYS62 4.9 41.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human SMYD3 in Complex with A MAP3K2 Peptide


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 SMYD3 in Complex with A MAP3K2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:34.6 occ:1.00 SG A:CYS263 2.2 31.8 1.0 SG A:CYS261 2.3 36.1 1.0 SG A:CYS266 2.3 33.4 1.0 SG A:CYS208 2.4 29.8 1.0 CB A:CYS208 3.2 31.8 1.0 CB A:CYS261 3.3 28.5 1.0 CB A:CYS266 3.3 37.9 1.0 CB A:CYS263 3.5 34.0 1.0 N A:CYS208 3.9 27.2 1.0 N A:CYS266 4.0 35.6 1.0 N A:CYS263 4.1 37.3 1.0 CA A:CYS208 4.2 29.2 1.0 CA A:CYS266 4.2 39.4 1.0 CA A:CYS263 4.2 38.5 1.0 NE2 A:HIS206 4.4 28.9 1.0 CA A:CYS261 4.5 34.9 1.0 C A:CYS261 4.5 37.9 1.0 O A:CYS263 4.5 38.3 1.0 C A:CYS263 4.7 38.6 1.0 NE A:ARG249 4.7 31.5 1.0 O A:CYS261 4.7 37.0 1.0 NH2 A:ARG249 4.7 32.8 1.0 CD2 A:HIS206 4.9 27.6 1.0 N A:ASP262 4.9 37.7 1.0 C A:ARG265 4.9 37.5 1.0 CB A:ARG265 5.0 35.5 1.0

W.Fu, N.Liu, Q.Qiao, M.Wang, J.Min, B.Zhu, R.M.Xu, N.Yang. Structural Basis For Substrate Preference of SMYD3, A Set Domain-Containing Protein Lysine Methyltransferase J.Biol.Chem. V. 291 9173 2016.
ISSN: ESSN 1083-351X
PubMed: 26929412
DOI: 10.1074/JBC.M115.709832