Zinc in PDB 5ex3: Crystal Structure of Human SMYD3 in Complex with A VEGFR1 Peptide

All present enzymatic activity of Crystal Structure of Human SMYD3 in Complex with A VEGFR1 Peptide:
2.1.1.43;

The structure of Crystal Structure of Human SMYD3 in Complex with A VEGFR1 Peptide, PDB code: 5ex3 was solved by Q.Qiao, W.Fu, N.Liu, 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)	30.00 / 2.41
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	53.378, 104.659, 117.599, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.3

The binding sites of Zinc atom in the Crystal Structure of Human SMYD3 in Complex with A VEGFR1 Peptide (pdb code 5ex3). 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 VEGFR1 Peptide, PDB code: 5ex3:
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 VEGFR1 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 VEGFR1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:58.2 occ:1.00 SG A:CYS75 2.3 68.4 1.0 SG A:CYS49 2.3 53.5 1.0 SG A:CYS71 2.5 60.3 1.0 SG A:CYS52 2.5 55.9 1.0 CB A:CYS75 3.1 64.9 1.0 CB A:CYS49 3.2 52.5 1.0 CB A:CYS52 3.4 52.8 1.0 CB A:CYS71 3.5 61.4 1.0 N A:CYS52 3.7 53.3 1.0 N A:CYS71 3.9 57.4 1.0 CA A:CYS52 4.1 57.6 1.0 CA A:CYS71 4.3 66.8 1.0 CB A:ARG51 4.4 56.1 1.0 CA A:CYS75 4.6 66.3 1.0 CA A:CYS49 4.6 51.9 1.0 CG A:ARG51 4.8 58.6 1.0 OG A:SER72 4.8 68.0 1.0 C A:ARG51 4.8 58.5 1.0 C A:CYS71 4.9 64.9 1.0 C A:CYS52 5.0 57.7 1.0 CA A:ARG51 5.0 50.8 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human SMYD3 in Complex with A VEGFR1 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 VEGFR1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:62.6 occ:1.00 NE2 A:HIS83 2.2 58.9 1.0 SG A:CYS65 2.3 61.7 1.0 SG A:CYS62 2.5 65.1 1.0 SG A:CYS87 2.5 63.8 1.0 CE1 A:HIS83 3.1 56.4 1.0 CB A:CYS62 3.2 65.5 1.0 CD2 A:HIS83 3.3 54.6 1.0 CB A:CYS65 3.3 73.8 1.0 CB A:CYS87 3.4 66.1 1.0 N A:CYS65 3.7 73.5 1.0 CA A:CYS87 3.9 66.2 1.0 CA A:CYS65 4.1 71.1 1.0 ND1 A:HIS83 4.2 58.5 1.0 CG A:HIS83 4.4 56.8 1.0 CB A:GLN64 4.4 89.6 1.0 O A:CYS87 4.6 73.0 1.0 CA A:CYS62 4.7 63.5 1.0 C A:CYS87 4.7 71.0 1.0 CB A:ALA68 4.8 53.3 1.0 C A:GLN64 4.8 94.3 1.0 N A:ARG66 4.9 94.6 1.0 C A:CYS65 4.9 72.5 1.0 C A:CYS62 5.0 68.6 1.0 O A:CYS62 5.0 67.2 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human SMYD3 in Complex with A VEGFR1 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 VEGFR1 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:59.6 occ:1.00 SG A:CYS261 2.4 62.2 1.0 SG A:CYS263 2.4 58.6 1.0 SG A:CYS208 2.4 56.6 1.0 SG A:CYS266 2.6 68.5 1.0 CB A:CYS208 3.2 58.1 1.0 CB A:CYS263 3.2 57.8 1.0 CB A:CYS261 3.2 60.8 1.0 CB A:CYS266 3.4 61.1 1.0 N A:CYS208 3.9 56.9 1.0 N A:CYS266 3.9 65.6 1.0 N A:CYS263 4.0 63.2 1.0 CA A:CYS263 4.0 61.1 1.0 CA A:CYS208 4.1 59.2 1.0 NE2 A:HIS206 4.2 55.2 1.0 CA A:CYS266 4.2 67.1 1.0 O A:CYS263 4.4 61.0 1.0 NH2 A:ARG249 4.4 60.5 1.0 CA A:CYS261 4.5 62.0 1.0 C A:CYS261 4.5 70.8 1.0 C A:CYS263 4.5 64.3 1.0 O A:CYS261 4.6 70.3 1.0 NE A:ARG249 4.6 52.4 1.0 CD2 A:HIS206 4.8 57.9 1.0 CB A:ARG265 4.9 64.5 1.0 C A:ARG265 4.9 65.0 1.0 N A:ASP262 5.0 71.0 1.0 C A:SER207 5.0 56.7 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