Magnesium 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:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin, PDB code: 3pdn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of SMYD3 in Complex with Methyltransferase Inhibitor Sinefungin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg439 b:26.0 occ:1.00 O A:HOH875 2.1 28.3 1.0 O A:HOH1002 2.1 27.4 1.0 O A:HOH932 2.1 23.7 1.0 O A:HOH751 2.1 23.5 1.0 O A:HOH791 2.1 26.8 1.0 O A:HOH1003 2.2 32.0 1.0 OD1 A:ASN134 4.0 20.6 1.0 OE2 A:GLU130 4.1 16.0 1.0 OE1 A:GLU130 4.1 17.4 1.0 O A:HOH994 4.2 21.0 1.0 OD1 A:ASN132 4.3 16.7 1.0 CD A:GLU130 4.4 22.2 1.0 CE A:LYS135 4.6 16.0 1.0 O A:HOH996 4.6 28.8 1.0 ND2 A:ASN134 4.7 22.3 1.0 CG A:ASN134 4.7 26.2 1.0 O A:HOH1006 4.9 32.7 1.0 NZ A:LYS135 5.0 23.3 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg440 b:27.0 occ:1.00 O A:HOH869 2.0 25.9 1.0 O A:HOH1006 2.0 32.7 1.0 O A:HOH1005 2.0 34.4 1.0 O A:HOH1004 2.2 31.4 1.0 O A:HOH896 2.3 24.5 1.0 O A:HOH792 4.1 28.5 1.0 O A:LEU129 4.2 11.2 1.0 O A:HOH674 4.2 15.5 1.0 OE2 A:GLU130 4.4 16.0 1.0 O A:ASP128 4.5 11.4 1.0 CA A:GLU130 4.5 9.1 1.0 O A:HOH957 4.6 30.1 1.0 N A:SER131 4.8 8.4 1.0 CD A:GLU130 4.8 22.2 1.0 C A:LEU129 4.8 12.4 1.0 OE1 A:GLU130 4.9 17.4 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