Magnesium in PDB 5eei: Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha

All present enzymatic activity of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha:
3.5.1.98;

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei was solved by Y.Hai, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.26 / 1.32
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.790, 83.551, 86.806, 90.00, 98.09, 90.00
R / Rfree (%)	12.5 / 14.8

The structure of Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha also contains other interesting chemical elements:

Potassium	(K)	4 atoms
Zinc	(Zn)	2 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Magnesium atom in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha (pdb code 5eei). 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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha, PDB code: 5eei:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2010 b:40.9 occ:0.66 MG A:MG2010 0.0 40.9 0.7 MG A:MG2010 1.9 45.5 0.3 O A:PHE793 2.9 19.2 1.0 HB3 A:PHE793 3.2 19.6 1.0 OH A:TYR662 3.5 21.0 1.0 CZ2 A:TRP794 3.6 17.5 1.0 CE2 A:TRP794 3.6 15.7 1.0 CZ A:TYR662 3.6 18.3 1.0 CH2 A:TRP794 3.7 18.0 1.0 HH A:TYR662 3.8 25.2 1.0 HE2 A:TYR662 3.8 22.9 1.0 CE2 A:TYR662 3.8 19.1 1.0 C A:PHE793 3.9 17.3 1.0 HZ2 A:TRP794 3.9 21.0 1.0 CD2 A:TRP794 3.9 14.9 1.0 CZ3 A:TRP794 3.9 18.2 1.0 CE3 A:TRP794 4.0 16.8 1.0 HA3 A:GLY661 4.0 19.6 1.0 CB A:PHE793 4.1 16.4 1.0 HH2 A:TRP794 4.1 21.6 1.0 NE1 A:TRP794 4.2 15.7 1.0 CE1 A:TYR662 4.3 17.5 1.0 HB2 A:PHE793 4.3 19.6 1.0 HA A:PHE793 4.4 19.9 1.0 CA A:PHE793 4.4 16.6 1.0 HZ3 A:TRP794 4.4 21.9 1.0 HA A:TRP794 4.5 19.5 1.0 HE1 A:TRP794 4.6 18.8 1.0 HE3 A:TRP794 4.6 20.2 1.0 HE1 A:TYR662 4.6 21.0 1.0 O A:HOH2350 4.6 41.4 1.0 CD2 A:TYR662 4.6 17.0 1.0 CG A:TRP794 4.6 14.3 1.0 CD1 A:TRP794 4.8 14.8 1.0 O A:HOH2254 4.8 37.1 1.0 O A:ARG660 4.8 18.8 1.0 N A:TRP794 4.9 16.4 1.0 CA A:GLY661 4.9 16.4 1.0 O A:GLY661 5.0 16.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha


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 Danio Rerio Histone Deacetylase 6 Catalytic Domain 2 in Complex with Saha within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2010 b:45.5 occ:0.34 MG A:MG2010 0.0 45.5 0.3 MG A:MG2010 1.9 40.9 0.7 O A:PHE793 3.0 19.2 1.0 HB3 A:PHE793 3.5 19.6 1.0 HA A:PHE793 3.8 19.9 1.0 OH A:TYR662 4.0 21.0 1.0 C A:PHE793 4.0 17.3 1.0 HE2 A:TYR662 4.0 22.9 1.0 CA A:PHE793 4.2 16.6 1.0 CB A:PHE793 4.3 16.4 1.0 HD1 A:PHE793 4.3 20.1 1.0 O A:HOH2254 4.4 37.1 1.0 HH A:TYR662 4.4 25.2 1.0 CE2 A:TYR662 4.5 19.1 1.0 CZ A:TYR662 4.5 18.3 1.0 O A:HOH2209 4.6 38.5 1.0 O A:HOH2340 4.7 31.4 1.0 HA3 A:GLY661 4.8 19.6 1.0 O A:ARG660 4.9 18.8 1.0 HB2 A:PHE793 4.9 19.6 1.0

Y.Hai, D.W.Christianson. Histone Deacetylase 6 Structure and Molecular Basis of Catalysis and Inhibition. Nat.Chem.Biol. V. 12 741 2016.
ISSN: ESSN 1552-4469
PubMed: 27454933
DOI: 10.1038/NCHEMBIO.2134