Cobalt in PDB 3mz3: Crystal Structure of CO2+ HDAC8 Complexed with M344

All present enzymatic activity of Crystal Structure of CO2+ HDAC8 Complexed with M344:
3.5.1.98;

The structure of Crystal Structure of CO2+ HDAC8 Complexed with M344, PDB code: 3mz3 was solved by D.P.Dowling, S.G.Gattis, C.A.Fierke, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.626, 86.143, 94.508, 90.00, 94.07, 90.00
R / Rfree (%)	20.4 / 25.6

The structure of Crystal Structure of CO2+ HDAC8 Complexed with M344 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Cobalt atom in the Crystal Structure of CO2+ HDAC8 Complexed with M344 (pdb code 3mz3). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of CO2+ HDAC8 Complexed with M344, PDB code: 3mz3:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of CO2+ HDAC8 Complexed with M344


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of CO2+ HDAC8 Complexed with M344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co400 b:74.2 occ:1.00 OD2 A:ASP267 1.8 55.0 1.0 OD2 A:ASP178 2.0 52.7 1.0 ND1 A:HIS180 2.3 48.3 1.0 O4 A:B3N390 2.3 68.0 1.0 O2 A:B3N390 2.5 66.6 1.0 CG A:ASP267 2.9 54.9 1.0 CG A:ASP178 3.0 53.1 1.0 CE1 A:HIS180 3.1 48.4 1.0 N3 A:B3N390 3.1 66.2 1.0 C1 A:B3N390 3.2 64.4 1.0 OD1 A:ASP178 3.3 52.9 1.0 OD1 A:ASP267 3.4 54.8 1.0 CG A:HIS180 3.5 48.0 1.0 N A:HIS180 3.8 47.1 1.0 CB A:HIS180 3.9 47.4 1.0 CA A:GLY304 4.0 56.8 1.0 N A:LEU179 4.0 47.6 1.0 CB A:ASP267 4.2 54.2 1.0 CB A:LEU179 4.3 45.5 1.0 NE2 A:HIS180 4.3 50.1 1.0 CB A:ASP178 4.3 52.4 1.0 CA A:LEU179 4.5 46.8 1.0 CA A:HIS180 4.5 48.5 1.0 CD2 A:HIS180 4.5 49.1 1.0 C A:LEU179 4.5 46.5 1.0 N A:GLY304 4.5 58.7 1.0 OH A:TYR306 4.6 57.7 1.0 CE1 A:TYR306 4.6 54.9 1.0 C5 A:B3N390 4.7 62.3 1.0 C A:ASP178 4.8 49.9 1.0 C A:GLY304 4.9 56.4 1.0 NE2 A:HIS142 4.9 53.8 1.0 CA A:ASP178 5.0 51.8 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of CO2+ HDAC8 Complexed with M344


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of CO2+ HDAC8 Complexed with M344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:70.4 occ:1.00 OD2 B:ASP178 1.8 52.9 1.0 OD2 B:ASP267 2.1 59.1 1.0 O4 B:B3N390 2.2 77.3 1.0 ND1 B:HIS180 2.3 47.5 1.0 O2 B:B3N390 2.4 73.7 1.0 CG B:ASP178 2.9 53.3 1.0 N3 B:B3N390 2.9 75.5 1.0 C1 B:B3N390 3.0 74.9 1.0 CE1 B:HIS180 3.2 46.8 1.0 CG B:ASP267 3.2 57.4 1.0 OD1 B:ASP178 3.2 54.9 1.0 CG B:HIS180 3.3 47.2 1.0 N B:HIS180 3.6 46.0 1.0 OD1 B:ASP267 3.7 57.4 1.0 CB B:HIS180 3.7 46.9 1.0 N B:LEU179 4.0 46.8 1.0 CA B:GLY304 4.1 56.7 1.0 CB B:ASP178 4.2 53.7 1.0 CA B:HIS180 4.3 46.8 1.0 NE2 B:HIS180 4.3 47.1 1.0 CB B:LEU179 4.4 43.9 1.0 CD2 B:HIS180 4.4 47.6 1.0 C B:LEU179 4.5 44.8 1.0 C5 B:B3N390 4.5 74.5 1.0 CA B:LEU179 4.5 45.0 1.0 CB B:ASP267 4.5 55.9 1.0 NE2 B:HIS142 4.6 58.4 1.0 N B:GLY304 4.6 58.5 1.0 C B:ASP178 4.7 50.7 1.0 OH B:TYR306 4.8 55.5 1.0 CE1 B:HIS142 4.8 58.3 1.0 NE2 B:HIS143 4.9 57.3 1.0 CE1 B:TYR306 4.9 53.7 1.0 CA B:ASP178 4.9 53.1 1.0 C6 B:B3N390 5.0 73.8 1.0

D.P.Dowling, S.G.Gattis, C.A.Fierke, D.W.Christianson. Structures of Metal-Substituted Human Histone Deacetylase 8 Provide Mechanistic Inferences on Biological Function. Biochemistry V. 49 5048 2010.
ISSN: ISSN 0006-2960
PubMed: 20545365
DOI: 10.1021/BI1005046