Manganese in PDB 3mz4: Crystal Structure of D101L MN2+ HDAC8 Complexed with M344

All present enzymatic activity of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344:
3.5.1.98;

The structure of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344, PDB code: 3mz4 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)	45.35 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.353, 91.148, 104.547, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.9

The structure of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344 also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Manganese atom in the Crystal Structure of D101L MN2+ HDAC8 Complexed with M344 (pdb code 3mz4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of D101L MN2+ HDAC8 Complexed with M344, PDB code: 3mz4:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of D101L MN2+ HDAC8 Complexed with M344


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn390 b:14.7 occ:1.00 O4 A:B3N501 1.9 7.7 0.3 OD2 A:ASP267 2.0 19.3 1.0 O A:HOH470 2.0 12.0 0.7 OD2 A:ASP178 2.1 15.5 1.0 ND1 A:HIS180 2.2 14.2 1.0 O A:HOH469 2.3 9.5 0.7 O2 A:B3N501 2.3 7.8 0.3 N3 A:B3N501 2.6 7.2 0.3 C1 A:B3N501 2.8 5.2 0.3 CG A:ASP178 2.9 14.4 1.0 CE1 A:HIS180 3.0 18.2 1.0 CG A:ASP267 3.1 19.0 1.0 OD1 A:ASP178 3.1 12.4 1.0 CG A:HIS180 3.3 14.3 1.0 OD1 A:ASP267 3.4 14.6 1.0 CB A:HIS180 3.7 15.2 1.0 N A:HIS180 3.9 15.1 1.0 O3 A:GOL705 4.0 32.9 0.7 CA A:GLY304 4.0 15.9 1.0 NE2 A:HIS180 4.2 16.1 1.0 N A:LEU179 4.3 12.5 1.0 C5 A:B3N501 4.3 7.2 0.3 N A:GLY304 4.3 16.2 1.0 CD2 A:HIS180 4.3 14.4 1.0 CB A:ASP178 4.3 11.7 1.0 CB A:ASP267 4.4 16.0 1.0 NE2 A:HIS142 4.4 12.9 1.0 CA A:HIS180 4.5 15.7 1.0 CB A:LEU179 4.5 14.2 1.0 OH A:TYR306 4.5 14.3 1.0 CE1 A:TYR306 4.7 13.9 1.0 CE1 A:HIS142 4.7 11.0 1.0 CA A:LEU179 4.7 14.9 1.0 C A:LEU179 4.8 15.8 1.0 C3 A:GOL705 4.8 33.9 0.7 C21 B:B3N501 4.9 36.6 0.7 C6 A:B3N501 4.9 11.3 0.3 NE2 A:HIS143 5.0 15.2 1.0 C A:ASP178 5.0 13.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of D101L MN2+ HDAC8 Complexed with M344


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D101L MN2+ HDAC8 Complexed with M344 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn390 b:14.4 occ:1.00 OD2 B:ASP178 2.0 15.2 1.0 OD2 B:ASP267 2.0 16.3 1.0 ND1 B:HIS180 2.2 17.4 1.0 O2 B:B3N501 2.2 13.1 0.7 O4 B:B3N501 2.3 15.0 0.7 C1 B:B3N501 2.7 21.8 0.7 N3 B:B3N501 2.7 20.4 0.7 CG B:ASP178 2.9 14.1 1.0 CG B:ASP267 3.1 17.5 1.0 OD1 B:ASP178 3.1 15.8 1.0 CE1 B:HIS180 3.1 13.4 1.0 CG B:HIS180 3.3 15.7 1.0 OD1 B:ASP267 3.4 13.6 1.0 CB B:HIS180 3.6 13.4 1.0 N B:HIS180 3.9 15.2 1.0 O3 B:GOL706 3.9 41.5 0.8 CA B:GLY304 4.0 15.1 1.0 C5 B:B3N501 4.0 25.0 0.7 CB B:ASP178 4.3 11.3 1.0 NE2 B:HIS142 4.3 12.8 1.0 NE2 B:HIS180 4.3 15.8 1.0 N B:LEU179 4.4 13.1 1.0 CD2 B:HIS180 4.4 17.2 1.0 N B:GLY304 4.4 15.1 1.0 CB B:ASP267 4.4 12.4 1.0 CA B:HIS180 4.4 15.0 1.0 CB B:LEU179 4.4 15.7 1.0 OH B:TYR306 4.5 19.3 1.0 C6 B:B3N501 4.7 23.7 0.7 CE1 B:HIS142 4.7 13.3 1.0 CA B:LEU179 4.7 14.9 1.0 CE1 B:TYR306 4.8 14.2 1.0 C B:LEU179 4.8 15.3 1.0 C21 A:B3N501 4.8 12.7 0.3 C B:ASP178 5.0 14.9 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