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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 3mz4:

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

Potassium (K) 4 atoms

Manganese Binding Sites:

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 3mz4

Go back to Manganese Binding Sites List in 3mz4
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 3mz4

Go back to Manganese Binding Sites List in 3mz4
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

Reference:

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
Page generated: Tue Dec 15 04:12:44 2020

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