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Zinc in PDB 3f07: Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form

Enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form

All present enzymatic activity of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form, PDB code: 3f07 was solved by D.P.Dowling, S.L.Gantt, 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) 31.50 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.381, 90.171, 92.267, 90.00, 94.74, 90.00
R / Rfree (%) 21.6 / 26

Other elements in 3f07:

The structure of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form also contains other interesting chemical elements:

Potassium (K) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form (pdb code 3f07). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form, PDB code: 3f07:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3f07

Go back to Zinc Binding Sites List in 3f07
Zinc binding site 1 out of 4 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:37.9
occ:1.00
 OD2 A:ASP178 2.0 39.6 1.0
ND1 A:HIS180 2.1 46.8 1.0
OD2 A:ASP267 2.1 35.7 1.0
O2 A:AGE500 2.4 63.0 0.7
O1 A:AGE500 2.6 59.5 0.7
C16 A:AGE500 2.6 62.8 0.7
N2 A:AGE500 2.7 61.5 0.7
CE1 A:HIS180 2.8 48.3 1.0
CG A:ASP178 2.9 38.0 1.0
CG A:ASP267 3.0 37.5 1.0
OD1 A:ASP178 3.1 37.7 1.0
CG A:HIS180 3.2 45.6 1.0
OD1 A:ASP267 3.4 37.9 1.0
CB A:HIS180 3.7 44.2 1.0
C15 A:AGE500 3.8 64.2 0.7
N A:HIS180 3.9 41.4 1.0
CA A:GLY304 3.9 50.8 1.0
NE2 A:HIS180 4.0 47.8 1.0
CB A:ASP267 4.2 38.7 1.0
CD2 A:HIS180 4.2 46.5 1.0
CB A:ASP178 4.3 37.1 1.0
NE2 A:HIS142 4.3 50.7 1.0
N A:LEU179 4.3 37.9 1.0
N A:GLY304 4.4 50.3 1.0
CA A:HIS180 4.5 42.9 1.0
C14 A:AGE500 4.5 65.7 0.7
CB A:LEU179 4.6 37.6 1.0
OH A:TYR306 4.6 61.6 1.0
CE1 A:TYR306 4.7 60.2 1.0
CE1 A:HIS142 4.7 50.9 1.0
NE2 A:HIS143 4.8 50.0 1.0
CA A:LEU179 4.8 38.7 1.0
C A:LEU179 4.8 40.1 1.0

Zinc binding site 2 out of 4 in 3f07

Go back to Zinc Binding Sites List in 3f07
Zinc binding site 2 out of 4 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:68.2
occ:0.70
 ND1 A:HIS90 2.0 86.6 1.0
NE2 A:HIS78 2.2 76.5 1.0
OD1 A:ASP92 2.6 72.8 1.0
OD2 A:ASP87 2.7 91.7 1.0
CG A:HIS90 2.7 87.8 1.0
CE1 A:HIS78 2.7 77.1 1.0
CB A:HIS90 2.8 88.7 1.0
CE1 A:HIS90 3.2 86.1 1.0
CG A:ASP92 3.5 73.3 1.0
CD2 A:HIS78 3.5 76.4 1.0
CG A:ASP87 3.6 93.2 1.0
N A:SER93 3.7 66.9 1.0
CA A:SER93 3.7 64.1 1.0
OD2 A:ASP92 3.8 73.4 1.0
CG1 A:VAL82 3.8 78.2 1.0
OD1 A:ASP87 3.9 92.4 1.0
CD2 A:HIS90 4.0 87.7 1.0
ND1 A:HIS78 4.0 77.0 1.0
CB A:SER93 4.0 64.6 1.0
CA A:HIS90 4.1 89.2 1.0
O A:HIS90 4.1 87.9 1.0
NE2 A:HIS90 4.2 86.2 1.0
C A:ASP92 4.3 69.9 1.0
C A:HIS90 4.4 87.3 1.0
CG A:HIS78 4.4 76.1 1.0
CB A:ASP92 4.7 73.1 1.0
O A:ASP92 4.8 69.0 1.0
CB A:ASP87 4.9 94.6 1.0
N A:ASP92 4.9 76.8 1.0
CA A:ASP92 4.9 72.9 1.0

Zinc binding site 3 out of 4 in 3f07

Go back to Zinc Binding Sites List in 3f07
Zinc binding site 3 out of 4 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:40.4
occ:1.00
 ND1 B:HIS180 2.0 47.4 1.0
OD2 B:ASP267 2.0 35.4 1.0
OD2 B:ASP178 2.1 34.8 1.0
C16 B:AGE501 2.3 68.2 0.7
N2 B:AGE501 2.4 67.7 0.7
O2 B:AGE501 2.4 68.1 0.7
O1 B:AGE501 2.5 68.3 0.7
CE1 B:HIS180 2.7 47.7 1.0
CG B:ASP178 2.9 35.6 1.0
CG B:ASP267 3.0 38.0 1.0
OD1 B:ASP178 3.1 35.3 1.0
CG B:HIS180 3.2 46.8 1.0
C15 B:AGE501 3.3 69.5 0.7
OD1 B:ASP267 3.4 38.4 1.0
CB B:HIS180 3.7 45.0 1.0
N B:HIS180 3.8 41.4 1.0
NE2 B:HIS180 3.9 46.2 1.0
CA B:GLY304 4.0 49.5 1.0
C14 B:AGE501 4.0 71.4 0.7
CD2 B:HIS180 4.2 46.8 1.0
CB B:ASP267 4.2 38.9 1.0
N B:LEU179 4.3 39.4 1.0
CB B:ASP178 4.3 36.7 1.0
NE2 B:HIS142 4.4 50.6 1.0
N B:GLY304 4.4 49.6 1.0
CA B:HIS180 4.4 43.1 1.0
CB B:LEU179 4.5 38.4 1.0
OH B:TYR306 4.6 63.4 1.0
CE1 B:TYR306 4.7 61.5 1.0
CE1 B:HIS142 4.7 51.1 1.0
CA B:LEU179 4.8 39.4 1.0
C B:LEU179 4.8 40.3 1.0
NE2 B:HIS143 4.8 52.6 1.0

Zinc binding site 4 out of 4 in 3f07

Go back to Zinc Binding Sites List in 3f07
Zinc binding site 4 out of 4 in the Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Human HDAC8 Complexed with Apha in A New Monoclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn406

b:48.2
occ:1.00
 ND1 C:HIS180 2.0 48.4 1.0
OD2 C:ASP267 2.0 43.5 1.0
OD2 C:ASP178 2.0 37.9 1.0
O C:HOH813 2.2 29.5 1.0
CE1 C:HIS180 2.7 49.3 1.0
CG C:ASP178 2.9 39.7 1.0
CG C:ASP267 3.0 44.0 1.0
OD1 C:ASP178 3.1 39.6 1.0
CG C:HIS180 3.1 48.0 1.0
OD1 C:ASP267 3.4 45.6 1.0
CB C:HIS180 3.7 46.6 1.0
N C:HIS180 3.8 44.2 1.0
NE2 C:HIS180 3.9 48.6 1.0
CA C:GLY304 4.0 53.6 1.0
CD2 C:HIS180 4.1 47.9 1.0
CB C:ASP267 4.2 41.9 1.0
N C:LEU179 4.2 41.5 1.0
CB C:ASP178 4.3 39.9 1.0
NE2 C:HIS142 4.3 55.7 1.0
CA C:HIS180 4.4 45.5 1.0
CB C:LEU179 4.5 39.8 1.0
N C:GLY304 4.5 53.6 1.0
OH C:TYR306 4.6 64.2 1.0
CE1 C:HIS142 4.7 55.9 1.0
CE1 C:TYR306 4.7 62.7 1.0
CA C:LEU179 4.7 42.3 1.0
C C:LEU179 4.8 43.5 1.0
NE2 C:HIS143 4.8 61.9 1.0

Reference:

D.P.Dowling, S.L.Gantt, S.G.Gattis, C.A.Fierke, D.W.Christianson. Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors. Biochemistry V. 47 13554 2008.
ISSN: ISSN 0006-2960
PubMed: 19053282
DOI: 10.1021/BI801610C
Page generated: Thu Oct 24 12:59:44 2024

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