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Calcium in PDB 3max: Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide

Enzymatic activity of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide

All present enzymatic activity of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide, PDB code: 3max was solved by R.J.Skene, A.J.Jennings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.311, 97.227, 138.849, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.4

Other elements in 3max:

The structure of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide (pdb code 3max). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide, PDB code: 3max:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 3max

Go back to Calcium Binding Sites List in 3max
Calcium binding site 1 out of 3 in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca380

b:24.8
occ:1.00
 O A:ASP181 2.6 23.3 1.0
O A:PHE203 2.7 30.2 1.0
OD1 A:ASP179 2.7 29.6 1.0
O A:HIS183 2.7 24.6 1.0
OG A:SER202 2.8 27.1 1.0
O A:ASP179 3.0 25.5 1.0
CG A:ASP179 3.3 27.5 1.0
C A:ASP179 3.6 25.7 1.0
C A:ASP181 3.6 26.0 1.0
C A:PHE203 3.6 28.8 1.0
C A:HIS183 3.7 25.3 1.0
N A:ASP181 3.7 24.0 1.0
N A:PHE203 3.8 26.7 1.0
CB A:ASP179 3.8 25.6 1.0
CB A:HIS204 3.9 27.2 1.0
CB A:ASP181 4.0 25.8 1.0
CA A:ASP181 4.0 24.9 1.0
CB A:SER202 4.1 28.3 1.0
N A:ILE180 4.2 26.7 1.0
OD2 A:ASP179 4.2 27.5 1.0
C A:ILE180 4.2 24.7 1.0
CA A:ILE180 4.3 21.8 1.0
CA A:HIS184 4.3 24.7 1.0
CA A:ASP179 4.3 26.8 1.0
N A:HIS184 4.3 26.4 1.0
CA A:HIS204 4.4 29.6 1.0
CA A:SER202 4.4 26.9 1.0
ND1 A:HIS204 4.4 28.0 1.0
N A:HIS204 4.4 28.2 1.0
N A:GLY185 4.4 29.5 1.0
N A:HIS183 4.4 24.7 1.0
CA A:PHE203 4.4 28.0 1.0
C A:SER202 4.5 29.0 1.0
O A:HOH397 4.6 24.4 1.0
CG A:HIS204 4.6 28.5 1.0
C A:ILE182 4.6 26.5 1.0
C A:HIS184 4.6 27.3 1.0
CA A:HIS183 4.7 25.0 1.0
CE1 A:HIS145 4.7 23.9 1.0
N A:ILE182 4.7 25.4 1.0
O A:ILE182 5.0 27.4 1.0
O A:ILE180 5.0 22.9 1.0

Calcium binding site 2 out of 3 in 3max

Go back to Calcium Binding Sites List in 3max
Calcium binding site 2 out of 3 in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca380

b:24.7
occ:1.00
 O B:ASP181 2.5 25.4 1.0
O B:PHE203 2.6 27.1 1.0
OD1 B:ASP179 2.6 25.4 1.0
O B:HIS183 2.6 22.1 1.0
OG B:SER202 2.9 25.2 1.0
O B:ASP179 2.9 23.2 1.0
CG B:ASP179 3.3 25.9 1.0
C B:ASP179 3.5 24.3 1.0
C B:ASP181 3.5 23.5 1.0
C B:PHE203 3.6 23.2 1.0
N B:ASP181 3.6 21.4 1.0
C B:HIS183 3.7 25.4 1.0
CB B:HIS204 3.9 24.7 1.0
N B:PHE203 3.9 24.9 1.0
CB B:ASP179 3.9 24.7 1.0
CA B:ASP181 4.0 22.0 1.0
CB B:ASP181 4.0 20.4 1.0
N B:ILE180 4.1 24.2 1.0
C B:ILE180 4.1 21.7 1.0
CB B:SER202 4.1 24.4 1.0
OD2 B:ASP179 4.1 26.3 1.0
CA B:ILE180 4.2 23.9 1.0
CA B:ASP179 4.3 24.0 1.0
CA B:HIS204 4.4 25.9 1.0
CA B:SER202 4.4 24.9 1.0
ND1 B:HIS204 4.4 25.5 1.0
N B:HIS183 4.4 22.1 1.0
CA B:HIS184 4.4 25.7 1.0
N B:HIS204 4.4 25.4 1.0
N B:HIS184 4.4 25.4 1.0
CA B:PHE203 4.4 26.1 1.0
N B:GLY185 4.4 26.4 1.0
O B:HOH3 4.5 21.4 1.0
C B:SER202 4.5 26.4 1.0
C B:ILE182 4.6 24.3 1.0
CG B:HIS204 4.6 25.8 1.0
N B:ILE182 4.6 23.0 1.0
CA B:HIS183 4.7 24.0 1.0
C B:HIS184 4.7 27.3 1.0
CE1 B:HIS145 4.8 20.9 1.0
O B:ILE180 4.9 21.2 1.0
CA B:ILE182 5.0 23.4 1.0
O B:ILE182 5.0 22.9 1.0

Calcium binding site 3 out of 3 in 3max

Go back to Calcium Binding Sites List in 3max
Calcium binding site 3 out of 3 in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca380

b:33.7
occ:1.00
 O C:ASP181 2.6 34.4 1.0
O C:PHE203 2.6 31.5 1.0
OD1 C:ASP179 2.6 34.1 1.0
O C:HIS183 2.7 33.4 1.0
O C:ASP179 2.8 34.0 1.0
OG C:SER202 2.9 34.2 1.0
CG C:ASP179 3.3 33.6 1.0
C C:ASP179 3.5 34.2 1.0
C C:ASP181 3.5 35.8 1.0
C C:PHE203 3.6 35.8 1.0
N C:ASP181 3.6 35.5 1.0
C C:HIS183 3.7 34.8 1.0
CB C:ASP179 3.8 34.3 1.0
N C:PHE203 3.8 34.2 1.0
CB C:HIS204 3.9 34.8 1.0
CA C:ASP181 4.0 34.7 1.0
CB C:ASP181 4.0 32.5 1.0
CB C:SER202 4.1 35.0 1.0
OD2 C:ASP179 4.1 32.4 1.0
C C:ILE180 4.1 36.4 1.0
N C:ILE180 4.1 34.3 1.0
CA C:ASP179 4.3 32.8 1.0
CA C:ILE180 4.3 35.3 1.0
N C:HIS183 4.4 33.5 1.0
ND1 C:HIS204 4.4 34.9 1.0
CA C:HIS184 4.4 36.5 1.0
CA C:PHE203 4.4 35.9 1.0
CA C:HIS204 4.4 37.0 1.0
CA C:SER202 4.4 35.8 1.0
N C:HIS184 4.4 35.3 1.0
N C:GLY185 4.4 36.5 1.0
N C:HIS204 4.4 35.1 1.0
C C:SER202 4.4 35.7 1.0
O C:HOH538 4.6 37.6 1.0
C C:ILE182 4.6 33.2 1.0
CG C:HIS204 4.6 35.6 1.0
N C:ILE182 4.7 35.2 1.0
CA C:HIS183 4.7 32.8 1.0
C C:HIS184 4.7 36.4 1.0
CE1 C:HIS145 4.8 34.7 1.0
O C:ILE180 4.9 38.1 1.0
O C:ILE182 5.0 32.4 1.0

Reference:

J.C.Bressi, A.J.Jennings, R.Skene, Y.Wu, R.Melkus, R.De Jong, S.O'connell, C.E.Grimshaw, M.Navre, A.R.Gangloff. Exploration of the HDAC2 Foot Pocket: Synthesis and Sar of Substituted N-(2-Aminophenyl)Benzamides. Bioorg.Med.Chem.Lett. V. 20 3142 2010.
ISSN: ISSN 0960-894X
PubMed: 20392638
DOI: 10.1016/J.BMCL.2010.03.091
Page generated: Tue Jul 8 14:34:02 2025

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