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Sodium 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:

Calcium (Ca) 3 atoms
Zinc (Zn) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Human HDAC2 Complexed with An N-(2-Aminophenyl) Benzamide, PDB code: 3max:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3max

Go back to Sodium Binding Sites List in 3max
Sodium 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 Sodium with other atoms in the Na 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:Na381

b:29.6
occ:1.00
O A:PHE192 2.2 27.0 1.0
O A:VAL198 2.3 30.2 1.0
O A:HOH396 2.4 27.9 1.0
O A:THR195 2.5 30.9 1.0
O A:HOH425 2.6 34.8 1.0
C A:PHE192 3.3 27.8 1.0
C A:VAL198 3.6 29.2 1.0
O A:TYR227 3.7 30.3 1.0
C A:THR195 3.7 32.2 1.0
CB A:PHE192 3.9 28.1 1.0
CB A:TYR227 3.9 29.4 1.0
CG2 A:THR195 4.1 31.0 1.0
N A:THR195 4.1 31.5 1.0
CA A:PHE192 4.2 28.6 1.0
N A:TYR193 4.2 26.0 1.0
C A:TYR227 4.2 30.7 1.0
C A:TYR193 4.3 30.9 1.0
CA A:TYR193 4.3 28.4 1.0
O A:TYR193 4.4 29.1 1.0
CA A:THR195 4.4 31.1 1.0
N A:MET199 4.5 28.1 1.0
CA A:VAL198 4.5 29.1 1.0
CA A:MET199 4.5 30.4 1.0
CB A:VAL198 4.6 27.7 1.0
N A:VAL198 4.6 28.1 1.0
CA A:GLY224 4.6 32.1 1.0
O A:GLY224 4.7 31.9 1.0
CA A:TYR227 4.7 29.1 1.0
N A:THR194 4.7 31.8 1.0
N A:ASP196 4.8 31.0 1.0
N A:THR200 4.9 28.1 1.0
CB A:THR195 4.9 31.9 1.0
CA A:ASP196 5.0 31.1 1.0

Sodium binding site 2 out of 3 in 3max

Go back to Sodium Binding Sites List in 3max
Sodium 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 Sodium with other atoms in the Na 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:Na381

b:28.8
occ:1.00
O B:HOH385 2.3 21.6 1.0
O B:VAL198 2.3 29.0 1.0
O B:PHE192 2.3 28.9 1.0
O B:THR195 2.5 30.8 1.0
O B:HOH441 2.5 33.5 1.0
C B:PHE192 3.5 27.5 1.0
C B:VAL198 3.6 30.1 1.0
O B:TYR227 3.6 34.6 1.0
C B:THR195 3.7 30.4 1.0
CB B:TYR227 3.7 28.7 1.0
CB B:PHE192 4.1 27.7 1.0
C B:TYR227 4.1 31.8 1.0
N B:THR195 4.1 30.1 1.0
CG2 B:THR195 4.3 28.9 1.0
O B:TYR193 4.3 32.5 1.0
C B:TYR193 4.3 30.6 1.0
N B:TYR193 4.3 28.9 1.0
CA B:TYR193 4.3 31.2 1.0
CA B:PHE192 4.4 27.9 1.0
CA B:THR195 4.4 30.9 1.0
N B:MET199 4.5 27.4 1.0
CA B:MET199 4.5 27.2 1.0
CA B:TYR227 4.5 30.6 1.0
CA B:VAL198 4.5 30.0 1.0
N B:VAL198 4.6 30.9 1.0
O B:GLY224 4.6 31.2 1.0
CB B:VAL198 4.6 29.9 1.0
CA B:GLY224 4.7 32.8 1.0
N B:ASP196 4.7 31.2 1.0
N B:ALA228 4.8 31.2 1.0
N B:THR200 4.8 26.2 1.0
N B:THR194 4.9 31.9 1.0
CA B:ASP196 4.9 31.6 1.0
CG B:TYR227 4.9 30.2 1.0
CB B:THR195 5.0 29.7 1.0

Sodium binding site 3 out of 3 in 3max

Go back to Sodium Binding Sites List in 3max
Sodium 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 Sodium with other atoms in the Na 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:Na381

b:32.5
occ:1.00
O C:HOH389 2.3 24.1 1.0
O C:PHE192 2.3 31.0 1.0
O C:VAL198 2.3 35.5 1.0
O C:THR195 2.4 33.8 1.0
O C:HOH464 2.7 45.8 1.0
C C:PHE192 3.5 33.6 1.0
C C:VAL198 3.6 35.0 1.0
C C:THR195 3.6 36.3 1.0
O C:TYR227 3.6 33.4 1.0
CB C:TYR227 3.8 35.0 1.0
CB C:PHE192 4.0 32.4 1.0
N C:THR195 4.1 35.2 1.0
CG2 C:THR195 4.1 34.6 1.0
C C:TYR227 4.2 35.8 1.0
C C:TYR193 4.2 34.7 1.0
O C:TYR193 4.3 30.9 1.0
CA C:THR195 4.3 36.1 1.0
CA C:PHE192 4.4 31.1 1.0
N C:TYR193 4.4 33.5 1.0
CA C:TYR193 4.4 34.6 1.0
CA C:GLY224 4.4 35.5 1.0
N C:MET199 4.5 35.0 1.0
CA C:MET199 4.5 36.4 1.0
CA C:VAL198 4.5 34.1 1.0
O C:GLY224 4.5 34.9 1.0
N C:VAL198 4.6 34.0 1.0
CA C:TYR227 4.6 34.3 1.0
N C:ASP196 4.6 35.5 1.0
CB C:VAL198 4.7 33.5 1.0
N C:THR194 4.7 32.7 1.0
CA C:ASP196 4.8 37.1 1.0
CB C:THR195 4.8 36.8 1.0
N C:ALA228 4.9 35.6 1.0
N C:THR200 5.0 36.9 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 Dec 15 06:17:23 2020

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