Atomistry » Sodium » PDB 3ma9-3mo9 » 3max
Atomistry »
  Sodium »
    PDB 3ma9-3mo9 »
      3max »

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: Mon Oct 7 11:28:08 2024

Last articles

Ca in 5KN0
Ca in 5KTH
Ca in 5KSA
Ca in 5KS9
Ca in 5KRU
Ca in 5KR5
Ca in 5KN9
Ca in 5KN8
Ca in 5KN3
Ca in 5KMH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy