Zinc in PDB 7cwa: Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine

Enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine

All present enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine, PDB code: 7cwa was solved by Y.Huang, X.-N.Wu, Q.Zhou, Y.Wu, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.26 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 76.261, 132.246, 101.916, 90, 90, 90
R / Rfree (%) 28.9 / 33.3

Other elements in 7cwa:

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Fluorine (F) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine (pdb code 7cwa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine, PDB code: 7cwa:

Zinc binding site 1 out of 1 in 7cwa

Go back to Zinc Binding Sites List in 7cwa
Zinc binding site 1 out of 1 in the Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:46.7
occ:1.00
 O A:HOH1001 2.0 43.1 1.0
OD2 A:ASP597 2.1 29.6 1.0
OD1 A:ASP726 2.1 25.9 1.0
O A:HOH1023 2.5 30.1 1.0
CG A:ASP726 2.9 25.8 1.0
NE2 A:HIS596 2.9 30.2 1.0
CD2 A:HIS596 3.0 30.0 1.0
CG A:ASP597 3.0 29.2 1.0
OD2 A:ASP726 3.1 25.9 1.0
NE2 A:HIS560 3.1 29.1 1.0
OD1 A:ASP597 3.3 29.0 1.0
O A:HOH1002 3.7 30.5 1.0
CD2 A:HIS560 4.1 29.0 1.0
CE1 A:HIS560 4.1 29.1 1.0
O A:HOH1040 4.1 28.6 1.0
MG A:MG902 4.2 42.2 1.0
CE1 A:HIS596 4.2 30.1 1.0
NE2 A:HIS556 4.3 29.4 1.0
CB A:ASP726 4.3 25.5 1.0
CG A:HIS596 4.3 29.9 1.0
C5' A:CFB903 4.4 33.1 1.0
CB A:ASP597 4.4 29.2 1.0
CD2 A:HIS556 4.4 29.3 1.0
O A:HOH1005 4.7 31.7 1.0
ND1 A:HIS596 4.9 30.0 1.0
O5' A:CFB903 5.0 33.1 1.0
CA A:ASP726 5.0 25.3 1.0

Reference:

Y.Huang, X.Wu, Q.Zhou, H.-B.Luo. Discovery of Highly Selective and Orally Bioavailable Phosphodiesterase-8A Inhibitors. Structure-Activity Relationship, Crystal Structures, and in Vivo Studies To Be Published.
Page generated: Fri Sep 24 17:04:27 2021

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