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Zinc in PDB 7b9h: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A, PDB code: 7b9h was solved by A.Torretta, S.Abbate, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.13 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.748, 98.628, 119.821, 90, 90, 90
R / Rfree (%) 19.4 / 22.1

Other elements in 7b9h:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A (pdb code 7b9h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A, PDB code: 7b9h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7b9h

Go back to Zinc Binding Sites List in 7b9h
Zinc binding site 1 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


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 the PDE4D Catalytic Domain in Complex with Gebr- 42A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:16.0
occ:1.00
O A:HOH632 2.0 16.4 1.0
OD2 A:ASP201 2.0 12.5 1.0
NE2 A:HIS164 2.2 13.2 1.0
OD1 A:ASP318 2.2 14.4 1.0
O A:HOH781 2.2 16.2 1.0
NE2 A:HIS200 2.2 12.0 1.0
CG A:ASP318 3.0 16.2 1.0
CD2 A:HIS200 3.1 12.5 1.0
CG A:ASP201 3.1 12.6 1.0
CE1 A:HIS164 3.1 14.0 1.0
CD2 A:HIS164 3.1 12.6 1.0
OD2 A:ASP318 3.2 24.0 1.0
CE1 A:HIS200 3.3 12.5 1.0
OD1 A:ASP201 3.6 12.7 1.0
MG A:MG502 3.7 11.9 1.0
O A:HOH854 4.0 14.3 1.0
O A:HOH708 4.2 17.3 1.0
CD2 A:HIS160 4.2 15.3 1.0
CG A:HIS200 4.3 11.0 1.0
ND1 A:HIS164 4.3 13.8 1.0
CB A:ASP201 4.3 13.0 1.0
CG A:HIS164 4.3 13.3 1.0
ND1 A:HIS200 4.3 12.1 1.0
NE2 A:HIS160 4.3 16.0 1.0
CB A:ASP318 4.4 14.6 1.0
C16 A:T3K524 4.5 24.5 0.8
O A:HOH713 4.7 13.3 1.0
CG2 A:VAL168 4.7 14.5 1.0
C17 A:T3K524 4.8 28.1 0.7
O A:HOH800 4.9 25.5 0.4
CA A:ASP318 5.0 15.5 1.0

Zinc binding site 2 out of 2 in 7b9h

Go back to Zinc Binding Sites List in 7b9h
Zinc binding site 2 out of 2 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:17.2
occ:1.00
OD2 B:ASP201 2.1 14.1 1.0
O B:HOH642 2.1 16.3 1.0
OD1 B:ASP318 2.1 14.8 1.0
NE2 B:HIS164 2.2 14.4 1.0
NE2 B:HIS200 2.2 17.0 1.0
O B:HOH726 2.3 19.0 1.0
CD2 B:HIS200 3.1 14.7 1.0
CG B:ASP318 3.1 19.7 1.0
CG B:ASP201 3.1 14.6 1.0
CE1 B:HIS164 3.1 16.7 1.0
CD2 B:HIS164 3.2 16.4 1.0
CE1 B:HIS200 3.2 16.7 1.0
OD2 B:ASP318 3.3 23.2 1.0
OD1 B:ASP201 3.5 14.9 1.0
MG B:MG502 3.7 12.2 1.0
O B:HOH801 4.0 14.9 1.0
CD2 B:HIS160 4.2 15.1 1.0
O B:HOH709 4.2 18.4 1.0
CG B:HIS200 4.3 15.7 1.0
ND1 B:HIS164 4.3 16.8 1.0
ND1 B:HIS200 4.3 14.9 1.0
CG B:HIS164 4.3 15.1 1.0
CB B:ASP201 4.3 15.1 1.0
NE2 B:HIS160 4.4 16.7 1.0
CB B:ASP318 4.4 13.9 1.0
O B:HOH684 4.7 14.3 1.0
CG2 B:VAL168 4.7 15.0 1.0
CA B:ASP318 5.0 13.1 1.0

Reference:

C.Brullo, F.Rapetti, S.Abbate, T.Prosdocimi, A.Torretta, M.Semrau, M.Massa, S.Alfei, P.Storici, E.Parisini, O.Bruno. Design, Synthesis, Biological Evaluation and Structural Characterization of Novel Gebr Library PDE4D Inhibitors Eur.J.Med.Chem. 2021.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2021.113638
Page generated: Thu Aug 21 22:45:44 2025

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