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Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A, PDB code: 7b9h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7b9h

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Magnesium binding site 1 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg502

b:11.9
occ:1.00
 O A:HOH713 2.1 13.3 1.0
OD1 A:ASP201 2.1 12.7 1.0
O A:HOH854 2.1 14.3 1.0
O A:HOH707 2.1 15.9 1.0
O A:HOH632 2.1 16.4 1.0
O A:HOH720 2.2 15.2 1.0
CG A:ASP201 3.1 12.6 1.0
OD2 A:ASP201 3.4 12.5 1.0
ZN A:ZN501 3.7 16.0 1.0
C16 A:T3K524 3.9 24.5 0.8
OE2 A:GLU230 4.1 18.2 1.0
O A:HOH781 4.1 16.2 1.0
CD2 A:HIS200 4.1 12.5 1.0
NE2 A:HIS233 4.1 13.6 1.0
O A:HIS200 4.2 12.3 1.0
O A:HOH826 4.3 20.1 1.0
OG1 A:THR271 4.3 15.4 1.0
O A:HOH620 4.4 35.1 1.0
OD2 A:ASP318 4.4 24.0 1.0
CD2 A:HIS233 4.4 11.9 1.0
CB A:ASP201 4.5 13.0 1.0
CD2 A:HIS204 4.5 13.2 1.0
N15 A:T3K524 4.5 27.5 0.4
NE2 A:HIS200 4.6 12.0 1.0
O A:THR271 4.7 17.8 1.0
NE2 A:HIS160 4.7 16.0 1.0
CA A:ASP201 4.8 12.5 1.0
CB A:THR271 4.8 16.7 1.0
NE2 A:HIS204 4.8 14.4 1.0
CD2 A:HIS160 4.8 15.3 1.0
CG A:GLU230 4.9 16.4 1.0
CD A:GLU230 4.9 18.8 1.0

Magnesium binding site 2 out of 8 in 7b9h

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Magnesium binding site 2 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg503

b:33.8
occ:1.00
 O A:HOH687 2.0 31.8 1.0
O A:HOH711 2.1 34.1 1.0
O A:HOH956 2.1 40.0 1.0
O A:HOH933 3.8 36.6 1.0
OD1 A:ASP187 4.1 26.0 1.0
O A:HOH738 4.3 33.5 1.0
OD2 A:ASP187 4.3 26.2 1.0
O A:HOH909 4.3 44.9 1.0
O A:HOH818 4.4 35.7 1.0
CG A:ASP187 4.6 29.3 1.0
O A:HOH948 4.7 39.3 1.0

Magnesium binding site 3 out of 8 in 7b9h

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Magnesium binding site 3 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 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:Mg504

b:39.5
occ:1.00
 O A:HOH827 2.0 45.5 1.0
O A:HOH817 2.1 46.5 1.0
OD1 A:ASN251 2.1 26.4 1.0
CG A:ASN251 3.2 29.2 1.0
ND2 A:ASN251 3.8 26.9 1.0
O A:GLN250 4.4 26.9 1.0
NE2 A:GLN250 4.5 38.7 1.0
CB A:ASN251 4.5 24.1 1.0
CA A:ASN251 4.7 24.8 1.0
C A:GLN250 4.9 27.3 1.0
CG A:GLN250 4.9 29.1 1.0

Magnesium binding site 4 out of 8 in 7b9h

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Magnesium binding site 4 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 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:Mg505

b:24.0
occ:1.00
 O A:HOH701 2.0 28.1 1.0
OD2 A:ASP305 2.1 24.7 1.0
OD2 A:ASP301 2.1 25.2 1.0
O A:HOH802 2.1 25.0 1.0
O A:HOH608 2.1 27.6 1.0
CG A:ASP305 3.1 30.5 1.0
CG A:ASP301 3.2 28.1 1.0
OD1 A:ASP305 3.5 26.7 1.0
CB A:ASP301 3.7 23.4 1.0
N A:ASP301 4.1 23.6 1.0
O2 A:EDO509 4.2 50.1 1.0
O A:HOH903 4.2 39.8 1.0
OD1 A:ASP301 4.3 28.7 1.0
CB A:ASP305 4.4 20.8 1.0
O A:LEU299 4.4 29.8 1.0
CE A:LYS291 4.5 30.7 1.0
C2 A:EDO509 4.5 40.9 1.0
CA A:ASP301 4.5 26.1 1.0
CA A:LEU300 4.9 21.8 1.0
O A:HOH613 4.9 30.6 1.0
C A:LEU300 4.9 27.6 1.0
C1 A:EDO509 5.0 35.4 1.0

Magnesium binding site 5 out of 8 in 7b9h

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Magnesium binding site 5 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 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:Mg506

b:47.6
occ:1.00
 O A:HOH633 2.0 38.5 1.0
OD1 A:ASN362 4.1 35.9 1.0
O A:HOH894 4.6 44.6 1.0
CG A:ASN362 4.7 37.0 1.0
ND2 A:ASN362 4.7 32.3 1.0
O A:HOH918 4.8 44.2 1.0

Magnesium binding site 6 out of 8 in 7b9h

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Magnesium binding site 6 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 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:Mg502

b:12.2
occ:1.00
 O B:HOH708 2.1 16.6 1.0
OD1 B:ASP201 2.1 14.9 1.0
O B:HOH801 2.1 14.9 1.0
O B:HOH642 2.1 16.3 1.0
O B:HOH684 2.1 14.3 1.0
O B:HOH730 2.2 15.4 1.0
CG B:ASP201 3.1 14.6 1.0
OD2 B:ASP201 3.5 14.1 1.0
ZN B:ZN501 3.7 17.2 1.0
OE2 B:GLU230 4.1 18.1 1.0
O B:HOH726 4.1 19.0 1.0
CD2 B:HIS200 4.1 14.7 1.0
NE2 B:HIS233 4.2 16.3 1.0
OG1 B:THR271 4.2 15.2 1.0
O B:HIS200 4.2 14.4 1.0
O B:HOH794 4.2 21.5 1.0
O B:HOH613 4.3 31.6 1.0
CD2 B:HIS233 4.4 13.3 1.0
CB B:ASP201 4.5 15.1 1.0
OD2 B:ASP318 4.5 23.2 1.0
CD2 B:HIS204 4.6 17.1 1.0
NE2 B:HIS200 4.6 17.0 1.0
O B:THR271 4.7 18.1 1.0
NE2 B:HIS160 4.7 16.7 1.0
CD2 B:HIS160 4.7 15.1 1.0
CB B:THR271 4.8 14.1 1.0
CA B:ASP201 4.8 14.2 1.0
NE2 B:HIS204 4.8 17.8 1.0
CG B:GLU230 4.8 16.4 1.0
CD B:GLU230 4.9 19.3 1.0

Magnesium binding site 7 out of 8 in 7b9h

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Magnesium binding site 7 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 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:Mg503

b:41.8
occ:1.00
 O B:HOH605 2.1 41.5 1.0
OD1 B:ASP334 3.5 51.9 1.0
OD2 B:ASP334 3.9 49.0 1.0
O B:HOH749 4.1 36.6 1.0
CG B:ASP334 4.1 44.1 1.0
CD B:ARG330 4.5 33.6 1.0

Magnesium binding site 8 out of 8 in 7b9h

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Magnesium binding site 8 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 42A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 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:Mg504

b:37.1
occ:1.00
 O B:HOH686 2.1 23.2 1.0
O B:HOH773 2.1 33.2 1.0
O B:HOH850 2.2 35.4 1.0
O B:HOH638 2.3 32.0 1.0
O B:HOH762 2.4 36.2 1.0
ND1 B:HIS378 3.8 21.8 1.0
OE2 B:GLU382 4.2 24.5 1.0
O B:HOH649 4.3 38.8 1.0
CE1 B:HIS378 4.3 24.0 1.0
O B:HOH747 4.4 27.1 1.0
O B:HOH869 4.5 36.8 1.0
OE1 B:GLU382 4.6 26.3 1.0
O B:ASP374 4.7 18.6 1.0
CD B:GLU382 4.7 24.4 1.0
CG B:HIS378 4.8 19.4 1.0
O1 B:EDO511 4.8 45.7 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 14 01:24:38 2025

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