Magnesium in PDB 7ay6: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B, PDB code: 7ay6 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) 49.33 / 1.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.838, 98.66, 120.239, 90, 90, 90
R / Rfree (%) 18.2 / 21.4

Other elements in 7ay6:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B 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- 41B (pdb code 7ay6). 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- 41B, PDB code: 7ay6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7ay6

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Magnesium binding site 1 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:8.7
occ:1.00
 OD1 A:ASP201 2.0 11.0 1.0
O A:HOH715 2.1 10.5 1.0
O A:HOH722 2.2 11.2 1.0
O A:HOH761 2.2 10.7 1.0
O A:HOH820 2.2 10.7 1.0
O A:HOH621 2.2 11.6 1.0
CG A:ASP201 3.0 12.2 1.0
OD2 A:ASP201 3.3 9.4 1.0
ZN A:ZN502 3.7 14.0 1.0
O A:HOH888 4.1 28.7 1.0
OE2 A:GLU230 4.1 14.1 1.0
O A:HOH767 4.1 12.5 1.0
CD2 A:HIS200 4.1 10.5 1.0
O A:HIS200 4.2 8.5 1.0
NE2 A:HIS233 4.2 10.6 1.0
OG1 A:THR271 4.3 13.6 1.0
O A:HOH839 4.4 18.0 1.0
CB A:ASP201 4.4 7.2 1.0
CD2 A:HIS233 4.4 8.2 1.0
OD2 A:ASP318 4.5 22.1 1.0
NE2 A:HIS200 4.5 9.7 1.0
CD2 A:HIS204 4.6 10.2 1.0
O A:THR271 4.7 15.7 1.0
NE2 A:HIS160 4.8 14.4 1.0
CA A:ASP201 4.8 9.3 1.0
CB A:THR271 4.8 14.2 1.0
CD2 A:HIS160 4.8 11.3 1.0
CG A:GLU230 4.9 10.9 1.0
NE2 A:HIS204 4.9 11.4 1.0
CD A:GLU230 4.9 15.7 1.0
C A:HIS200 5.0 9.3 1.0

Magnesium binding site 2 out of 8 in 7ay6

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Magnesium binding site 2 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:39.9
occ:1.00
 O A:HOH683 2.1 38.0 1.0
O A:HOH692 2.2 35.2 1.0
O A:HOH957 2.2 44.4 1.0
O A:HOH939 3.8 45.8 1.0
O A:HOH787 3.9 45.0 1.0
OD1 A:ASP187 4.1 25.1 1.0
OD2 A:ASP187 4.3 24.9 1.0
O A:HOH842 4.4 34.0 1.0
O A:HOH718 4.4 31.4 1.0
O A:HOH951 4.4 43.5 1.0
CG A:ASP187 4.7 26.8 1.0
O A:HOH949 4.7 40.1 1.0

Magnesium binding site 3 out of 8 in 7ay6

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Magnesium binding site 3 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:34.6
occ:1.00
 O A:HOH728 1.9 32.8 1.0
O A:HOH834 2.1 41.3 1.0
OD1 A:ASN251 2.1 23.0 1.0
CG A:ASN251 3.2 20.8 1.0
ND2 A:ASN251 3.8 18.8 1.0
O A:GLN250 4.3 24.0 1.0
CB A:ASN251 4.5 19.3 1.0
NE2 A:GLN250 4.5 39.6 1.0
CA A:ASN251 4.6 22.7 1.0
C A:GLN250 4.8 21.1 1.0
CG A:GLN250 4.9 26.5 1.0

Magnesium binding site 4 out of 8 in 7ay6

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Magnesium binding site 4 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:23.2
occ:1.00
 OD2 A:ASP301 2.1 20.2 1.0
OD2 A:ASP305 2.1 21.9 1.0
O A:HOH626 2.2 21.5 1.0
O A:HOH677 2.2 28.5 1.0
CG A:ASP305 3.1 29.0 1.0
CG A:ASP301 3.2 22.8 1.0
OD1 A:ASP305 3.4 26.6 1.0
CB A:ASP301 3.7 19.7 1.0
N A:ASP301 4.1 24.1 1.0
O A:HOH841 4.3 37.1 1.0
OD1 A:ASP301 4.3 25.7 1.0
O2 A:EDO510 4.3 46.5 1.0
O A:HOH899 4.4 31.9 1.0
CB A:ASP305 4.4 15.6 1.0
O A:LEU299 4.5 26.6 1.0
C2 A:EDO510 4.5 41.8 1.0
CE A:LYS291 4.5 27.1 1.0
CA A:ASP301 4.6 24.9 1.0
C1 A:EDO510 4.8 35.9 1.0
CA A:LEU300 5.0 15.7 1.0
C A:LEU300 5.0 24.1 1.0

Magnesium binding site 5 out of 8 in 7ay6

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Magnesium binding site 5 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:49.8
occ:1.00
 O A:HOH653 2.1 32.2 1.0
O A:HOH919 2.3 51.6 1.0
OD1 A:ASN362 4.1 30.6 1.0
O A:HOH925 4.6 44.6 1.0
O A:HOH900 4.6 42.1 1.0
ND2 A:ASN362 4.6 27.5 1.0
CG A:ASN362 4.7 33.3 1.0

Magnesium binding site 6 out of 8 in 7ay6

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Magnesium binding site 6 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:9.2
occ:1.00
 O B:HOH813 2.0 12.0 1.0
O B:HOH716 2.1 13.3 1.0
OD1 B:ASP201 2.1 12.2 1.0
O B:HOH646 2.1 13.2 1.0
O B:HOH699 2.1 10.3 1.0
O B:HOH740 2.1 10.5 1.0
CG B:ASP201 3.1 13.3 1.0
OD2 B:ASP201 3.4 11.5 1.0
ZN B:ZN502 3.8 14.8 1.0
O B:HOH843 3.8 30.4 1.0
OE2 B:GLU230 4.0 16.5 1.0
O B:HOH755 4.1 16.2 1.0
CD2 B:HIS200 4.2 13.3 1.0
NE2 B:HIS233 4.2 11.4 1.0
O B:HOH819 4.2 16.4 1.0
O B:HIS200 4.2 10.1 1.0
OG1 B:THR271 4.3 14.0 1.0
O B:HOH879 4.3 43.2 1.0
CD2 B:HIS233 4.4 8.9 1.0
CB B:ASP201 4.5 11.0 1.0
OD2 B:ASP318 4.5 23.7 1.0
NE2 B:HIS200 4.6 13.2 1.0
CD2 B:HIS204 4.6 14.6 1.0
O B:THR271 4.7 14.9 1.0
NE2 B:HIS160 4.7 16.5 1.0
CD2 B:HIS160 4.8 11.0 1.0
CA B:ASP201 4.8 10.2 1.0
NE2 B:HIS204 4.8 13.7 1.0
CB B:THR271 4.8 11.7 1.0
CD B:GLU230 4.8 17.4 1.0
CG B:GLU230 4.9 11.1 1.0

Magnesium binding site 7 out of 8 in 7ay6

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Magnesium binding site 7 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:36.9
occ:1.00
 O B:HOH656 2.0 41.5 1.0
O B:HOH921 2.1 38.8 1.0
O B:HOH606 2.1 31.9 1.0
OD2 B:ASP334 3.6 47.8 1.0
OD1 B:ASP334 4.0 49.2 1.0
O B:HOH787 4.1 34.3 1.0
CG B:ASP334 4.2 39.2 1.0
CD B:ARG330 4.6 35.9 1.0

Magnesium binding site 8 out of 8 in 7ay6

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Magnesium binding site 8 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 41B


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- 41B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg505

b:33.2
occ:1.00
 O B:HOH681 2.1 19.6 1.0
O B:HOH842 2.2 28.6 1.0
O B:HOH648 2.3 31.6 1.0
O B:HOH796 2.5 34.9 1.0
ND1 B:HIS378 3.9 19.5 1.0
O B:HOH692 4.1 34.3 1.0
OE1 B:GLU382 4.2 21.7 1.0
O B:HOH912 4.2 36.3 1.0
CE1 B:HIS378 4.4 22.6 1.0
O B:HOH724 4.5 24.0 1.0
O B:HOH874 4.5 34.6 1.0
OE2 B:GLU382 4.6 26.1 1.0
O B:ASP374 4.6 16.9 1.0
CD B:GLU382 4.7 29.1 1.0
CG B:HIS378 4.9 17.1 1.0
O B:HOH795 5.0 32.6 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: Sun Jul 11 15:42:12 2021

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