Atomistry » Magnesium » PDB 7aom-7b19 » 7ay6
Atomistry »
  Magnesium »
    PDB 7aom-7b19 »
      7ay6 »

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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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

Go back to Magnesium Binding Sites List in 7ay6
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: Wed Oct 2 10:15:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy