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Magnesium in PDB 6f8v: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B, PDB code: 6f8v was solved by T.Prosdocimi, S.Donini, E.Parisini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.49 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.558, 98.314, 120.089, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.4

Other elements in 6f8v:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B 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- 18B (pdb code 6f8v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B, PDB code: 6f8v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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- 18B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:12.5
occ:1.00
 OD1 A:ASP367 2.0 14.1 1.0
O A:HOH731 2.0 15.0 1.0
O A:HOH906 2.1 14.1 1.0
O A:HOH748 2.1 12.8 1.0
O A:HOH817 2.2 12.1 1.0
O A:HOH803 2.2 13.3 1.0
CG A:ASP367 3.1 15.8 1.0
OD2 A:ASP367 3.4 11.6 1.0
ZN A:ZN601 3.8 18.5 1.0
H01 A:D0B605 3.9 20.4 1.0
H19 A:D0B605 4.0 20.4 1.0
O A:HIS366 4.1 14.4 1.0
NE2 A:HIS399 4.1 10.8 1.0
O A:HOH814 4.1 18.5 1.0
OE2 A:GLU396 4.2 17.2 1.0
CD2 A:HIS366 4.2 11.6 1.0
O A:HOH874 4.2 15.0 1.0
OG1 A:THR437 4.3 11.2 1.0
CD2 A:HIS399 4.3 8.7 1.0
C15 A:D0B605 4.3 17.0 1.0
CB A:ASP367 4.4 12.2 1.0
O A:HOH784 4.4 23.2 1.0
CD2 A:HIS370 4.5 9.9 1.0
OD2 A:ASP484 4.5 18.8 1.0
C16 A:D0B605 4.6 26.8 1.0
NE2 A:HIS366 4.6 11.7 1.0
CA A:ASP367 4.8 13.1 1.0
NE2 A:HIS370 4.8 12.8 1.0
O A:THR437 4.8 19.9 1.0
NE2 A:HIS326 4.8 13.2 1.0
CB A:THR437 4.8 13.7 1.0
O04 A:D0B605 4.8 28.7 1.0
CD2 A:HIS326 4.9 11.3 1.0
CG A:GLU396 4.9 12.1 1.0
CD A:GLU396 4.9 15.4 1.0
C A:HIS366 4.9 14.3 1.0
H20 A:D0B605 5.0 24.2 1.0

Magnesium binding site 2 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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- 18B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:34.0
occ:1.00
 O A:HOH798 2.1 32.1 1.0
O A:HOH710 2.6 32.9 1.0
OD2 A:ASP264 3.7 39.8 1.0
OD1 A:ASP264 3.7 37.6 1.0
CG A:ASP264 4.1 37.2 1.0
O A:HOH869 4.3 34.8 1.0
CE A:LYS260 4.3 34.5 1.0
O A:LYS260 4.4 27.3 1.0
OE1 A:GLU263 4.8 39.7 1.0

Magnesium binding site 3 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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- 18B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:33.1
occ:1.00
 OD2 A:ASP471 2.0 28.5 1.0
OD2 A:ASP467 2.1 26.0 1.0
O A:HOH800 2.2 31.8 1.0
O A:HOH820 2.2 28.6 1.0
O A:HOH809 2.2 27.0 1.0
CG A:ASP471 3.0 27.1 1.0
CG A:ASP467 3.3 28.3 1.0
OD1 A:ASP471 3.4 28.6 1.0
CB A:ASP467 4.0 30.1 1.0
N A:ASP467 4.1 25.2 1.0
O A:HOH890 4.2 33.8 1.0
OD1 A:ASP467 4.3 33.5 1.0
CB A:ASP471 4.3 21.1 1.0
O A:HOH917 4.5 32.7 1.0
O A:LEU465 4.6 28.8 1.0
CA A:ASP467 4.7 31.3 1.0
CA A:LEU466 4.9 21.5 1.0
C A:LEU466 5.0 30.9 1.0

Magnesium binding site 4 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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- 18B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:10.5
occ:1.00
 O B:HOH712 2.1 16.8 1.0
OD1 B:ASP367 2.1 11.4 1.0
O B:HOH801 2.1 12.5 1.0
O B:HOH779 2.1 15.1 1.0
O B:HOH751 2.2 13.5 1.0
O B:HOH807 2.2 11.2 1.0
CG B:ASP367 3.1 10.4 1.0
OD2 B:ASP367 3.4 14.5 1.0
H01 B:D0B603 3.7 23.8 1.0
ZN B:ZN601 3.7 19.1 1.0
H19 B:D0B603 4.0 23.8 1.0
O B:HOH753 4.1 13.2 1.0
CD2 B:HIS366 4.2 15.0 1.0
O B:HOH853 4.2 14.6 1.0
O B:HIS366 4.2 11.3 1.0
NE2 B:HIS399 4.2 15.2 1.0
OG1 B:THR437 4.2 12.5 1.0
C15 B:D0B603 4.3 19.8 1.0
OE2 B:GLU396 4.3 15.3 1.0
OD2 B:ASP484 4.4 19.5 1.0
CD2 B:HIS399 4.4 13.0 1.0
CB B:ASP367 4.4 14.4 1.0
O B:HOH723 4.5 19.1 1.0
NE2 B:HIS326 4.5 14.8 1.0
C16 B:D0B603 4.5 25.6 1.0
NE2 B:HIS366 4.5 14.6 1.0
CD2 B:HIS370 4.6 15.8 1.0
O B:THR437 4.6 16.4 1.0
CD2 B:HIS326 4.6 11.7 1.0
O04 B:D0B603 4.7 19.4 1.0
CB B:THR437 4.8 10.1 1.0
CA B:ASP367 4.8 9.7 1.0
NE2 B:HIS370 4.9 11.2 1.0
CG B:GLU396 5.0 12.6 1.0

Reference:

T.Prosdocimi, L.Mollica, S.Donini, M.S.Semrau, A.P.Lucarelli, E.Aiolfi, A.Cavalli, P.Storici, S.Alfei, C.Brullo, O.Bruno, E.Parisini. Molecular Bases of PDE4D Inhibition By Memory-Enhancing Gebr Library Compounds. Biochemistry V. 57 2876 2018.
ISSN: ISSN 1520-4995
PubMed: 29652483
DOI: 10.1021/ACS.BIOCHEM.8B00288
Page generated: Tue Oct 1 00:12:00 2024

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