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Magnesium in PDB 6f8u: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B, PDB code: 6f8u 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) 49.33 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.672, 98.669, 119.644, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 21.9

Other elements in 6f8u:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B also contains other interesting chemical elements:

Fluorine (F) 6 atoms
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- 20B (pdb code 6f8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B, PDB code: 6f8u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6f8u

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Magnesium binding site 1 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:10.2
occ:1.00
 O A:HOH769 2.0 13.8 1.0
O A:HOH890 2.0 12.2 1.0
OD1 A:ASP367 2.0 12.5 1.0
O A:HOH796 2.1 12.6 1.0
O A:HOH778 2.1 10.6 1.0
O A:HOH868 2.2 13.0 1.0
CG A:ASP367 3.0 17.3 1.0
OD2 A:ASP367 3.3 12.5 1.0
ZN A:ZN601 3.7 19.2 1.0
O A:HOH703 3.8 25.9 1.0
O A:HOH871 4.0 19.0 1.0
OE2 A:GLU396 4.0 15.9 1.0
CD2 A:HIS366 4.1 11.2 1.0
O A:HIS366 4.2 14.4 1.0
O A:HOH777 4.2 18.6 1.0
NE2 A:HIS399 4.2 13.0 1.0
OG1 A:THR437 4.3 13.0 1.0
CD2 A:HIS399 4.3 9.7 1.0
CB A:ASP367 4.4 10.4 1.0
OD2 A:ASP484 4.5 22.4 1.0
NE2 A:HIS366 4.5 8.9 1.0
CD2 A:HIS370 4.6 10.9 1.0
CD2 A:HIS326 4.7 14.1 1.0
NE2 A:HIS326 4.7 16.4 1.0
O A:THR437 4.8 19.0 1.0
CA A:ASP367 4.8 12.5 1.0
CB A:THR437 4.8 14.0 1.0
NE2 A:HIS370 4.8 15.1 1.0
CG A:GLU396 4.9 10.8 1.0
CD A:GLU396 4.9 18.0 1.0
C A:HIS366 4.9 11.0 1.0

Magnesium binding site 2 out of 5 in 6f8u

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Magnesium binding site 2 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:44.7
occ:1.00
 O A:HOH737 2.1 26.3 1.0
O A:HOH931 2.2 32.6 1.0
O A:HOH923 3.9 39.6 1.0
OD1 A:ASP353 4.0 20.5 1.0
O A:HOH897 4.1 43.9 1.0
O A:HOH793 4.2 30.2 1.0
OD2 A:ASP353 4.2 22.0 1.0
CG A:ASP353 4.5 26.1 1.0

Magnesium binding site 3 out of 5 in 6f8u

Go back to Magnesium Binding Sites List in 6f8u
Magnesium binding site 3 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:32.4
occ:1.00
 OD2 A:ASP467 2.1 24.7 1.0
O A:HOH803 2.1 24.6 1.0
O A:HOH815 2.1 23.6 1.0
O A:HOH750 2.1 31.6 1.0
OD2 A:ASP471 2.1 23.6 1.0
CG A:ASP471 3.0 27.5 1.0
CG A:ASP467 3.2 27.7 1.0
OD1 A:ASP471 3.4 22.2 1.0
CB A:ASP467 3.7 27.5 1.0
N A:ASP467 4.0 30.9 1.0
O A:HOH922 4.0 39.4 1.0
OD1 A:ASP467 4.2 33.0 1.0
CB A:ASP471 4.3 21.9 1.0
O A:LEU465 4.4 27.3 1.0
CA A:ASP467 4.5 29.5 1.0
CD A:LYS457 4.6 45.2 1.0
C A:LEU466 4.8 28.7 1.0
CA A:LEU466 4.9 28.1 1.0

Magnesium binding site 4 out of 5 in 6f8u

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Magnesium binding site 4 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:50.8
occ:1.00
 OD1 A:ASP567 3.7 28.8 1.0
OD2 A:ASP567 3.9 30.6 1.0
CG A:ASP567 4.0 25.6 1.0
O A:HOH906 4.6 42.5 1.0
CB A:ASP567 4.9 25.5 1.0

Magnesium binding site 5 out of 5 in 6f8u

Go back to Magnesium Binding Sites List in 6f8u
Magnesium binding site 5 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 20B


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- 20B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:10.9
occ:1.00
 O B:HOH753 1.9 15.7 1.0
OD1 B:ASP367 2.0 14.0 1.0
O B:HOH800 2.0 14.7 1.0
O B:HOH777 2.0 15.1 1.0
O B:HOH765 2.1 15.1 1.0
O B:HOH815 2.2 12.7 1.0
CG B:ASP367 3.1 16.7 1.0
OD2 B:ASP367 3.4 15.4 1.0
ZN B:ZN601 3.7 20.1 1.0
O B:HOH787 3.9 17.6 1.0
OE2 B:GLU396 4.0 18.3 1.0
O B:HOH837 4.0 28.4 1.0
O B:HOH834 4.1 21.3 1.0
CD2 B:HIS366 4.1 13.9 1.0
O B:HOH708 4.2 26.1 1.0
O B:HIS366 4.2 12.6 1.0
NE2 B:HIS399 4.2 11.0 1.0
OG1 B:THR437 4.2 12.2 1.0
OD2 B:ASP484 4.4 27.1 1.0
CD2 B:HIS399 4.4 14.2 1.0
CB B:ASP367 4.4 13.9 1.0
NE2 B:HIS326 4.5 20.2 1.0
CD2 B:HIS370 4.5 13.8 1.0
NE2 B:HIS366 4.6 12.7 1.0
CD2 B:HIS326 4.6 15.2 1.0
CA B:ASP367 4.8 9.1 1.0
CB B:THR437 4.8 12.4 1.0
O B:THR437 4.8 17.2 1.0
NE2 B:HIS370 4.9 16.6 1.0
CD B:GLU396 4.9 16.1 1.0
CG B:GLU396 4.9 11.4 1.0
C B:HIS366 5.0 11.5 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 00:11:59 2024

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