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Magnesium in PDB 6f8x: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G, PDB code: 6f8x 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) 49.21 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.547, 119.820, 64.502, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.5

Other elements in 6f8x:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G 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- 26G (pdb code 6f8x). 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- 26G, PDB code: 6f8x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6f8x

Go back to Magnesium Binding Sites List in 6f8x
Magnesium binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G


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- 26G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:8.7
occ:1.00
 O A:HOH801 2.1 10.0 1.0
OD1 A:ASP367 2.1 12.3 1.0
O A:HOH725 2.2 12.6 1.0
O A:HOH838 2.2 13.5 1.0
O A:HOH860 2.2 11.2 1.0
O A:HOH814 2.2 13.0 1.0
CG A:ASP367 3.0 12.7 1.0
OD2 A:ASP367 3.3 11.4 1.0
O A:HOH735 3.7 30.9 1.0
ZN A:ZN601 3.7 11.4 0.8
O A:HOH702 3.8 16.2 1.0
O A:HIS366 4.1 10.7 1.0
CD2 A:HIS366 4.1 9.6 1.0
OE2 A:GLU396 4.2 18.5 1.0
NE2 A:HIS399 4.2 9.2 1.0
O A:HOH835 4.2 16.3 1.0
O A:HOH791 4.2 19.6 1.0
CD2 A:HIS399 4.3 8.0 1.0
OG1 A:THR437 4.3 12.1 1.0
CB A:ASP367 4.4 8.1 1.0
O A:HOH724 4.5 32.8 1.0
OD2 A:ASP484 4.5 18.2 1.0
NE2 A:HIS366 4.5 9.1 1.0
CD2 A:HIS370 4.6 9.9 1.0
O A:THR437 4.7 14.7 1.0
CB A:THR437 4.7 11.3 1.0
CA A:ASP367 4.8 7.6 1.0
NE2 A:HIS326 4.8 14.8 1.0
CD2 A:HIS326 4.8 13.5 1.0
NE2 A:HIS370 4.9 12.5 1.0
CG A:GLU396 4.9 11.9 1.0
O03 A:D08605 4.9 31.9 0.7
C A:HIS366 4.9 9.5 1.0
CD A:GLU396 5.0 17.8 1.0

Magnesium binding site 2 out of 4 in 6f8x

Go back to Magnesium Binding Sites List in 6f8x
Magnesium binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G


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- 26G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:38.9
occ:1.00
 O A:HOH704 2.2 31.3 1.0
OD1 A:ASP264 3.8 40.4 1.0
OD2 A:ASP264 3.9 40.4 1.0
O A:HOH824 4.1 44.0 1.0
CG A:ASP264 4.3 44.4 1.0
OE1 A:GLU263 4.7 46.0 1.0

Magnesium binding site 3 out of 4 in 6f8x

Go back to Magnesium Binding Sites List in 6f8x
Magnesium binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G


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- 26G within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:23.6
occ:1.00
 O A:HOH769 2.0 21.2 1.0
OD2 A:ASP467 2.1 20.3 1.0
OD2 A:ASP471 2.1 21.6 1.0
O A:HOH782 2.1 25.3 1.0
CG A:ASP471 3.0 27.4 1.0
CG A:ASP467 3.2 26.1 1.0
OD1 A:ASP471 3.3 23.6 1.0
CB A:ASP467 3.7 22.3 1.0
N A:ASP467 4.0 23.1 1.0
OD1 A:ASP467 4.3 27.7 1.0
O A:HOH901 4.4 32.2 1.0
O A:LEU465 4.4 21.6 1.0
CB A:ASP471 4.4 21.3 1.0
CE A:LYS457 4.4 24.5 1.0
CA A:ASP467 4.5 22.9 1.0
NZ A:LYS457 4.8 27.1 1.0
O A:HOH733 4.8 31.8 1.0
CA A:LEU466 4.9 18.7 1.0
C A:LEU466 4.9 27.2 1.0

Magnesium binding site 4 out of 4 in 6f8x

Go back to Magnesium Binding Sites List in 6f8x
Magnesium binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 26G


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- 26G within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:9.0
occ:1.00
 O B:HOH758 2.0 15.3 1.0
OD1 B:ASP367 2.0 11.9 1.0
O B:HOH765 2.1 11.3 1.0
O B:HOH796 2.1 13.1 1.0
O B:HOH837 2.2 12.5 1.0
O B:HOH804 2.2 13.1 1.0
CG B:ASP367 3.1 12.0 1.0
OD2 B:ASP367 3.4 14.0 1.0
O B:HOH731 3.7 30.3 1.0
ZN B:ZN601 3.7 17.3 1.0
O B:HOH705 3.8 17.6 1.0
CD2 B:HIS366 4.1 12.0 1.0
O B:HIS366 4.1 11.4 1.0
OE2 B:GLU396 4.1 16.3 1.0
O B:HOH786 4.2 18.3 1.0
NE2 B:HIS399 4.2 12.1 1.0
OG1 B:THR437 4.2 14.5 1.0
O B:HOH798 4.3 18.0 1.0
CD2 B:HIS399 4.4 11.6 1.0
CB B:ASP367 4.4 15.3 1.0
H17 B:D08604 4.5 34.6 0.7
O B:HOH748 4.5 29.4 1.0
NE2 B:HIS366 4.5 16.0 1.0
OD2 B:ASP484 4.5 25.0 1.0
CD2 B:HIS370 4.6 15.1 1.0
O B:THR437 4.7 15.8 1.0
CB B:THR437 4.8 16.1 1.0
CD2 B:HIS326 4.8 12.1 1.0
NE2 B:HIS326 4.8 13.5 1.0
CA B:ASP367 4.8 12.0 1.0
O03 B:D08604 4.8 26.6 0.7
NE2 B:HIS370 4.8 12.2 1.0
C B:HIS366 5.0 12.9 1.0
CG B:GLU396 5.0 13.3 1.0
CD B:GLU396 5.0 17.3 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 00:13:06 2024

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