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Magnesium in PDB 6f8r: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54, PDB code: 6f8r 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) 49.27 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.671, 98.303, 120.091, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23

Other elements in 6f8r:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54 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- 54 (pdb code 6f8r). 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- 54, PDB code: 6f8r:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6f8r

Go back to Magnesium Binding Sites List in 6f8r
Magnesium binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54


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

b:9.5
occ:1.00
 OD1 A:ASP367 2.0 9.5 1.0
O A:HOH781 2.0 10.8 1.0
O A:HOH726 2.1 10.4 1.0
O A:HOH832 2.1 12.8 1.0
O A:HOH906 2.1 11.8 1.0
O A:HOH844 2.1 13.2 1.0
CG A:ASP367 3.0 15.6 1.0
OD2 A:ASP367 3.3 8.6 1.0
ZN A:ZN605 3.7 15.4 1.0
CD2 A:HIS366 4.1 14.2 1.0
OE2 A:GLU396 4.1 14.2 1.0
NE2 A:HIS399 4.1 11.7 1.0
O A:HIS366 4.2 12.2 1.0
O A:HOH864 4.2 14.2 1.0
OG1 A:THR437 4.3 13.2 1.0
O A:HOH825 4.3 15.4 1.0
CD2 A:HIS399 4.4 8.6 1.0
CB A:ASP367 4.4 11.3 1.0
OD2 A:ASP484 4.4 19.7 1.0
NE2 A:HIS366 4.4 8.9 1.0
CD2 A:HIS370 4.6 10.7 1.0
O A:THR437 4.6 15.9 1.0
H30 A:CZK601 4.7 33.0 1.0
NE2 A:HIS326 4.8 17.1 1.0
CA A:ASP367 4.8 11.8 1.0
CB A:THR437 4.8 11.8 1.0
CD2 A:HIS326 4.8 13.0 1.0
NE2 A:HIS370 4.9 15.0 1.0
CG A:GLU396 4.9 13.1 1.0
CD A:GLU396 4.9 16.1 1.0
C A:HIS366 5.0 11.1 1.0

Magnesium binding site 2 out of 4 in 6f8r

Go back to Magnesium Binding Sites List in 6f8r
Magnesium binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54


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

b:22.6
occ:1.00
 O A:HOH816 2.0 22.7 1.0
OD2 A:ASP467 2.0 21.4 1.0
OD2 A:ASP471 2.1 20.6 1.0
O A:HOH770 2.2 25.4 1.0
CG A:ASP471 3.1 22.9 1.0
CG A:ASP467 3.2 20.9 1.0
OD1 A:ASP471 3.4 24.0 1.0
CB A:ASP467 3.8 20.1 1.0
O A:HOH960 4.0 32.2 1.0
N A:ASP467 4.1 23.9 1.0
OD1 A:ASP467 4.2 25.1 1.0
O A:HOH949 4.4 43.1 1.0
CB A:ASP471 4.4 17.5 1.0
O A:LEU465 4.4 22.4 1.0
O A:HOH946 4.5 30.0 1.0
CA A:ASP467 4.6 21.9 1.0
NZ A:LYS457 4.8 28.6 1.0
CD A:LYS457 4.9 33.0 1.0
CA A:LEU466 4.9 18.0 1.0
C A:LEU466 5.0 22.7 1.0
O A:HOH731 5.0 31.9 1.0

Magnesium binding site 3 out of 4 in 6f8r

Go back to Magnesium Binding Sites List in 6f8r
Magnesium binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54


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

b:33.5
occ:1.00
 O A:HOH843 2.1 36.5 1.0
OD1 A:ASN417 2.1 21.9 1.0
O A:HOH713 2.3 36.2 1.0
CG A:ASN417 3.3 24.5 1.0
ND2 A:ASN417 3.9 19.1 1.0
O A:GLN416 4.5 22.7 1.0
CB A:ASN417 4.5 22.1 1.0
NE2 A:GLN416 4.6 29.1 1.0
CA A:ASN417 4.7 25.2 1.0
C A:GLN416 5.0 23.1 1.0

Magnesium binding site 4 out of 4 in 6f8r

Go back to Magnesium Binding Sites List in 6f8r
Magnesium binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 54


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

b:10.5
occ:1.00
 O B:HOH831 2.0 14.3 1.0
OD1 B:ASP367 2.1 13.7 1.0
O B:HOH858 2.1 14.2 1.0
O B:HOH722 2.1 14.7 1.0
O B:HOH861 2.2 15.5 1.0
O B:HOH760 2.2 13.6 1.0
CG B:ASP367 3.1 13.7 1.0
OD2 B:ASP367 3.4 13.9 1.0
ZN B:ZN603 3.6 17.7 1.0
O B:HOH701 3.9 22.1 1.0
O B:HOH902 4.0 30.1 1.0
O B:HOH863 4.0 16.5 1.0
CD2 B:HIS366 4.1 13.5 1.0
OE2 B:GLU396 4.1 15.4 1.0
O B:HIS366 4.2 11.2 1.0
NE2 B:HIS399 4.2 14.1 1.0
O B:HOH871 4.2 16.7 1.0
OG1 B:THR437 4.2 13.0 1.0
CD2 B:HIS399 4.4 12.0 1.0
CB B:ASP367 4.5 14.0 1.0
NE2 B:HIS366 4.5 12.7 1.0
OD2 B:ASP484 4.5 19.6 1.0
O B:HOH738 4.5 38.1 1.0
CD2 B:HIS370 4.6 15.2 1.0
O B:HOH935 4.6 32.4 1.0
O B:THR437 4.6 12.4 1.0
NE2 B:HIS326 4.7 15.4 1.0
CB B:THR437 4.7 12.8 1.0
CD2 B:HIS326 4.8 13.5 1.0
CA B:ASP367 4.8 11.8 1.0
NE2 B:HIS370 4.9 13.4 1.0
CD B:GLU396 4.9 12.1 1.0
CG B:GLU396 5.0 12.1 1.0
C B:HIS366 5.0 15.6 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 00:11:25 2024

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