Magnesium in PDB 6fdc: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A, PDB code: 6fdc 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) 49.32 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.692, 98.608, 120.165, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.9

Other elements in 6fdc:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A also contains other interesting chemical elements:

Fluorine (F) 4 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- 32A (pdb code 6fdc). 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- 32A, PDB code: 6fdc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6fdc

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Magnesium binding site 1 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:8.8
occ:1.00
 O A:HOH725 2.0 13.4 1.0
O A:HOH895 2.1 12.8 1.0
OD1 A:ASP367 2.1 10.9 1.0
O A:HOH769 2.1 12.3 1.0
O A:HOH798 2.1 13.9 1.0
O A:HOH815 2.1 12.1 1.0
CG A:ASP367 3.1 11.0 1.0
OD2 A:ASP367 3.4 10.7 1.0
O A:HOH701 3.7 15.6 1.0
ZN A:ZN601 3.8 13.8 1.0
OE2 A:GLU396 4.0 15.9 1.0
O A:HOH839 4.1 13.3 1.0
CD2 A:HIS366 4.1 10.2 1.0
NE2 A:HIS399 4.2 11.7 1.0
O A:HIS366 4.2 10.8 1.0
O A:HOH887 4.2 16.8 1.0
OG1 A:THR437 4.3 13.8 1.0
CD2 A:HIS399 4.4 10.7 1.0
CB A:ASP367 4.4 11.3 1.0
OD2 A:ASP484 4.4 21.0 1.0
NE2 A:HIS366 4.5 10.2 1.0
CD2 A:HIS370 4.6 11.1 1.0
O A:THR437 4.6 15.4 1.0
NE2 A:HIS326 4.7 14.2 1.0
CA A:ASP367 4.8 10.1 1.0
CD2 A:HIS326 4.8 12.6 1.0
H27 A:DD5606 4.8 26.1 0.7
CB A:THR437 4.8 13.7 1.0
CG A:GLU396 4.9 12.6 1.0
CD A:GLU396 4.9 15.2 1.0
NE2 A:HIS370 4.9 12.5 1.0
C A:HIS366 5.0 10.5 1.0

Magnesium binding site 2 out of 5 in 6fdc

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Magnesium binding site 2 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:20.5
occ:1.00
 OD2 A:ASP467 2.0 19.9 1.0
O A:HOH783 2.1 21.1 1.0
OD2 A:ASP471 2.1 20.0 1.0
O A:HOH742 2.1 23.0 1.0
CG A:ASP471 3.1 23.4 1.0
CG A:ASP467 3.2 21.8 1.0
OD1 A:ASP471 3.4 21.9 1.0
CB A:ASP467 3.7 20.1 1.0
N A:ASP467 4.1 19.2 1.0
OD1 A:ASP467 4.2 22.7 1.0
O A:HOH937 4.3 35.5 1.0
CB A:ASP471 4.4 17.4 1.0
O A:HOH929 4.4 33.1 1.0
O A:LEU465 4.4 25.6 1.0
CA A:ASP467 4.6 20.4 1.0
CE A:LYS457 4.6 25.1 1.0
O A:HOH712 4.9 30.1 1.0
C A:LEU466 5.0 22.9 1.0
CA A:LEU466 5.0 18.5 1.0
NZ A:LYS457 5.0 28.5 1.0

Magnesium binding site 3 out of 5 in 6fdc

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Magnesium binding site 3 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:32.4
occ:1.00
 OD1 A:ASN417 2.1 22.1 1.0
O A:HOH867 2.1 39.4 1.0
O A:HOH918 2.1 37.5 1.0
O A:HOH842 2.3 41.8 1.0
CG A:ASN417 3.2 20.3 1.0
ND2 A:ASN417 3.8 22.0 1.0
O A:HOH954 4.1 41.8 1.0
O A:GLN416 4.4 24.6 1.0
OE1 A:GLN416 4.4 38.7 1.0
CB A:ASN417 4.5 21.6 1.0
CA A:ASN417 4.7 19.5 1.0
C A:GLN416 4.8 22.2 1.0
CG A:GLN416 4.8 26.2 1.0

Magnesium binding site 4 out of 5 in 6fdc

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Magnesium binding site 4 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:9.9
occ:1.00
 O B:HOH871 2.0 14.1 1.0
O B:HOH793 2.1 15.3 1.0
OD1 B:ASP367 2.1 13.2 1.0
O B:HOH720 2.1 14.3 1.0
O B:HOH799 2.1 13.3 1.0
O B:HOH762 2.1 13.2 1.0
CG B:ASP367 3.1 13.8 1.0
OD2 B:ASP367 3.4 12.8 1.0
O B:HOH705 3.7 14.8 1.0
ZN B:ZN601 3.8 15.0 1.0
O B:HOH890 3.9 27.7 1.0
OE2 B:GLU396 4.0 15.4 1.0
O B:HOH838 4.1 16.2 1.0
NE2 B:HIS399 4.1 13.9 1.0
CD2 B:HIS366 4.2 11.8 1.0
O B:HIS366 4.2 13.4 1.0
O B:HOH855 4.2 18.9 1.0
OG1 B:THR437 4.3 14.2 1.0
CD2 B:HIS399 4.4 11.5 1.0
CB B:ASP367 4.5 13.3 1.0
OD2 B:ASP484 4.5 23.6 1.0
CD2 B:HIS370 4.5 14.3 1.0
NE2 B:HIS366 4.6 13.7 1.0
O B:THR437 4.6 15.0 1.0
NE2 B:HIS326 4.7 16.4 1.0
CD2 B:HIS326 4.8 15.2 1.0
CB B:THR437 4.8 12.7 1.0
NE2 B:HIS370 4.8 14.2 1.0
CA B:ASP367 4.8 11.5 1.0
CG B:GLU396 4.9 13.1 1.0
CD B:GLU396 4.9 14.1 1.0

Magnesium binding site 5 out of 5 in 6fdc

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Magnesium binding site 5 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 32A


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- 32A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg603

b:32.3
occ:0.60
 O B:HOH754 2.1 34.4 1.0
O B:HOH730 2.1 26.6 1.0
O B:HOH891 2.3 36.4 1.0
ND1 B:HIS544 3.8 19.8 1.0
O B:HOH896 4.3 41.6 1.0
CE1 B:HIS544 4.3 20.8 1.0
OE1 B:GLU548 4.3 26.7 1.0
O B:HOH739 4.3 36.7 1.0
O B:HOH777 4.5 25.1 1.0
O B:ASP540 4.6 18.6 1.0
OE2 B:GLU548 4.7 27.6 1.0
CG B:HIS544 4.7 17.4 1.0
CD B:GLU548 4.8 25.9 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: Mon Dec 14 22:41:16 2020

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