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Magnesium in PDB 6f8w: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A

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

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

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A, PDB code: 6f8w 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) 45.69 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.039, 98.717, 120.765, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 21.9

Other elements in 6f8w:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A 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- 18A (pdb code 6f8w). 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- 18A, PDB code: 6f8w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6f8w

Go back to Magnesium Binding Sites List in 6f8w
Magnesium binding site 1 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A


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

b:15.1
occ:1.00
 OD1 A:ASP367 2.1 17.2 1.0
O A:HOH793 2.1 18.8 1.0
O A:HOH749 2.1 18.9 1.0
O A:HOH872 2.1 17.6 1.0
O A:HOH781 2.1 17.8 1.0
O A:HOH813 2.2 17.3 1.0
CG A:ASP367 3.1 20.6 1.0
OD2 A:ASP367 3.4 18.3 1.0
ZN A:ZN601 3.8 21.2 1.0
O A:HOH701 3.8 28.6 1.0
H01 A:D0E605 3.8 20.9 0.8
H19 A:D0E605 4.1 20.9 0.8
O A:HOH850 4.1 19.3 1.0
CD2 A:HIS366 4.1 15.8 1.0
O A:HOH857 4.1 20.6 1.0
NE2 A:HIS399 4.1 17.2 1.0
OE2 A:GLU396 4.2 21.4 1.0
O A:HIS366 4.2 18.3 1.0
OG1 A:THR437 4.3 17.3 1.0
C15 A:D0E605 4.3 17.4 0.8
CD2 A:HIS399 4.4 15.6 1.0
CB A:ASP367 4.4 18.3 1.0
OD2 A:ASP484 4.5 23.6 1.0
O A:HOH742 4.5 25.3 1.0
C16 A:D0E605 4.5 22.6 0.8
NE2 A:HIS366 4.5 18.0 1.0
O04 A:D0E605 4.6 26.6 0.8
CD2 A:HIS370 4.6 18.3 1.0
NE2 A:HIS326 4.7 19.7 1.0
CD2 A:HIS326 4.7 17.1 1.0
CB A:THR437 4.8 16.9 1.0
O A:THR437 4.8 20.1 1.0
CA A:ASP367 4.8 16.6 1.0
NE2 A:HIS370 4.9 19.8 1.0
CG A:GLU396 4.9 16.3 1.0
CD A:GLU396 4.9 18.7 1.0

Magnesium binding site 2 out of 5 in 6f8w

Go back to Magnesium Binding Sites List in 6f8w
Magnesium binding site 2 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A


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

b:44.7
occ:1.00
 O A:HOH764 2.1 29.9 1.0
O A:HOH765 2.2 37.0 1.0
O A:HOH901 2.5 41.9 1.0
O A:HOH878 2.6 39.1 1.0
O A:HOH919 3.8 51.2 1.0
ND1 A:HIS544 3.9 25.5 1.0
OE1 A:GLU548 4.3 29.7 1.0
CE1 A:HIS544 4.5 29.3 1.0
O A:ASP540 4.6 23.6 1.0
O A:HOH837 4.6 33.1 1.0
OE2 A:GLU548 4.8 26.4 1.0
CG A:HIS544 4.8 23.9 1.0
CD A:GLU548 4.9 31.0 1.0

Magnesium binding site 3 out of 5 in 6f8w

Go back to Magnesium Binding Sites List in 6f8w
Magnesium binding site 3 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A


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

b:41.9
occ:1.00
 O A:HOH760 2.2 38.7 1.0
O A:HOH939 2.3 45.3 1.0
O A:HOH724 2.3 40.7 1.0
OD2 A:ASP560 4.2 34.5 1.0
OD1 A:ASP560 4.4 29.9 1.0
CG A:ASP560 4.8 30.3 1.0

Magnesium binding site 4 out of 5 in 6f8w

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Magnesium binding site 4 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A


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

b:15.4
occ:1.00
 O B:HOH749 2.0 19.0 1.0
OD1 B:ASP367 2.1 17.7 1.0
O B:HOH799 2.1 16.2 1.0
O B:HOH890 2.1 15.8 1.0
O B:HOH824 2.2 16.8 1.0
O B:HOH774 2.2 18.0 1.0
CG B:ASP367 3.1 17.8 1.0
OD2 B:ASP367 3.4 15.7 1.0
O B:HOH701 3.7 28.3 1.0
ZN B:ZN601 3.8 20.6 1.0
H01 B:D0E604 3.9 25.7 0.8
O B:HOH853 4.1 18.7 1.0
CD2 B:HIS366 4.1 14.0 1.0
NE2 B:HIS399 4.2 15.6 1.0
O B:HIS366 4.2 17.1 1.0
OE2 B:GLU396 4.2 21.1 1.0
O B:HOH843 4.2 20.9 1.0
H19 B:D0E604 4.3 25.7 0.8
OG1 B:THR437 4.3 18.3 1.0
CD2 B:HIS399 4.4 13.8 1.0
CB B:ASP367 4.4 15.9 1.0
C15 B:D0E604 4.4 21.4 0.8
OD2 B:ASP484 4.5 24.1 1.0
NE2 B:HIS366 4.5 16.1 1.0
O B:HOH730 4.5 26.6 1.0
CD2 B:HIS370 4.6 15.8 1.0
C16 B:D0E604 4.6 27.2 0.8
O04 B:D0E604 4.7 27.8 0.8
NE2 B:HIS326 4.7 18.9 1.0
CA B:ASP367 4.8 15.3 1.0
CD2 B:HIS326 4.8 16.6 1.0
CB B:THR437 4.8 18.2 1.0
O B:THR437 4.8 20.7 1.0
NE2 B:HIS370 4.8 18.0 1.0
CG B:GLU396 4.9 15.8 1.0
CD B:GLU396 4.9 19.9 1.0
C B:HIS366 5.0 16.2 1.0

Magnesium binding site 5 out of 5 in 6f8w

Go back to Magnesium Binding Sites List in 6f8w
Magnesium binding site 5 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18A


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

b:30.8
occ:1.00
 O B:HOH790 2.0 29.1 1.0
OD2 B:ASP467 2.0 30.4 1.0
O B:HOH776 2.1 35.7 1.0
OD2 B:ASP471 2.1 31.1 1.0
O B:HOH771 2.1 34.5 1.0
CG B:ASP471 3.1 35.5 1.0
CG B:ASP467 3.1 32.1 1.0
OD1 B:ASP471 3.5 32.8 1.0
CB B:ASP467 3.6 31.3 1.0
O B:HOH921 3.9 47.3 1.0
N B:ASP467 4.1 32.6 1.0
OD1 B:ASP467 4.2 37.4 1.0
O B:HOH904 4.4 41.4 1.0
CB B:ASP471 4.4 25.5 1.0
CA B:ASP467 4.5 32.5 1.0
CE B:LYS457 4.7 37.5 1.0
O B:LEU465 4.7 33.6 1.0
O B:HOH755 4.9 37.2 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 00:12:44 2024

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