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Magnesium in PDB 6f8t: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A, PDB code: 6f8t 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) 45.63 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.531, 98.717, 119.623, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21.2

Other elements in 6f8t:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A 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- 4A (pdb code 6f8t). 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- 4A, PDB code: 6f8t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6f8t

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Magnesium binding site 1 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A


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- 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:9.9
occ:1.00
 OD1 A:ASP367 2.0 11.2 1.0
O A:HOH803 2.1 11.2 1.0
O A:HOH756 2.1 10.9 1.0
O A:HOH933 2.1 10.1 1.0
O A:HOH857 2.2 12.2 1.0
O A:HOH867 2.2 10.7 1.0
CG A:ASP367 3.0 13.6 1.0
OD2 A:ASP367 3.4 8.5 1.0
ZN A:ZN601 3.7 15.1 1.0
O A:HOH707 3.9 29.4 1.0
O A:HOH966 4.0 29.6 1.0
OE2 A:GLU396 4.1 12.8 1.0
CD2 A:HIS366 4.1 9.7 1.0
O A:HOH840 4.2 15.1 1.0
O A:HIS366 4.2 11.3 1.0
NE2 A:HIS399 4.2 10.2 1.0
O A:HOH829 4.2 13.9 1.0
OG1 A:THR437 4.2 11.8 1.0
CD2 A:HIS399 4.4 9.3 1.0
CB A:ASP367 4.4 9.4 1.0
OD2 A:ASP484 4.5 19.6 1.0
NE2 A:HIS366 4.5 9.0 1.0
CD2 A:HIS370 4.6 9.5 1.0
O A:THR437 4.7 13.4 1.0
NE2 A:HIS326 4.7 13.5 1.0
CA A:ASP367 4.8 9.8 1.0
CB A:THR437 4.8 11.0 1.0
CD2 A:HIS326 4.8 11.7 1.0
NE2 A:HIS370 4.8 13.2 1.0
CG A:GLU396 4.9 9.8 1.0
CD A:GLU396 4.9 14.7 1.0
C A:HIS366 5.0 9.0 1.0

Magnesium binding site 2 out of 5 in 6f8t

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Magnesium binding site 2 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A


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- 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:21.5
occ:1.00
 OD2 A:ASP333 2.6 13.9 1.0
ND1 A:HIS330 2.8 8.8 1.0
ND2 A:ASN487 3.0 12.5 1.0
CH2 A:TRP498 3.2 14.2 1.0
CZ2 A:TRP498 3.3 15.0 1.0
CZ3 A:TRP498 3.4 16.6 1.0
CE2 A:TRP498 3.4 14.4 1.0
OH A:TYR325 3.4 10.1 1.0
CG A:ASP333 3.5 13.0 1.0
CE3 A:TRP498 3.5 16.0 1.0
CD2 A:TRP498 3.6 13.8 1.0
CB A:ASP333 3.7 9.7 1.0
CE1 A:HIS330 3.7 10.2 1.0
CG A:HIS330 3.8 10.6 1.0
CG A:ASN487 3.9 12.6 1.0
CA A:HIS330 3.9 11.4 1.0
OD1 A:ASN487 3.9 13.7 1.0
CZ A:TYR325 3.9 13.5 1.0
CB A:HIS330 4.1 9.9 1.0
NE1 A:TRP498 4.2 13.7 1.0
O A:HIS330 4.2 11.5 1.0
CE2 A:TYR325 4.3 12.4 1.0
O A:HOH745 4.4 13.3 1.0
CG A:TRP498 4.4 13.7 1.0
C A:HIS330 4.6 11.8 1.0
OD1 A:ASP333 4.7 15.8 1.0
CD1 A:TRP498 4.7 16.5 1.0
CE1 A:TYR325 4.7 13.1 1.0
NE2 A:HIS330 4.9 7.7 1.0
N A:HIS330 5.0 11.5 1.0
CG2 A:VAL334 5.0 9.9 1.0
CD2 A:HIS330 5.0 7.9 1.0

Magnesium binding site 3 out of 5 in 6f8t

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Magnesium binding site 3 out of 5 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 4A


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- 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg604

b:36.1
occ:1.00
 O A:HOH714 2.2 27.1 1.0
OD2 A:ASP264 3.9 41.6 1.0
OD1 A:ASP264 4.0 35.9 1.0
CG A:ASP264 4.4 40.4 1.0
OE1 A:GLU263 4.7 41.8 1.0
O A:LYS260 4.8 31.3 1.0
CE A:LYS260 4.9 45.1 1.0

Magnesium binding site 4 out of 5 in 6f8t

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


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- 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg605

b:25.0
occ:1.00
 OD2 A:ASP467 2.0 19.3 1.0
OD2 A:ASP471 2.1 19.4 1.0
O A:HOH779 2.2 23.2 1.0
O A:HOH814 2.2 23.8 1.0
CG A:ASP471 3.1 24.3 1.0
CG A:ASP467 3.2 22.6 1.0
OD1 A:ASP471 3.4 21.6 1.0
CB A:ASP467 3.7 19.3 1.0
N A:ASP467 3.9 21.6 1.0
OD1 A:ASP467 4.2 25.9 1.0
O A:LEU465 4.4 23.4 1.0
CB A:ASP471 4.4 16.2 1.0
O A:HOH977 4.5 33.9 1.0
CA A:ASP467 4.5 20.8 1.0
O A:HOH976 4.5 36.3 1.0
NZ A:LYS457 4.8 27.5 1.0
C A:LEU466 4.8 21.2 1.0
CA A:LEU466 4.9 13.6 1.0
CE A:LYS457 4.9 29.6 1.0

Magnesium binding site 5 out of 5 in 6f8t

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


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- 4A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:11.3
occ:1.00
 OD1 B:ASP367 2.1 11.0 1.0
O B:HOH832 2.1 11.9 1.0
O B:HOH726 2.1 12.6 1.0
O B:HOH868 2.1 12.2 1.0
O B:HOH758 2.1 11.6 1.0
O B:HOH848 2.2 12.5 1.0
CG B:ASP367 3.1 15.9 1.0
OD2 B:ASP367 3.4 12.6 1.0
ZN B:ZN601 3.7 16.5 1.0
O B:HOH929 3.9 27.8 1.0
OE2 B:GLU396 4.1 12.3 1.0
CD2 B:HIS366 4.1 12.4 1.0
O B:HOH838 4.1 17.8 1.0
O B:HIS366 4.2 11.9 1.0
NE2 B:HIS399 4.2 10.7 1.0
O B:HOH863 4.2 18.5 1.0
OG1 B:THR437 4.3 13.0 1.0
CD2 B:HIS399 4.4 9.7 1.0
CB B:ASP367 4.4 12.3 1.0
OD2 B:ASP484 4.5 20.4 1.0
NE2 B:HIS366 4.5 11.0 1.0
CD2 B:HIS370 4.6 13.7 1.0
NE2 B:HIS326 4.7 17.6 1.0
O B:HOH830 4.7 32.0 1.0
O B:THR437 4.7 12.6 1.0
CD2 B:HIS326 4.7 13.9 1.0
CA B:ASP367 4.8 8.7 1.0
CB B:THR437 4.8 11.5 1.0
NE2 B:HIS370 4.9 12.3 1.0
CD B:GLU396 4.9 15.1 1.0
CG B:GLU396 4.9 12.2 1.0
C B:HIS366 5.0 12.7 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 00:11:30 2024

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