Atomistry » Magnesium » PDB 6f6u-6fch » 6f8v
Atomistry »
  Magnesium »
    PDB 6f6u-6fch »
      6f8v »

Magnesium in PDB 6f8v: Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B

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

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

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B, PDB code: 6f8v 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) 45.49 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.558, 98.314, 120.089, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 25.4

Other elements in 6f8v:

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B 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- 18B (pdb code 6f8v). 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- 18B, PDB code: 6f8v:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 1 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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

b:12.5
occ:1.00
 OD1 A:ASP367 2.0 14.1 1.0
O A:HOH731 2.0 15.0 1.0
O A:HOH906 2.1 14.1 1.0
O A:HOH748 2.1 12.8 1.0
O A:HOH817 2.2 12.1 1.0
O A:HOH803 2.2 13.3 1.0
CG A:ASP367 3.1 15.8 1.0
OD2 A:ASP367 3.4 11.6 1.0
ZN A:ZN601 3.8 18.5 1.0
H01 A:D0B605 3.9 20.4 1.0
H19 A:D0B605 4.0 20.4 1.0
O A:HIS366 4.1 14.4 1.0
NE2 A:HIS399 4.1 10.8 1.0
O A:HOH814 4.1 18.5 1.0
OE2 A:GLU396 4.2 17.2 1.0
CD2 A:HIS366 4.2 11.6 1.0
O A:HOH874 4.2 15.0 1.0
OG1 A:THR437 4.3 11.2 1.0
CD2 A:HIS399 4.3 8.7 1.0
C15 A:D0B605 4.3 17.0 1.0
CB A:ASP367 4.4 12.2 1.0
O A:HOH784 4.4 23.2 1.0
CD2 A:HIS370 4.5 9.9 1.0
OD2 A:ASP484 4.5 18.8 1.0
C16 A:D0B605 4.6 26.8 1.0
NE2 A:HIS366 4.6 11.7 1.0
CA A:ASP367 4.8 13.1 1.0
NE2 A:HIS370 4.8 12.8 1.0
O A:THR437 4.8 19.9 1.0
NE2 A:HIS326 4.8 13.2 1.0
CB A:THR437 4.8 13.7 1.0
O04 A:D0B605 4.8 28.7 1.0
CD2 A:HIS326 4.9 11.3 1.0
CG A:GLU396 4.9 12.1 1.0
CD A:GLU396 4.9 15.4 1.0
C A:HIS366 4.9 14.3 1.0
H20 A:D0B605 5.0 24.2 1.0

Magnesium binding site 2 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 2 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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

b:34.0
occ:1.00
 O A:HOH798 2.1 32.1 1.0
O A:HOH710 2.6 32.9 1.0
OD2 A:ASP264 3.7 39.8 1.0
OD1 A:ASP264 3.7 37.6 1.0
CG A:ASP264 4.1 37.2 1.0
O A:HOH869 4.3 34.8 1.0
CE A:LYS260 4.3 34.5 1.0
O A:LYS260 4.4 27.3 1.0
OE1 A:GLU263 4.8 39.7 1.0

Magnesium binding site 3 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 3 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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

b:33.1
occ:1.00
 OD2 A:ASP471 2.0 28.5 1.0
OD2 A:ASP467 2.1 26.0 1.0
O A:HOH800 2.2 31.8 1.0
O A:HOH820 2.2 28.6 1.0
O A:HOH809 2.2 27.0 1.0
CG A:ASP471 3.0 27.1 1.0
CG A:ASP467 3.3 28.3 1.0
OD1 A:ASP471 3.4 28.6 1.0
CB A:ASP467 4.0 30.1 1.0
N A:ASP467 4.1 25.2 1.0
O A:HOH890 4.2 33.8 1.0
OD1 A:ASP467 4.3 33.5 1.0
CB A:ASP471 4.3 21.1 1.0
O A:HOH917 4.5 32.7 1.0
O A:LEU465 4.6 28.8 1.0
CA A:ASP467 4.7 31.3 1.0
CA A:LEU466 4.9 21.5 1.0
C A:LEU466 5.0 30.9 1.0

Magnesium binding site 4 out of 4 in 6f8v

Go back to Magnesium Binding Sites List in 6f8v
Magnesium binding site 4 out of 4 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Gebr- 18B


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

b:10.5
occ:1.00
 O B:HOH712 2.1 16.8 1.0
OD1 B:ASP367 2.1 11.4 1.0
O B:HOH801 2.1 12.5 1.0
O B:HOH779 2.1 15.1 1.0
O B:HOH751 2.2 13.5 1.0
O B:HOH807 2.2 11.2 1.0
CG B:ASP367 3.1 10.4 1.0
OD2 B:ASP367 3.4 14.5 1.0
H01 B:D0B603 3.7 23.8 1.0
ZN B:ZN601 3.7 19.1 1.0
H19 B:D0B603 4.0 23.8 1.0
O B:HOH753 4.1 13.2 1.0
CD2 B:HIS366 4.2 15.0 1.0
O B:HOH853 4.2 14.6 1.0
O B:HIS366 4.2 11.3 1.0
NE2 B:HIS399 4.2 15.2 1.0
OG1 B:THR437 4.2 12.5 1.0
C15 B:D0B603 4.3 19.8 1.0
OE2 B:GLU396 4.3 15.3 1.0
OD2 B:ASP484 4.4 19.5 1.0
CD2 B:HIS399 4.4 13.0 1.0
CB B:ASP367 4.4 14.4 1.0
O B:HOH723 4.5 19.1 1.0
NE2 B:HIS326 4.5 14.8 1.0
C16 B:D0B603 4.5 25.6 1.0
NE2 B:HIS366 4.5 14.6 1.0
CD2 B:HIS370 4.6 15.8 1.0
O B:THR437 4.6 16.4 1.0
CD2 B:HIS326 4.6 11.7 1.0
O04 B:D0B603 4.7 19.4 1.0
CB B:THR437 4.8 10.1 1.0
CA B:ASP367 4.8 9.7 1.0
NE2 B:HIS370 4.9 11.2 1.0
CG B:GLU396 5.0 12.6 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 00:12:00 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy