Atomistry » Magnesium » PDB 6fch-6fjk » 6fdc
Atomistry »
  Magnesium »
    PDB 6fch-6fjk »
      6fdc »

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

Go back to Magnesium Binding Sites List in 6fdc
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

Go back to Magnesium Binding Sites List in 6fdc
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

Go back to Magnesium Binding Sites List in 6fdc
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

Go back to Magnesium Binding Sites List in 6fdc
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

Go back to Magnesium Binding Sites List in 6fdc
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: Tue Oct 1 00:24:30 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy