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Magnesium in PDB 1zkn: Structure of PDE4D2-Ibmx

Enzymatic activity of Structure of PDE4D2-Ibmx

All present enzymatic activity of Structure of PDE4D2-Ibmx:
3.1.4.17;

Protein crystallography data

The structure of Structure of PDE4D2-Ibmx, PDB code: 1zkn was solved by Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.704, 111.703, 159.387, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26

Other elements in 1zkn:

The structure of Structure of PDE4D2-Ibmx also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of PDE4D2-Ibmx (pdb code 1zkn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of PDE4D2-Ibmx, PDB code: 1zkn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1zkn

Go back to Magnesium Binding Sites List in 1zkn
Magnesium binding site 1 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of PDE4D2-Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:30.4
occ:1.00
 O A:HOH637 2.3 21.1 1.0
O A:HOH635 2.3 19.4 1.0
OD1 A:ASP201 2.4 17.0 1.0
O A:HOH634 2.5 21.8 1.0
CG A:ASP201 3.4 17.1 1.0
OD2 A:ASP201 3.7 19.9 1.0
OE2 A:GLU230 4.0 22.5 1.0
ZN A:ZN601 4.0 25.0 1.0
O A:HOH622 4.1 20.4 1.0
OG1 A:THR271 4.1 23.6 1.0
O A:HIS200 4.1 17.5 1.0
O A:HOH621 4.1 29.3 1.0
NE2 A:HIS233 4.1 16.4 1.0
CD2 A:HIS200 4.3 20.4 1.0
CD2 A:HIS233 4.3 16.4 1.0
OD2 A:ASP318 4.6 26.0 1.0
CB A:THR271 4.6 25.2 1.0
CB A:ASP201 4.7 17.8 1.0
O A:THR271 4.8 26.5 1.0
CD2 A:HIS204 4.8 17.2 1.0
NE2 A:HIS200 4.9 22.6 1.0
CD2 A:HIS160 4.9 15.0 1.0
CD A:GLU230 4.9 21.4 1.0
CA A:ASP201 5.0 18.0 1.0
CG A:GLU230 5.0 21.4 1.0
NE2 A:HIS160 5.0 14.7 1.0
C A:HIS200 5.0 17.5 1.0

Magnesium binding site 2 out of 4 in 1zkn

Go back to Magnesium Binding Sites List in 1zkn
Magnesium binding site 2 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of PDE4D2-Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:44.7
occ:1.00
 OD1 B:ASP201 2.3 23.8 1.0
O B:HOH625 2.4 32.6 1.0
O B:HOH627 2.5 22.2 1.0
O B:HOH606 2.5 24.7 1.0
CG B:ASP201 3.3 23.5 1.0
OD2 B:ASP201 3.5 24.9 1.0
O B:HOH624 3.7 34.5 1.0
ZN B:ZN601 3.9 27.9 1.0
OE2 B:GLU230 4.2 26.5 1.0
NE2 B:HIS233 4.3 21.9 1.0
CD2 B:HIS160 4.4 20.8 1.0
O B:HIS200 4.4 19.4 1.0
CD2 B:HIS200 4.4 21.8 1.0
CD2 B:HIS204 4.4 20.5 1.0
NE2 B:HIS160 4.5 18.5 1.0
CD2 B:HIS233 4.6 21.7 1.0
OD2 B:ASP318 4.6 27.6 1.0
OG1 B:THR271 4.6 26.3 1.0
NE2 B:HIS204 4.6 19.8 1.0
CB B:ASP201 4.6 23.5 1.0
NE2 B:HIS200 4.7 22.6 1.0
O B:THR271 4.9 29.1 1.0

Magnesium binding site 3 out of 4 in 1zkn

Go back to Magnesium Binding Sites List in 1zkn
Magnesium binding site 3 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of PDE4D2-Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:35.2
occ:1.00
 O C:HOH621 2.4 25.1 1.0
OD1 C:ASP201 2.4 21.2 1.0
O C:HOH611 2.4 24.0 1.0
O C:HOH616 2.5 20.1 1.0
CG C:ASP201 3.3 21.3 1.0
OD2 C:ASP201 3.6 22.3 1.0
ZN C:ZN601 3.9 28.4 1.0
O C:HOH619 4.1 31.7 1.0
O C:HIS200 4.2 20.0 1.0
CD2 C:HIS200 4.2 21.1 1.0
NE2 C:HIS233 4.2 15.6 1.0
OE2 C:GLU230 4.3 24.9 1.0
OG1 C:THR271 4.4 27.4 1.0
CD2 C:HIS233 4.4 15.8 1.0
CD2 C:HIS204 4.6 17.9 1.0
CD2 C:HIS160 4.6 22.0 1.0
CB C:ASP201 4.7 21.1 1.0
NE2 C:HIS160 4.7 21.8 1.0
O C:THR271 4.7 28.9 1.0
NE2 C:HIS200 4.7 23.4 1.0
OD2 C:ASP318 4.7 30.1 1.0
NE2 C:HIS204 4.9 18.2 1.0
CB C:THR271 4.9 26.9 1.0
CA C:ASP201 5.0 20.6 1.0

Magnesium binding site 4 out of 4 in 1zkn

Go back to Magnesium Binding Sites List in 1zkn
Magnesium binding site 4 out of 4 in the Structure of PDE4D2-Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of PDE4D2-Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg602

b:29.1
occ:1.00
 OD1 D:ASP201 2.3 22.8 1.0
O D:HOH640 2.3 19.5 1.0
O D:HOH639 2.3 23.6 1.0
O D:HOH629 2.5 19.2 1.0
O D:HOH618 2.5 22.6 1.0
CG D:ASP201 3.3 21.1 1.0
OD2 D:ASP201 3.6 22.3 1.0
ZN D:ZN601 4.0 25.4 1.0
O D:HIS200 4.1 18.4 1.0
OE2 D:GLU230 4.1 26.0 1.0
CD2 D:HIS200 4.1 17.5 1.0
OG1 D:THR271 4.2 23.4 1.0
O D:HOH619 4.2 32.6 1.0
NE2 D:HIS233 4.2 20.2 1.0
O D:HOH638 4.3 53.5 1.0
CD2 D:HIS233 4.4 19.3 1.0
NE2 D:HIS200 4.6 19.5 1.0
OD2 D:ASP318 4.6 24.8 1.0
O D:THR271 4.7 26.0 1.0
CB D:ASP201 4.7 20.9 1.0
CD2 D:HIS160 4.7 23.4 1.0
CD2 D:HIS204 4.7 19.9 1.0
CB D:THR271 4.8 24.6 1.0
NE2 D:HIS160 4.8 25.1 1.0
CA D:ASP201 4.9 18.1 1.0
CD D:GLU230 4.9 25.1 1.0
CG D:GLU230 5.0 23.7 1.0
C D:HIS200 5.0 18.0 1.0
NE2 D:HIS204 5.0 20.3 1.0

Reference:

Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke. Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor 3-Isobutyl-1-Methylxanthine Suggest A Conformation Determinant of Inhibitor Selectivity J.Biol.Chem. V. 279 13095 2004.
ISSN: ISSN 0021-9258
PubMed: 14668322
DOI: 10.1074/JBC.M311556200
Page generated: Mon Dec 14 07:12:10 2020

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