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Magnesium in PDB 4wzi: Crystal Structure of Crosslink Stabilized Long-Form PDE4B

Enzymatic activity of Crystal Structure of Crosslink Stabilized Long-Form PDE4B

All present enzymatic activity of Crystal Structure of Crosslink Stabilized Long-Form PDE4B:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B, PDB code: 4wzi was solved by P.Cedervall, J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.01 / 2.58
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.830, 137.830, 141.740, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 20.6

Other elements in 4wzi:

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Iodine (I) 2 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B (pdb code 4wzi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B, PDB code: 4wzi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4wzi

Go back to Magnesium Binding Sites List in 4wzi
Magnesium binding site 1 out of 2 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B


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 Crosslink Stabilized Long-Form PDE4B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:53.6
occ:1.00
O A:HOH1090 2.3 54.2 1.0
OD1 A:ASP447 2.4 28.9 1.0
O A:HOH950 2.4 23.1 1.0
O A:HOH1089 2.4 40.4 1.0
O A:HOH956 2.5 31.0 1.0
CG A:ASP447 3.3 29.6 1.0
OD2 A:ASP447 3.5 37.4 1.0
ZN A:ZN801 3.8 30.6 1.0
OD2 A:ASP564 4.3 34.8 1.0
O A:HOH996 4.3 43.4 1.0
CD2 A:HIS446 4.3 26.3 1.0
NE2 A:HIS406 4.4 28.0 1.0
CD2 A:HIS406 4.4 28.5 1.0
OE2 A:GLU476 4.5 37.2 1.0
O A:HIS446 4.5 24.3 1.0
CD2 A:HIS450 4.6 25.9 1.0
O A:THR517 4.6 31.4 1.0
NE2 A:HIS479 4.6 24.9 1.0
OG1 A:THR517 4.6 28.9 1.0
NE2 A:HIS446 4.6 27.2 1.0
CB A:ASP447 4.7 20.5 1.0
NE2 A:HIS450 4.8 26.1 1.0
CD2 A:HIS479 4.9 24.6 1.0

Magnesium binding site 2 out of 2 in 4wzi

Go back to Magnesium Binding Sites List in 4wzi
Magnesium binding site 2 out of 2 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B


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 Crosslink Stabilized Long-Form PDE4B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:65.6
occ:1.00
O B:HOH918 2.2 33.9 1.0
OD1 B:ASP447 2.3 44.2 1.0
O B:HOH1040 2.4 54.1 1.0
O B:HOH1041 2.4 61.9 1.0
O B:HOH937 2.5 45.7 1.0
O B:HOH1039 2.6 59.4 1.0
CG B:ASP447 3.2 42.7 1.0
OD2 B:ASP447 3.5 47.3 1.0
ZN B:ZN801 3.9 39.9 1.0
CD2 B:HIS446 4.1 34.6 1.0
O B:HIS446 4.1 34.7 1.0
OG1 B:THR517 4.2 32.7 1.0
OE2 B:GLU476 4.3 47.4 1.0
OD2 B:ASP564 4.3 43.0 1.0
NE2 B:HIS479 4.4 32.0 1.0
O B:THR517 4.4 43.1 1.0
NE2 B:HIS446 4.5 35.2 1.0
CD2 B:HIS479 4.6 31.8 1.0
CB B:ASP447 4.6 32.8 1.0
O B:HOH1020 4.6 54.0 1.0
CD2 B:HIS406 4.7 36.1 1.0
CD2 B:HIS450 4.7 33.7 1.0
CB B:THR517 4.7 38.0 1.0
NE2 B:HIS406 4.8 36.5 1.0
O B:HOH1003 4.8 51.2 1.0
CA B:ASP447 4.9 31.2 1.0
C B:HIS446 4.9 33.4 1.0

Reference:

P.Cedervall, A.Aulabaugh, K.F.Geoghegan, T.J.Mclellan, J.Pandit. Engineered Stabilization and Structural Analysis of the Autoinhibited Conformation of PDE4 Proc. Natl. Acad. Sci. 2015.
Page generated: Mon Dec 14 19:43:00 2020

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