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Iodine 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:

Magnesium (Mg) 2 atoms
Zinc (Zn) 3 atoms
Sodium (Na) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B, PDB code: 4wzi:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 4wzi

Go back to Iodine Binding Sites List in 4wzi
Iodine 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 Iodine with other atoms in the I 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:I805

b:59.6
occ:1.00
O A:HOH980 3.4 37.3 1.0
NE A:ARG503 3.5 41.3 1.0
NH2 A:ARG503 3.5 27.4 1.0
O A:HOH1036 3.8 46.4 1.0
CE1 A:PHE484 3.8 24.7 1.0
CZ A:ARG503 3.9 55.7 1.0
CD1 A:PHE484 4.0 24.5 1.0
O A:ARG503 4.1 34.0 1.0
CB A:ARG503 4.2 27.7 1.0
CB A:ARG507 4.2 25.9 1.0
CD A:ARG507 4.4 22.9 1.0
CD1 A:LEU487 4.5 23.4 1.0
CD2 A:PHE495 4.5 27.5 1.0
CD A:ARG503 4.6 35.0 1.0
CG A:ARG503 4.7 35.7 1.0
C A:ARG503 4.7 34.8 1.0
CA A:ARG503 4.7 29.6 1.0
CG A:ARG507 4.8 31.4 1.0
O B:HOH1016 5.0 69.9 1.0
CZ A:PHE484 5.0 25.7 1.0

Iodine binding site 2 out of 2 in 4wzi

Go back to Iodine Binding Sites List in 4wzi
Iodine 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 Iodine with other atoms in the I 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:I804

b:53.9
occ:1.00
O B:HOH945 3.3 38.5 1.0
NE B:ARG503 3.5 43.3 1.0
NH2 B:ARG503 3.8 37.4 1.0
CE1 B:PHE484 3.8 27.6 1.0
O B:HOH967 4.0 47.5 1.0
CD1 B:PHE484 4.0 28.2 1.0
CZ B:ARG503 4.1 54.7 1.0
O B:ARG503 4.1 36.8 1.0
CB B:ARG503 4.2 30.2 1.0
CB B:ARG507 4.2 28.8 1.0
CD B:ARG507 4.3 23.4 1.0
CD1 B:LEU487 4.5 31.0 1.0
CD2 B:PHE495 4.5 33.7 1.0
CD B:ARG503 4.6 38.6 1.0
CG B:ARG503 4.6 39.7 1.0
C B:ARG503 4.7 37.8 1.0
CA B:ARG503 4.7 32.4 1.0
CG B:ARG507 4.7 25.0 1.0
O A:HOH1054 4.8 63.5 1.0
CZ B:PHE484 5.0 26.4 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: Sun Dec 13 19:37:38 2020

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