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Zinc in PDB 4x0f: Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram

Enzymatic activity of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram

All present enzymatic activity of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram, PDB code: 4x0f 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) 119.00 / 3.22
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 137.400, 137.400, 142.970, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 22.2

Other elements in 4x0f:

The structure of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iodine (I) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram (pdb code 4x0f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram, PDB code: 4x0f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4x0f

Go back to Zinc Binding Sites List in 4x0f
Zinc binding site 1 out of 3 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:47.5
occ:1.00
 OD2 A:ASP447 1.9 55.4 1.0
NE2 A:HIS446 2.0 35.7 1.0
NE2 A:HIS410 2.1 35.8 1.0
OD1 A:ASP564 2.2 55.8 1.0
CD2 A:HIS446 2.9 35.9 1.0
CG A:ASP447 3.0 52.7 1.0
CE1 A:HIS410 3.0 36.4 1.0
CD2 A:HIS410 3.1 35.9 1.0
CG A:ASP564 3.1 54.5 1.0
CE1 A:HIS446 3.1 35.5 1.0
OD2 A:ASP564 3.3 62.6 1.0
OD1 A:ASP447 3.6 56.8 1.0
CG A:HIS446 4.0 34.0 1.0
CD2 A:HIS406 4.1 34.2 1.0
CB A:ASP447 4.1 32.6 1.0
ND1 A:HIS446 4.1 35.9 1.0
CG A:HIS410 4.2 35.8 1.0
ND1 A:HIS410 4.2 37.9 1.0
NE2 A:HIS406 4.3 34.1 1.0
CB A:ASP564 4.4 37.6 1.0
MG A:MG805 4.6 34.8 1.0
CG2 A:VAL414 4.7 31.1 1.0

Zinc binding site 2 out of 3 in 4x0f

Go back to Zinc Binding Sites List in 4x0f
Zinc binding site 2 out of 3 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn802

b:48.3
occ:1.00
 ND1 A:HIS491 1.9 48.1 1.0
CE1 A:HIS491 2.8 48.9 1.0
CG A:HIS491 3.0 45.7 1.0
OD2 A:ASP386 3.4 70.2 1.0
CB A:HIS491 3.5 41.2 1.0
NE2 A:HIS491 3.9 49.2 1.0
CD2 A:HIS491 4.1 47.8 1.0
CG A:ASP386 4.3 62.0 1.0
OD1 A:ASP386 4.5 64.0 1.0
CA A:HIS491 5.0 39.8 1.0
OG1 A:THR390 5.0 36.6 1.0

Zinc binding site 3 out of 3 in 4x0f

Go back to Zinc Binding Sites List in 4x0f
Zinc binding site 3 out of 3 in the Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Crosslink Stabilized Long-Form PDE4B in Complex with (R)-(-)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:50.4
occ:1.00
 OD2 B:ASP447 2.0 63.2 1.0
NE2 B:HIS410 2.0 51.3 1.0
NE2 B:HIS446 2.1 44.3 1.0
OD1 B:ASP564 2.1 62.7 1.0
CE1 B:HIS410 2.9 52.7 1.0
CG B:ASP564 3.0 61.9 1.0
CD2 B:HIS446 3.0 43.8 1.0
CD2 B:HIS410 3.0 51.1 1.0
CG B:ASP447 3.1 57.5 1.0
CE1 B:HIS446 3.1 44.0 1.0
OD2 B:ASP564 3.2 62.7 1.0
OD1 B:ASP447 3.7 60.9 1.0
CD2 B:HIS406 4.1 49.5 1.0
ND1 B:HIS410 4.1 53.7 1.0
CG B:HIS410 4.1 50.5 1.0
CG B:HIS446 4.1 41.5 1.0
MG B:MG804 4.2 39.7 1.0
ND1 B:HIS446 4.2 43.9 1.0
CB B:ASP447 4.2 38.7 1.0
NE2 B:HIS406 4.3 50.0 1.0
CB B:ASP564 4.3 55.9 1.0
CG2 B:VAL414 4.6 48.7 1.0
CA B:ASP564 4.9 56.2 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 Oct 27 10:10:15 2024

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