Atomistry » Zinc » PDB 4wnv-4x3r » 4x0f
Atomistry »
  Zinc »
    PDB 4wnv-4x3r »
      4x0f »

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

Last articles

Fe in 1ZLQ
Fe in 1YRQ
Fe in 1ZJ9
Fe in 1ZJ8
Fe in 1ZGN
Fe in 1Z1N
Fe in 1ZBZ
Fe in 1ZBY
Fe in 1ZA5
Fe in 1Z9N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy