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Zinc in PDB 3iak: Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine.

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine.

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine.:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine., PDB code: 3iak was solved by R.K.Y.Cheng, L.Crawley, J.Barker, M.Wood, B.Felicetti, M.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.75 / 2.80
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 83.502, 83.502, 148.144, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 29.1

Other elements in 3iak:

The structure of Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine. (pdb code 3iak). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine., PDB code: 3iak:

Zinc binding site 1 out of 1 in 3iak

Go back to Zinc Binding Sites List in 3iak
Zinc binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine.


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 Human Phosphodiesterase 4D (PDE4D) with Papaverine. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:78.5
occ:1.00
 OD2 A:ASP201 2.0 49.9 1.0
OD1 A:ASP318 2.2 59.2 1.0
NE2 A:HIS164 2.2 52.5 1.0
O A:HOH5 2.3 50.6 1.0
NE2 A:HIS200 2.7 49.4 1.0
O A:HOH4 2.7 52.1 1.0
CG A:ASP318 3.2 59.1 1.0
CD2 A:HIS164 3.2 52.6 1.0
CG A:ASP201 3.2 49.4 1.0
CE1 A:HIS164 3.2 52.4 1.0
OD2 A:ASP318 3.5 60.0 1.0
CD2 A:HIS200 3.5 49.2 1.0
CE1 A:HIS200 3.6 49.5 1.0
OD1 A:ASP201 3.8 49.2 1.0
MG A:MG414 3.9 96.8 1.0
CD2 A:HIS160 4.1 50.3 1.0
O A:HOH8 4.2 84.0 1.0
ND1 A:HIS164 4.3 52.5 1.0
CG A:HIS164 4.3 52.4 1.0
CB A:ASP201 4.4 48.9 1.0
NE2 A:HIS160 4.5 49.9 1.0
CB A:ASP318 4.5 58.8 1.0
ND1 A:HIS200 4.6 49.3 1.0
CG A:HIS200 4.6 48.8 1.0
CG2 A:VAL168 4.7 54.3 1.0
O A:HOH7 4.8 49.6 1.0
CE2 A:TYR159 5.0 55.7 1.0

Reference:

R.K.Y.Cheng, L.Crawley, J.Barker, M.Wood, B.Felicetti, M.Whittaker. Crystal Structure of Human Phosphodiesterase 4D (PDE4D) with Papaverine. To Be Published.
Page generated: Sat Oct 26 06:53:13 2024

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