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Zinc in PDB 3k4s: The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone

Enzymatic activity of The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone

All present enzymatic activity of The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone:
3.1.4.17;

Protein crystallography data

The structure of The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone, PDB code: 3k4s was solved by L.Crawley, R.K.Y.Cheng, M.Wood, J.Barker, B.Felicetti, M.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.15 / 2.05
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 83.217, 83.217, 148.766, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.2

Other elements in 3k4s:

The structure of The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone (pdb code 3k4s). 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 The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone, PDB code: 3k4s:

Zinc binding site 1 out of 1 in 3k4s

Go back to Zinc Binding Sites List in 3k4s
Zinc binding site 1 out of 1 in the The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of the Catalytic Domain of Human PDE4D with 4- (3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:41.0
occ:1.00
 OD2 A:ASP201 2.1 33.4 1.0
OD1 A:ASP318 2.2 29.5 1.0
NE2 A:HIS200 2.3 34.5 1.0
NE2 A:HIS164 2.3 21.0 1.0
O A:HOH547 2.3 30.5 1.0
O A:HOH542 2.5 32.7 1.0
CD2 A:HIS200 3.1 30.2 1.0
CG A:ASP318 3.2 30.9 1.0
CG A:ASP201 3.2 29.0 1.0
CD2 A:HIS164 3.3 23.0 1.0
CE1 A:HIS164 3.3 25.9 1.0
CE1 A:HIS200 3.4 32.8 1.0
OD2 A:ASP318 3.4 33.7 1.0
MG A:MG415 3.6 52.4 1.0
OD1 A:ASP201 3.7 31.2 1.0
O A:HOH619 4.0 39.9 1.0
O A:HOH543 4.0 30.2 1.0
CD2 A:HIS160 4.1 25.6 1.0
O A:HOH548 4.1 42.0 1.0
CG A:HIS200 4.3 28.8 1.0
O A:HOH565 4.4 44.3 1.0
NE2 A:HIS160 4.4 26.7 1.0
CB A:ASP201 4.4 26.9 1.0
ND1 A:HIS200 4.4 31.8 1.0
CG A:HIS164 4.4 28.1 1.0
ND1 A:HIS164 4.4 22.0 1.0
CB A:ASP318 4.6 29.0 1.0
O A:HOH540 4.8 29.1 1.0
CG2 A:VAL168 4.8 24.6 1.0

Reference:

L.Crawley, R.K.Y.Cheng, M.Wood, J.Barker, B.Felicetti, M.Whittaker. The Structure of the Catalytic Domain of Human PDE4D with 4-(3-Butoxy-4-Methoxyphenyl)Methyl-2-Imidazolidone To Be Published.
Page generated: Sat Oct 26 07:40:30 2024

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