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Zinc in PDB 5k6j: Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor

Enzymatic activity of Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor

All present enzymatic activity of Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor:
3.1.4.53;

Protein crystallography data

The structure of Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor, PDB code: 5k6j was solved by F.L.Rock, Y.Zhou, D.Sullivan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.46 / 1.86
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 53.839, 53.839, 229.850, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.5

Other elements in 5k6j:

The structure of Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor (pdb code 5k6j). 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 Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor, PDB code: 5k6j:

Zinc binding site 1 out of 1 in 5k6j

Go back to Zinc Binding Sites List in 5k6j
Zinc binding site 1 out of 1 in the Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Phospodiesterase 4B in Complex with Pyridyloxy-Benzoxaborole Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:24.8
occ:1.00
 OD2 A:ASP275 2.1 21.5 1.0
O19 A:6QQ503 2.2 24.4 0.8
NE2 A:HIS274 2.2 19.6 1.0
NE2 A:HIS238 2.2 21.1 1.0
OD1 A:ASP392 2.2 20.2 1.0
O18 A:6QQ503 2.3 25.5 0.8
B17 A:6QQ503 2.7 29.6 0.8
CD2 A:HIS274 3.0 18.8 1.0
CG A:ASP392 3.0 22.6 1.0
CE1 A:HIS238 3.1 19.2 1.0
CG A:ASP275 3.2 21.1 1.0
CD2 A:HIS238 3.2 20.0 1.0
OD2 A:ASP392 3.2 24.9 1.0
CE1 A:HIS274 3.3 18.9 1.0
OD1 A:ASP275 3.6 20.3 1.0
O16 A:6QQ503 3.6 26.0 0.8
MG A:MG502 3.8 16.5 1.0
O A:HOH666 3.9 31.3 1.0
C20 A:6QQ503 4.0 32.1 0.8
CG A:HIS274 4.2 19.0 1.0
CD2 A:HIS234 4.3 23.6 1.0
ND1 A:HIS238 4.3 19.8 1.0
ND1 A:HIS274 4.3 19.4 1.0
CG A:HIS238 4.4 20.3 1.0
CB A:ASP275 4.4 19.9 1.0
CB A:ASP392 4.4 21.6 1.0
C21 A:6QQ503 4.5 34.7 0.8
NE2 A:HIS234 4.6 22.8 1.0
O A:HOH603 4.8 21.8 1.0
CG2 A:VAL242 4.8 18.0 1.0
C15 A:6QQ503 4.9 31.0 0.8
CA A:ASP392 5.0 21.6 1.0

Reference:

C.Dong, K.Jarnagin. To Be Published To Be Published.
Page generated: Sun Oct 27 20:07:53 2024

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