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Zinc in PDB 2qyl: Crystal Structure of PDE4B2B in Complex with Inhibitor Npv

Protein crystallography data

The structure of Crystal Structure of PDE4B2B in Complex with Inhibitor Npv, PDB code: 2qyl was solved by H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 91.758, 105.353, 87.827, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 23.9

Other elements in 2qyl:

The structure of Crystal Structure of PDE4B2B in Complex with Inhibitor Npv also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE4B2B in Complex with Inhibitor Npv (pdb code 2qyl). 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 PDE4B2B in Complex with Inhibitor Npv, PDB code: 2qyl:

Zinc binding site 1 out of 1 in 2qyl

Go back to Zinc Binding Sites List in 2qyl
Zinc binding site 1 out of 1 in the Crystal Structure of PDE4B2B in Complex with Inhibitor Npv


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 PDE4B2B in Complex with Inhibitor Npv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:38.2
occ:1.00
O A:HOH504 2.2 36.7 1.0
NE2 A:HIS238 2.3 29.7 1.0
OD2 A:ASP275 2.3 35.0 1.0
OD1 A:ASP392 2.3 32.1 1.0
NE2 A:HIS274 2.4 34.2 1.0
O A:HOH505 2.4 33.5 1.0
CD2 A:HIS274 3.0 34.6 1.0
CG A:ASP392 3.1 33.5 1.0
CD2 A:HIS238 3.2 31.3 1.0
CG A:ASP275 3.2 35.9 1.0
CE1 A:HIS238 3.3 30.9 1.0
OD2 A:ASP392 3.3 38.4 1.0
CE1 A:HIS274 3.5 34.2 1.0
MG A:MG502 3.6 39.9 1.0
OD1 A:ASP275 3.7 33.3 1.0
O A:HOH508 4.1 31.4 1.0
O A:HOH525 4.2 33.1 1.0
CD2 A:HIS234 4.2 31.3 1.0
CG A:HIS274 4.3 32.0 1.0
NE2 A:HIS234 4.4 31.7 1.0
CG A:HIS238 4.4 32.1 1.0
ND1 A:HIS238 4.4 29.1 1.0
CB A:ASP275 4.4 34.8 1.0
ND1 A:HIS274 4.4 34.6 1.0
CB A:ASP392 4.5 34.4 1.0
CG2 A:VAL242 4.7 28.9 1.0
O A:HOH509 4.9 35.4 1.0

Reference:

H.Wang, M.S.Peng, Y.Chen, J.Geng, H.Robinson, M.D.Houslay, J.Cai, H.Ke. Structures of the Four Subfamilies of Phosphodiesterase-4 Provide Insight Into the Selectivity of Their Inhibitors. Biochem.J. V. 408 193 2007.
ISSN: ISSN 0264-6021
PubMed: 17727341
DOI: 10.1042/BJ20070970
Page generated: Wed Dec 16 03:51:14 2020

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