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Zinc in PDB 1y2h: Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2h was solved by G.L.Card, L.Blasdel, B.P.England, C.Zhang, Y.Suzuki, S.Gillette, D.Fong, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.541, 94.178, 106.819, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 29.9

Other elements in 1y2h:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y2h

Go back to Zinc Binding Sites List in 1y2h
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:42.5
occ:1.00
 O A:HOH1007 1.7 24.3 1.0
OD2 A:ASP392 2.1 31.8 1.0
NE2 A:HIS274 2.2 26.4 1.0
NE2 A:HIS238 2.3 28.8 1.0
O A:HOH1008 2.5 16.5 1.0
OD2 A:ASP275 2.5 27.9 1.0
CD2 A:HIS238 3.0 29.6 1.0
CG A:ASP392 3.1 32.4 1.0
CD2 A:HIS274 3.1 22.4 1.0
CE1 A:HIS274 3.1 26.0 1.0
OD1 A:ASP392 3.3 32.9 1.0
CG A:ASP275 3.4 25.2 1.0
CE1 A:HIS238 3.4 29.4 1.0
MG A:MG1002 3.9 27.6 1.0
OD1 A:ASP275 3.9 22.2 1.0
O A:HOH1006 4.0 39.5 1.0
ND1 A:HIS274 4.2 25.6 1.0
CG A:HIS274 4.2 26.2 1.0
CG A:HIS238 4.2 29.8 1.0
ND1 A:HIS238 4.4 29.3 1.0
CB A:ASP275 4.4 25.6 1.0
CB A:ASP392 4.5 32.9 1.0
CG2 A:VAL242 4.7 30.1 1.0
CD2 A:HIS234 4.8 30.1 1.0
O A:HOH1004 4.8 57.5 1.0
CA A:ASP392 4.9 32.9 1.0

Zinc binding site 2 out of 2 in 1y2h

Go back to Zinc Binding Sites List in 1y2h
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 1-(2- Chloro-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:45.5
occ:1.00
 O B:HOH2007 1.9 42.3 1.0
OD2 B:ASP275 2.0 21.9 1.0
NE2 B:HIS274 2.1 21.7 1.0
OD2 B:ASP392 2.2 35.0 1.0
NE2 B:HIS238 2.3 29.1 1.0
O B:HOH2008 2.9 68.9 1.0
CE1 B:HIS274 3.0 23.8 1.0
CG B:ASP275 3.1 25.6 1.0
CD2 B:HIS274 3.1 25.1 1.0
CD2 B:HIS238 3.2 27.9 1.0
CE1 B:HIS238 3.2 27.8 1.0
CG B:ASP392 3.2 34.8 1.0
OD1 B:ASP392 3.5 33.5 1.0
OD1 B:ASP275 3.6 24.1 1.0
MG B:MG1002 3.8 53.1 1.0
O B:HOH12 4.1 56.5 1.0
ND1 B:HIS274 4.1 27.4 1.0
CG B:HIS274 4.2 25.9 1.0
O B:HOH2006 4.2 54.9 1.0
CD2 B:HIS234 4.3 28.7 1.0
NE2 B:HIS234 4.3 31.5 1.0
ND1 B:HIS238 4.3 27.3 1.0
CB B:ASP275 4.4 26.1 1.0
CG B:HIS238 4.4 28.9 1.0
O B:HOH2004 4.5 29.7 1.0
CB B:ASP392 4.6 35.7 1.0
CG2 B:VAL242 4.6 29.6 1.0

Reference:

G.L.Card, L.Blasdel, B.P.England, C.Zhang, Y.Suzuki, S.Gillette, D.Fong, P.N.Ibrahim, D.R.Artis, G.Bollag, M.V.Milburn, S.-H.Kim, J.Schlessinger, K.Y.J.Zhang. A Family of Phosphodiesterase Inhibitors Discovered By Cocrystallography and Scaffold-Based Drug Design Nat.Biotechnol. V. 23 201 2005.
ISSN: ISSN 1087-0156
PubMed: 15685167
DOI: 10.1038/NBT1059
Page generated: Wed Oct 16 20:45:12 2024

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