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Zinc in PDB 1y2d: Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

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

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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 4D in Complex with 1-(4- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2d 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) 81.65 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.804, 79.146, 164.617, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.9

Other elements in 1y2d:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2d). 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 4D in Complex with 1-(4- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2d:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y2d

Go back to Zinc Binding Sites List in 1y2d
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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 4D in Complex with 1-(4- Methoxy-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:17.2
occ:1.00
 O A:HOH1007 2.1 14.9 1.0
OD2 A:ASP201 2.2 7.0 1.0
NE2 A:HIS164 2.2 6.8 1.0
OD1 A:ASP318 2.2 7.5 1.0
NE2 A:HIS200 2.2 7.0 1.0
O A:HOH1008 2.2 14.2 1.0
CD2 A:HIS200 3.1 7.7 1.0
CD2 A:HIS164 3.1 7.5 1.0
CG A:ASP318 3.1 10.5 1.0
CG A:ASP201 3.2 6.2 1.0
CE1 A:HIS164 3.2 9.8 1.0
CE1 A:HIS200 3.3 8.6 1.0
OD2 A:ASP318 3.3 12.5 1.0
OD1 A:ASP201 3.6 7.2 1.0
MG A:MG1002 3.7 10.9 1.0
O A:HOH1006 3.9 14.9 1.0
CD2 A:HIS160 4.2 7.9 1.0
O A:HOH1016 4.2 19.1 1.0
CG A:HIS200 4.3 5.9 1.0
ND1 A:HIS164 4.3 6.6 1.0
CG A:HIS164 4.3 8.2 1.0
ND1 A:HIS200 4.3 6.7 1.0
NE2 A:HIS160 4.4 9.0 1.0
CB A:ASP201 4.4 6.5 1.0
CB A:ASP318 4.5 8.4 1.0
O A:HOH1109 4.6 39.2 1.0
CG2 A:VAL168 4.8 8.7 1.0
O A:HOH1004 4.8 12.9 1.0
CA A:ASP318 5.0 8.6 1.0

Zinc binding site 2 out of 2 in 1y2d

Go back to Zinc Binding Sites List in 1y2d
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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 4D in Complex with 1-(4- Methoxy-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:16.2
occ:1.00
 O B:HOH2007 2.1 14.8 1.0
OD1 B:ASP318 2.2 6.5 1.0
OD2 B:ASP201 2.2 7.6 1.0
NE2 B:HIS164 2.2 8.1 1.0
NE2 B:HIS200 2.2 6.1 1.0
O B:HOH2008 2.3 14.0 1.0
CD2 B:HIS200 3.1 8.3 1.0
CG B:ASP318 3.1 10.2 1.0
CD2 B:HIS164 3.1 9.4 1.0
CG B:ASP201 3.2 8.2 1.0
CE1 B:HIS164 3.3 10.1 1.0
OD2 B:ASP318 3.3 14.6 1.0
CE1 B:HIS200 3.3 6.9 1.0
OD1 B:ASP201 3.6 5.7 1.0
MG B:MG1002 3.7 9.9 1.0
O B:HOH2006 3.9 13.3 1.0
O B:HOH2019 4.2 18.1 1.0
CD2 B:HIS160 4.2 10.6 1.0
CG B:HIS200 4.3 7.2 1.0
CG B:HIS164 4.3 8.0 1.0
ND1 B:HIS164 4.3 7.8 1.0
ND1 B:HIS200 4.4 7.5 1.0
CB B:ASP201 4.4 7.5 1.0
CB B:ASP318 4.5 8.7 1.0
O B:HOH2120 4.5 37.7 1.0
NE2 B:HIS160 4.5 11.1 1.0
O B:HOH2004 4.8 12.2 1.0
CG2 B:VAL168 4.8 8.3 1.0
CA B:ASP318 5.0 8.7 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 20:44:32 2024

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