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Zinc in PDB 1y2b: Catalytic Domain of Human Phosphodiesterase 4D in Complex with 3,5- Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

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

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with 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 3,5- Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2b 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 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.469, 79.009, 164.141, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 18.5

Other elements in 1y2b:

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with 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 3,5- Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2b). 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 3,5- Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y2b

Go back to Zinc Binding Sites List in 1y2b
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 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 3,5- Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:14.1
occ:1.00
 OD2 A:ASP201 2.1 7.7 1.0
O A:HOH1007 2.1 14.5 1.0
OD1 A:ASP318 2.2 8.4 1.0
O A:HOH1008 2.2 16.3 1.0
NE2 A:HIS200 2.2 7.7 1.0
NE2 A:HIS164 2.2 7.3 1.0
CD2 A:HIS200 3.0 8.4 1.0
CG A:ASP318 3.1 9.5 1.0
CG A:ASP201 3.1 7.1 1.0
CD2 A:HIS164 3.1 7.1 1.0
CE1 A:HIS164 3.2 7.2 1.0
CE1 A:HIS200 3.2 8.7 1.0
OD2 A:ASP318 3.3 10.6 1.0
OD1 A:ASP201 3.6 8.0 1.0
MG A:MG1002 3.7 11.0 1.0
O A:HOH1006 3.9 15.3 1.0
O A:HOH1032 4.1 18.7 1.0
CD2 A:HIS160 4.2 9.0 1.0
CG A:HIS200 4.2 6.8 1.0
ND1 A:HIS164 4.3 6.8 1.0
CG A:HIS164 4.3 7.2 1.0
ND1 A:HIS200 4.3 8.0 1.0
CB A:ASP201 4.3 7.4 1.0
CB A:ASP318 4.5 8.8 1.0
NE2 A:HIS160 4.5 9.8 1.0
O A:HOH1118 4.5 32.6 1.0
CG2 A:VAL168 4.7 8.1 1.0
O A:HOH1004 4.8 11.8 1.0
CA A:ASP318 5.0 8.6 1.0

Zinc binding site 2 out of 2 in 1y2b

Go back to Zinc Binding Sites List in 1y2b
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 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 3,5- Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:13.3
occ:1.00
 O B:HOH2007 2.0 14.3 1.0
OD2 B:ASP201 2.1 8.6 1.0
OD1 B:ASP318 2.1 8.5 1.0
NE2 B:HIS200 2.2 8.0 1.0
O B:HOH2008 2.2 14.4 1.0
NE2 B:HIS164 2.2 9.0 1.0
CD2 B:HIS200 3.0 9.1 1.0
CG B:ASP318 3.1 8.3 1.0
CG B:ASP201 3.1 7.7 1.0
CE1 B:HIS164 3.1 8.0 1.0
CD2 B:HIS164 3.2 8.8 1.0
CE1 B:HIS200 3.2 8.9 1.0
OD2 B:ASP318 3.3 11.9 1.0
OD1 B:ASP201 3.6 8.1 1.0
MG B:MG1002 3.7 10.6 1.0
O B:HOH2006 3.9 14.8 1.0
CD2 B:HIS160 4.2 9.3 1.0
O B:HOH2028 4.2 17.3 1.0
CG B:HIS200 4.2 8.5 1.0
ND1 B:HIS164 4.3 8.2 1.0
ND1 B:HIS200 4.3 9.2 1.0
CG B:HIS164 4.3 7.8 1.0
CB B:ASP201 4.3 7.6 1.0
CB B:ASP318 4.4 8.3 1.0
O B:HOH2131 4.5 37.1 1.0
NE2 B:HIS160 4.5 11.3 1.0
CG2 B:VAL168 4.7 8.0 1.0
O B:HOH2004 4.8 12.4 1.0
O B:HOH2217 4.8 42.8 1.0
CA B:ASP318 5.0 8.1 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 Aug 20 00:30:15 2025

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