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Zinc in PDB 1y2j: Catalytic Domain of Human Phosphodiesterase 4B in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester

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

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-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 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2j 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 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.484, 94.235, 106.843, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 29.7

Other elements in 1y2j:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-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 4B in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2j). 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 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2j:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1y2j

Go back to Zinc Binding Sites List in 1y2j
Zinc binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-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 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:36.3
occ:1.00
OD2 A:ASP392 2.0 12.0 1.0
OD2 A:ASP275 2.1 4.7 1.0
O A:HOH1007 2.1 15.5 1.0
NE2 A:HIS274 2.3 13.6 1.0
NE2 A:HIS238 2.4 2.0 1.0
OD1 A:ASP392 2.5 2.0 1.0
CG A:ASP392 2.6 9.7 1.0
O A:HOH1008 2.8 9.4 1.0
CD2 A:HIS274 3.1 9.1 1.0
CG A:ASP275 3.2 8.5 1.0
CD2 A:HIS238 3.3 4.7 1.0
CE1 A:HIS274 3.3 10.7 1.0
CE1 A:HIS238 3.5 3.5 1.0
OD1 A:ASP275 3.7 2.3 1.0
O A:HOH1006 3.8 19.1 1.0
O21 A:7DE101 3.8 49.1 1.0
MG A:MG1002 3.8 25.5 1.0
CB A:ASP392 4.2 12.9 1.0
CG A:HIS274 4.3 15.3 1.0
ND1 A:HIS274 4.3 15.8 1.0
CB A:ASP275 4.4 12.1 1.0
N19 A:7DE101 4.5 54.4 1.0
CG A:HIS238 4.5 4.8 1.0
CD2 A:HIS234 4.5 24.6 1.0
ND1 A:HIS238 4.6 2.0 1.0
O20 A:7DE101 4.6 54.2 1.0
O A:HOH21 4.7 48.9 1.0
CG2 A:VAL242 4.8 15.2 1.0
CA A:ASP392 4.8 13.8 1.0
NE2 A:HIS234 5.0 25.4 1.0
O A:HOH1004 5.0 31.4 1.0

Zinc binding site 2 out of 2 in 1y2j

Go back to Zinc Binding Sites List in 1y2j
Zinc binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-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 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:37.2
occ:1.00
O B:HOH2007 1.9 12.5 1.0
OD2 B:ASP275 2.0 4.0 1.0
NE2 B:HIS238 2.1 2.0 1.0
OD2 B:ASP392 2.2 6.6 1.0
NE2 B:HIS274 2.5 2.0 1.0
CD2 B:HIS238 3.0 3.9 1.0
CG B:ASP275 3.0 10.0 1.0
O B:HOH2008 3.0 24.5 1.0
CG B:ASP392 3.1 10.3 1.0
CE1 B:HIS238 3.2 2.0 1.0
CE1 B:HIS274 3.2 2.0 1.0
OD1 B:ASP392 3.3 6.1 1.0
CD2 B:HIS274 3.3 2.0 1.0
OD1 B:ASP275 3.4 4.1 1.0
MG B:MG1002 3.9 37.8 1.0
O B:HOH2006 3.9 22.7 1.0
CG B:HIS238 4.2 3.8 1.0
ND1 B:HIS274 4.2 5.2 1.0
ND1 B:HIS238 4.3 2.0 1.0
CD2 B:HIS234 4.3 25.1 1.0
NE2 B:HIS234 4.3 26.3 1.0
CG B:HIS274 4.3 6.1 1.0
CB B:ASP275 4.4 11.1 1.0
O21 B:7DE102 4.4 55.4 1.0
O B:HOH2004 4.5 35.2 1.0
CB B:ASP392 4.5 14.1 1.0
N19 B:7DE102 4.7 56.8 1.0
CG2 B:VAL242 4.8 16.2 1.0
O B:HOH2005 4.8 38.3 1.0
O20 B:7DE102 4.9 57.5 1.0
CA B:ASP392 4.9 15.2 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 Dec 16 03:13:37 2020

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