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Magnesium in PDB 1y2k: Catalytic Domain of Human Phosphodiesterase 4D 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 4D 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 4D 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 4D in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2k 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 / 1.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.349, 78.886, 164.010, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 18.8

Other elements in 1y2k:

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

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 3,5- Dimethyl-1-(3-Nitro-Phenyl)-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1y2k

Go back to Magnesium Binding Sites List in 1y2k
Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D 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 Magnesium with other atoms in the Mg binding site number 1 of Catalytic Domain of Human Phosphodiesterase 4D 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:Mg1002

b:8.8
occ:1.00
 O A:HOH1007 2.1 12.5 1.0
OD1 A:ASP201 2.1 7.1 1.0
O A:HOH1006 2.1 12.9 1.0
O A:HOH1004 2.2 10.8 1.0
O A:HOH1005 2.2 12.2 1.0
O A:HOH1003 2.2 11.5 1.0
CG A:ASP201 3.1 6.8 1.0
OD2 A:ASP201 3.4 7.1 1.0
ZN A:ZN1001 3.7 13.2 1.0
OE2 A:GLU230 4.1 9.4 1.0
CD2 A:HIS200 4.1 6.5 1.0
O A:HOH1008 4.1 12.8 1.0
O A:HIS200 4.2 7.0 1.0
NE2 A:HIS233 4.2 6.7 1.0
O20 A:7DE602 4.2 27.1 1.0
O A:HOH1030 4.3 15.6 1.0
OG1 A:THR271 4.3 8.6 1.0
CD2 A:HIS233 4.4 6.9 1.0
OD2 A:ASP318 4.4 10.3 0.7
NE2 A:HIS200 4.5 6.3 1.0
CB A:ASP201 4.5 6.5 1.0
OD1 A:ASP318 4.5 6.6 0.3
CD2 A:HIS204 4.6 7.3 1.0
C13 A:7DE602 4.7 24.2 1.0
O A:THR271 4.7 9.5 1.0
C2 A:EDO723 4.7 25.7 1.0
NE2 A:HIS160 4.8 8.4 1.0
CD2 A:HIS160 4.8 7.9 1.0
CA A:ASP201 4.8 6.5 1.0
CB A:THR271 4.8 9.2 1.0
CG A:GLU230 4.9 7.9 1.0
CD A:GLU230 4.9 8.4 1.0
NE2 A:HIS204 5.0 7.4 1.0
N19 A:7DE602 5.0 26.0 1.0
C A:HIS200 5.0 6.5 1.0

Magnesium binding site 2 out of 2 in 1y2k

Go back to Magnesium Binding Sites List in 1y2k
Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D 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 Magnesium with other atoms in the Mg binding site number 2 of Catalytic Domain of Human Phosphodiesterase 4D 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:Mg1002

b:8.4
occ:1.00
 O B:HOH2006 2.1 11.9 1.0
O B:HOH2007 2.1 11.9 1.0
OD1 B:ASP201 2.1 7.9 1.0
O B:HOH2004 2.1 11.4 1.0
O B:HOH2005 2.1 12.5 1.0
O B:HOH2003 2.2 12.2 1.0
CG B:ASP201 3.1 7.5 1.0
OD2 B:ASP201 3.4 8.1 1.0
ZN B:ZN1001 3.7 12.5 1.0
OE2 B:GLU230 4.0 9.8 1.0
O B:HOH2008 4.1 11.9 1.0
NE2 B:HIS233 4.1 6.5 1.0
CD2 B:HIS200 4.2 6.3 1.0
O20 B:7DE601 4.2 26.8 1.0
O B:HIS200 4.2 6.7 1.0
OG1 B:THR271 4.3 9.2 1.0
O B:HOH2019 4.3 15.5 1.0
CD2 B:HIS233 4.3 6.8 1.0
OD2 B:ASP318 4.4 10.3 0.7
CB B:ASP201 4.5 7.0 1.0
OD2 B:ASP318 4.5 8.2 0.3
NE2 B:HIS200 4.5 7.1 1.0
O B:THR271 4.6 10.2 1.0
CD2 B:HIS204 4.6 7.6 1.0
C13 B:7DE601 4.6 24.2 1.0
CD2 B:HIS160 4.8 8.5 1.0
NE2 B:HIS160 4.8 9.8 1.0
CB B:THR271 4.8 9.6 1.0
CA B:ASP201 4.8 6.8 1.0
CG B:GLU230 4.9 8.5 1.0
CD B:GLU230 4.9 8.4 1.0
NE2 B:HIS204 4.9 7.9 1.0
N19 B:7DE601 5.0 25.3 1.0
C B:HIS200 5.0 6.7 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: Tue Aug 13 18:30:36 2024

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