Atomistry » Magnesium » PDB 1xyl-1ydf » 1y2j
Atomistry »
  Magnesium »
    PDB 1xyl-1ydf »
      1y2j »

Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1y2j

Go back to Magnesium Binding Sites List in 1y2j
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1002

b:25.5
occ:1.00
 O A:HOH1003 1.8 32.3 1.0
O A:HOH1005 2.0 26.5 1.0
O A:HOH1007 2.0 15.5 1.0
OD1 A:ASP275 2.0 2.3 1.0
O A:HOH1004 2.4 31.4 1.0
O A:HOH1006 2.4 19.1 1.0
CG A:ASP275 3.0 8.5 1.0
OD2 A:ASP275 3.3 4.7 1.0
OE2 A:GLU304 3.7 9.8 1.0
ZN A:ZN1001 3.8 36.3 1.0
O A:HIS274 4.1 13.9 1.0
NE2 A:HIS307 4.1 14.7 1.0
OG1 A:THR345 4.1 13.7 1.0
O20 A:7DE101 4.1 54.2 1.0
O A:HOH1008 4.1 9.4 1.0
OD1 A:ASP392 4.2 2.0 1.0
CD2 A:HIS307 4.3 13.3 1.0
O A:THR345 4.3 13.3 1.0
CB A:ASP275 4.4 12.1 1.0
CD2 A:HIS274 4.5 9.1 1.0
CD A:GLU304 4.6 12.3 1.0
CD2 A:HIS278 4.7 21.0 1.0
CG A:GLU304 4.7 16.4 1.0
CB A:THR345 4.7 15.4 1.0
CA A:ASP275 4.7 12.9 1.0
O A:HOH23 4.7 35.7 1.0
C13 A:7DE101 4.7 53.6 1.0
C A:HIS274 4.9 13.4 1.0
NE2 A:HIS274 4.9 13.6 1.0
N19 A:7DE101 4.9 54.4 1.0

Magnesium binding site 2 out of 2 in 1y2j

Go back to Magnesium Binding Sites List in 1y2j
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1002

b:37.8
occ:1.00
 O B:HOH2005 1.8 38.3 1.0
OD1 B:ASP275 1.9 4.1 1.0
O B:HOH2004 2.0 35.2 1.0
O B:HOH2003 2.0 33.0 1.0
O B:HOH2007 2.2 12.5 1.0
O B:HOH2006 2.3 22.7 1.0
CG B:ASP275 3.1 10.0 1.0
OD2 B:ASP275 3.6 4.0 1.0
O B:HIS274 3.7 10.0 1.0
ZN B:ZN1001 3.9 37.2 1.0
NE2 B:HIS307 3.9 16.7 1.0
O B:HOH2008 4.0 24.5 1.0
OE2 B:GLU304 4.1 16.2 1.0
CD2 B:HIS307 4.2 16.2 1.0
CD2 B:HIS278 4.3 15.2 1.0
CB B:ASP275 4.3 11.1 1.0
CD2 B:HIS274 4.3 2.0 1.0
NE2 B:HIS278 4.3 17.6 1.0
OG1 B:THR345 4.3 15.1 1.0
CA B:ASP275 4.5 11.1 1.0
C B:HIS274 4.5 9.9 1.0
O B:THR345 4.5 17.0 1.0
NE2 B:HIS234 4.6 26.3 1.0
OD1 B:ASP392 4.6 6.1 1.0
O20 B:7DE102 4.6 57.5 1.0
CD2 B:HIS234 4.7 25.1 1.0
NE2 B:HIS274 4.7 2.0 1.0
CB B:THR345 4.8 16.6 1.0
N B:ASP275 4.8 10.2 1.0
CG B:GLU304 4.9 14.3 1.0
CD B:GLU304 4.9 15.5 1.0
CG B:HIS274 4.9 6.1 1.0
CE1 B:HIS307 5.0 16.6 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: Sun Aug 10 07:41:21 2025

Last articles

Mg in 4UXO
Mg in 4UX3
Mg in 4UW9
Mg in 4UVD
Mg in 4UVG
Mg in 4UVE
Mg in 4USX
Mg in 4UUX
Mg in 4UUW
Mg in 4UU1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy