Atomistry » Magnesium » PDB 1xyl-1ydf » 1y2e
Atomistry »
  Magnesium »
    PDB 1xyl-1ydf »
      1y2e »

Magnesium in PDB 1y2e: Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Amino-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- Amino-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- Amino-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- Amino-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2e 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 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.880, 79.442, 164.265, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.8

Other elements in 1y2e:

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Amino-Phenyl)-3,5-Dimethyl-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 1-(4- Amino-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2e). 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 1-(4- Amino-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1y2e

Go back to Magnesium Binding Sites List in 1y2e
Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Amino-Phenyl)-3,5-Dimethyl-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 1-(4- Amino-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:18.4
occ:1.00
 O A:HOH1007 2.0 18.2 1.0
O A:HOH1009 2.2 23.9 1.0
OD1 A:ASP201 2.2 11.9 1.0
O A:HOH1008 2.2 22.0 1.0
O A:HOH1005 2.2 22.4 1.0
O A:HOH1006 2.3 19.2 1.0
CG A:ASP201 3.2 9.6 1.0
OD2 A:ASP201 3.5 8.6 1.0
ZN A:ZN1001 3.7 28.2 1.0
N14 A:5DE1003 3.8 27.9 1.0
OE2 A:GLU230 4.0 13.6 1.0
CD2 A:HIS200 4.1 10.3 1.0
O A:HIS200 4.2 10.0 1.0
O A:HOH1028 4.2 22.9 1.0
O A:HOH1010 4.2 18.9 1.0
OG1 A:THR271 4.2 12.5 1.0
NE2 A:HIS233 4.3 9.6 1.0
O A:THR271 4.4 11.7 1.0
CD2 A:HIS233 4.4 6.5 1.0
NE2 A:HIS200 4.5 12.1 1.0
CB A:ASP201 4.6 9.9 1.0
OD2 A:ASP318 4.6 8.8 1.0
CB A:THR271 4.7 11.5 1.0
CD2 A:HIS204 4.7 8.2 1.0
O A:HOH1047 4.8 30.7 1.0
NE2 A:HIS160 4.8 8.2 1.0
CA A:ASP201 4.9 9.6 1.0
CD A:GLU230 4.9 11.3 1.0
CD2 A:HIS160 4.9 9.3 1.0
C13 A:5DE1003 4.9 27.3 1.0
CG A:GLU230 4.9 8.8 1.0
NE2 A:HIS204 4.9 8.1 1.0
C A:HIS200 5.0 10.1 1.0

Magnesium binding site 2 out of 2 in 1y2e

Go back to Magnesium Binding Sites List in 1y2e
Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Amino-Phenyl)-3,5-Dimethyl-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 1-(4- Amino-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:11.9
occ:1.00
 O B:HOH2007 2.0 23.2 1.0
OD2 B:ASP201 2.1 5.3 1.0
O B:HOH2003 2.1 16.9 1.0
O B:HOH2004 2.1 21.2 1.0
O B:HOH2006 2.1 17.4 1.0
O B:HOH2005 2.2 17.4 1.0
CG B:ASP201 3.1 8.7 1.0
OD1 B:ASP201 3.4 8.3 1.0
ZN B:ZN1001 3.7 27.8 1.0
N14 B:5DE1003 3.9 26.7 1.0
OE2 B:GLU230 4.1 11.8 1.0
O B:HIS200 4.1 9.0 1.0
CD2 B:HIS200 4.1 10.1 1.0
NE2 B:HIS233 4.2 7.2 1.0
O B:HOH2032 4.2 25.7 1.0
O B:HOH2008 4.2 22.6 1.0
OG1 B:THR271 4.3 9.6 1.0
CD2 B:HIS233 4.4 7.4 1.0
NE2 B:HIS200 4.4 11.2 1.0
CB B:ASP201 4.5 7.5 1.0
OD2 B:ASP318 4.5 13.3 1.0
CD2 B:HIS204 4.5 7.1 1.0
NE2 B:HIS160 4.6 9.8 1.0
O B:HOH2056 4.6 28.7 1.0
CD2 B:HIS160 4.7 8.1 1.0
NE2 B:HIS204 4.7 4.3 1.0
CB B:THR271 4.7 11.1 1.0
O B:THR271 4.8 11.1 1.0
CG B:GLU230 4.8 11.6 1.0
CA B:ASP201 4.9 7.9 1.0
CD B:GLU230 4.9 11.8 1.0
O B:HOH2060 4.9 25.1 1.0
C B:HIS200 5.0 9.3 1.0
C13 B:5DE1003 5.0 26.6 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: Tue Aug 13 18:30:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy