Atomistry » Magnesium » PDB 1xyl-1ydf » 1y2d
Atomistry »
  Magnesium »
    PDB 1xyl-1ydf »
      1y2d »

Magnesium in PDB 1y2d: Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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- Methoxy-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- Methoxy-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- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2d 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.804, 79.146, 164.617, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.9

Other elements in 1y2d:

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester (pdb code 1y2d). 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- Methoxy-Phenyl)-3,5-Dimethyl-1H-Pyrazole-4-Carboxylic Acid Ethyl Ester, PDB code: 1y2d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1y2d

Go back to Magnesium Binding Sites List in 1y2d
Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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- Methoxy-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:10.9
occ:1.00
 O A:HOH1007 2.1 14.9 1.0
O A:HOH1004 2.1 12.9 1.0
OD1 A:ASP201 2.1 7.2 1.0
O A:HOH1006 2.2 14.9 1.0
O A:HOH1005 2.2 14.8 1.0
O A:HOH1003 2.2 14.2 1.0
CG A:ASP201 3.2 6.2 1.0
OD2 A:ASP201 3.4 7.0 1.0
ZN A:ZN1001 3.7 17.2 1.0
OE2 A:GLU230 4.1 8.0 1.0
CD2 A:HIS200 4.2 7.7 1.0
NE2 A:HIS233 4.2 8.6 1.0
O A:HOH1008 4.2 14.2 1.0
O A:HIS200 4.2 7.2 1.0
O A:HOH1024 4.2 18.3 1.0
O A:HOH1109 4.2 39.2 1.0
OG1 A:THR271 4.3 10.8 1.0
CD2 A:HIS233 4.4 7.9 1.0
CB A:ASP201 4.5 6.5 1.0
OD2 A:ASP318 4.5 12.5 1.0
NE2 A:HIS200 4.5 7.0 1.0
CD2 A:HIS204 4.6 11.5 1.0
O A:HOH1092 4.7 36.0 1.0
O A:THR271 4.7 10.8 1.0
CG A:GLU230 4.8 7.7 1.0
NE2 A:HIS160 4.8 9.0 1.0
CD2 A:HIS160 4.8 7.9 1.0
CB A:THR271 4.8 10.9 1.0
CA A:ASP201 4.9 7.0 1.0
NE2 A:HIS204 4.9 9.2 1.0
CD A:GLU230 4.9 8.5 1.0
C A:HIS200 5.0 7.0 1.0

Magnesium binding site 2 out of 2 in 1y2d

Go back to Magnesium Binding Sites List in 1y2d
Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with 1-(4- Methoxy-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- Methoxy-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:9.9
occ:1.00
 O B:HOH2007 2.0 14.8 1.0
OD1 B:ASP201 2.1 5.7 1.0
O B:HOH2003 2.2 11.6 1.0
O B:HOH2004 2.2 12.2 1.0
O B:HOH2006 2.2 13.3 1.0
O B:HOH2005 2.3 14.3 1.0
CG B:ASP201 3.1 8.2 1.0
OD2 B:ASP201 3.4 7.6 1.0
ZN B:ZN1001 3.7 16.2 1.0
CD2 B:HIS200 4.1 8.3 1.0
O B:HOH2008 4.1 14.0 1.0
OE2 B:GLU230 4.2 10.3 1.0
O B:HIS200 4.2 9.0 1.0
O B:HOH2120 4.2 37.7 1.0
NE2 B:HIS233 4.2 7.2 1.0
OG1 B:THR271 4.3 10.1 1.0
O B:HOH2036 4.3 21.1 1.0
CB B:ASP201 4.4 7.5 1.0
CD2 B:HIS233 4.4 7.1 1.0
OD2 B:ASP318 4.5 14.6 1.0
NE2 B:HIS200 4.5 6.1 1.0
CD2 B:HIS204 4.6 9.0 1.0
O B:HOH2187 4.6 39.3 1.0
CD2 B:HIS160 4.8 10.6 1.0
CA B:ASP201 4.8 8.0 1.0
O B:THR271 4.8 10.1 1.0
NE2 B:HIS204 4.8 8.7 1.0
CB B:THR271 4.8 9.2 1.0
CG B:GLU230 4.9 9.6 1.0
NE2 B:HIS160 4.9 11.1 1.0
CD B:GLU230 5.0 10.4 1.0
C B:HIS200 5.0 8.9 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 18:29:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy