Atomistry » Magnesium » PDB 1t5t-1tkd » 1tbb
Atomistry »
  Magnesium »
    PDB 1t5t-1tkd »
      1tbb »

Magnesium in PDB 1tbb: Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram, PDB code: 1tbb was solved by K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D.Hsieh, J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.-H.Kim, J.Schlessinger, G.Bollag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.65 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.106, 79.019, 164.548, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 20.4

Other elements in 1tbb:

The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram 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 Rolipram (pdb code 1tbb). 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 Rolipram, PDB code: 1tbb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1tbb

Go back to Magnesium Binding Sites List in 1tbb
Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram


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 Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:15.7
occ:1.00
OD1 A:ASP201 2.1 6.8 1.0
O A:HOH1224 2.1 18.2 1.0
O A:HOH1225 2.1 19.5 1.0
O A:HOH1222 2.2 17.0 1.0
O A:HOH1221 2.2 18.3 1.0
O A:HOH1223 2.2 17.9 1.0
CG A:ASP201 3.1 8.8 1.0
OD2 A:ASP201 3.3 7.6 1.0
ZN A:ZN1001 3.6 20.6 1.0
O A:HOH1226 3.9 16.3 1.0
CD2 A:HIS200 4.1 4.8 1.0
OE2 A:GLU230 4.2 10.4 1.0
O A:HIS200 4.2 7.5 1.0
NE2 A:HIS233 4.3 6.3 1.0
OG1 A:THR271 4.3 7.4 1.0
O A:HOH1006 4.3 23.4 1.0
CD2 A:HIS233 4.5 6.6 1.0
CB A:ASP201 4.5 7.4 1.0
OD2 A:ASP318 4.6 11.8 1.0
CD2 A:HIS204 4.6 8.7 1.0
NE2 A:HIS200 4.6 2.8 1.0
O A:THR271 4.7 9.5 1.0
CB A:THR271 4.8 8.7 1.0
CA A:ASP201 4.8 7.3 1.0
NE2 A:HIS204 4.9 7.6 1.0
CG A:GLU230 4.9 8.2 1.0
SD A:MET273 4.9 8.4 0.3
CD2 A:HIS160 4.9 10.1 1.0
NE2 A:HIS160 5.0 10.9 1.0
C A:HIS200 5.0 7.4 1.0
CD A:GLU230 5.0 9.5 1.0

Magnesium binding site 2 out of 2 in 1tbb

Go back to Magnesium Binding Sites List in 1tbb
Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Rolipram


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 Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1002

b:16.3
occ:1.00
OD1 B:ASP201 2.1 4.8 1.0
O B:HOH1220 2.1 18.9 1.0
O B:HOH1219 2.1 18.9 1.0
O B:HOH1218 2.1 19.2 1.0
O B:HOH1217 2.2 17.8 1.0
O B:HOH1216 2.2 19.9 1.0
CG B:ASP201 3.1 6.5 1.0
OD2 B:ASP201 3.3 6.5 1.0
ZN B:ZN1001 3.7 22.2 1.0
O B:HOH1072 4.0 39.0 1.0
O B:HOH1221 4.0 17.9 1.0
CD2 B:HIS200 4.1 5.5 1.0
O B:HIS200 4.2 6.8 1.0
OE2 B:GLU230 4.2 8.8 1.0
NE2 B:HIS233 4.2 5.6 1.0
O B:HOH1021 4.3 23.5 1.0
OG1 B:THR271 4.3 8.3 1.0
CD2 B:HIS233 4.4 6.5 1.0
CB B:ASP201 4.5 5.8 1.0
OD2 B:ASP318 4.6 11.4 1.0
NE2 B:HIS200 4.6 4.7 1.0
CD2 B:HIS204 4.6 8.2 1.0
O B:THR271 4.7 9.8 1.0
CA B:ASP201 4.8 5.9 1.0
CE1 B:HIS160 4.8 6.1 1.0
CB B:THR271 4.8 9.0 1.0
NE2 B:HIS204 4.9 7.3 1.0
CG B:GLU230 4.9 6.8 1.0
ND1 B:HIS160 4.9 10.8 1.0
C B:HIS200 5.0 6.0 1.0
CD B:GLU230 5.0 8.1 1.0

Reference:

K.Y.J.Zhang, G.L.Card, Y.Suzuki, D.R.Artis, D.Fong, S.Gillette, D.Hsieh, J.Neiman, B.L.West, C.Zhang, M.V.Milburn, S.-H.Kim, J.Schlessinger, G.Bollag. A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases Mol.Cell V. 15 279 2004.
ISSN: ISSN 1097-2765
PubMed: 15260978
DOI: 10.1016/J.MOLCEL.2004.07.005
Page generated: Tue Aug 13 14:30:43 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