Atomistry » Magnesium » PDB 1t5s-1tk8 » 1tb5
Atomistry »
  Magnesium »
    PDB 1t5s-1tk8 »
      1tb5 »

Magnesium in PDB 1tb5: Catalytic Domain of Human Phosphodiesterase 4B in Complex with Amp

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Amp

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

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Amp, PDB code: 1tb5 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) 70.71 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.547, 94.241, 107.243, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 26.8

Other elements in 1tb5:

The structure of Catalytic Domain of Human Phosphodiesterase 4B in Complex with Amp 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 Amp (pdb code 1tb5). 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 Amp, PDB code: 1tb5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1tb5

Go back to Magnesium Binding Sites List in 1tb5
Magnesium binding site 1 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Amp


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

b:22.2
occ:1.00
O A:HOH1004 2.0 32.2 1.0
O A:HOH1003 2.0 36.2 1.0
O1P A:AMP102 2.1 30.2 0.8
OD1 A:ASP275 2.1 25.9 1.0
O A:HOH1007 2.1 36.0 1.0
O A:HOH1005 2.2 25.0 1.0
CG A:ASP275 3.1 26.6 1.0
P A:AMP102 3.3 40.6 0.8
OD2 A:ASP275 3.3 23.7 1.0
ZN A:ZN1001 3.7 33.4 1.0
O2P A:AMP102 3.7 18.3 0.8
O5' A:AMP102 3.8 40.7 0.8
O A:HOH58 4.0 45.7 1.0
OE2 A:GLU304 4.0 24.1 1.0
CE1 A:HIS307 4.1 23.4 1.0
OG1 A:THR345 4.2 27.1 1.0
O A:HIS274 4.2 23.0 1.0
ND1 A:HIS307 4.4 23.4 1.0
CD2 A:HIS274 4.5 19.3 1.0
CB A:ASP275 4.5 23.6 1.0
O A:THR345 4.5 26.6 1.0
O3P A:AMP102 4.6 33.6 0.8
CD2 A:HIS278 4.6 24.1 1.0
OD1 A:ASP392 4.7 24.8 1.0
CB A:THR345 4.7 28.0 1.0
NE2 A:HIS274 4.8 17.9 1.0
CA A:ASP275 4.9 23.7 1.0
CD A:GLU304 4.9 28.0 1.0
NE2 A:HIS278 5.0 21.2 1.0
CG A:GLU304 5.0 26.5 1.0

Magnesium binding site 2 out of 2 in 1tb5

Go back to Magnesium Binding Sites List in 1tb5
Magnesium binding site 2 out of 2 in the Catalytic Domain of Human Phosphodiesterase 4B in Complex with Amp


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

b:25.2
occ:1.00
O B:HOH2007 2.0 31.2 1.0
O1P B:AMP101 2.1 43.9 0.8
O B:HOH2004 2.1 31.4 1.0
OD1 B:ASP275 2.1 22.8 1.0
O B:HOH2005 2.2 36.3 1.0
O B:HOH2003 2.2 29.9 1.0
CG B:ASP275 3.2 24.9 1.0
P B:AMP101 3.2 47.8 0.8
OD2 B:ASP275 3.5 22.0 1.0
O5' B:AMP101 3.6 55.6 0.8
ZN B:ZN1001 3.6 39.2 1.0
O2P B:AMP101 3.9 45.3 0.8
O B:HOH13 4.0 37.6 1.0
CD2 B:HIS274 4.1 23.2 1.0
OE2 B:GLU304 4.1 24.9 1.0
OG1 B:THR345 4.2 28.0 1.0
CE1 B:HIS307 4.2 22.7 1.0
O B:HIS274 4.2 26.5 1.0
OD1 B:ASP392 4.4 27.2 1.0
NE2 B:HIS274 4.5 11.9 1.0
O3P B:AMP101 4.5 49.9 0.8
CD2 B:HIS278 4.5 23.0 1.0
CB B:ASP275 4.5 24.3 1.0
ND1 B:HIS307 4.6 25.7 1.0
NE2 B:HIS278 4.6 21.4 1.0
CB B:THR345 4.6 26.9 1.0
O B:THR345 4.8 28.4 1.0
CA B:ASP275 4.9 24.5 1.0
C5' B:AMP101 4.9 63.5 0.8
NE2 B:HIS234 4.9 25.9 1.0
CG B:GLU304 4.9 23.5 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: Mon Dec 14 06:51:06 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy