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Magnesium in PDB 1tbf: Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil

Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil

All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil:
3.1.4.17;

Protein crystallography data

The structure of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil, PDB code: 1tbf 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) 65.94 / 1.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.097, 76.097, 99.272, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 18.5

Other elements in 1tbf:

The structure of Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil (pdb code 1tbf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil, PDB code: 1tbf:

Magnesium binding site 1 out of 1 in 1tbf

Go back to Magnesium Binding Sites List in 1tbf
Magnesium binding site 1 out of 1 in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil


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 5A in Complex with Sildenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:11.3
occ:1.00
 O A:HOH1175 2.1 13.1 1.0
O A:HOH1178 2.1 14.0 1.0
O A:HOH1176 2.1 12.1 1.0
OD1 A:ASP654 2.1 7.5 1.0
O A:HOH1179 2.1 13.0 1.0
O A:HOH1177 2.1 12.5 1.0
CG A:ASP654 3.1 6.3 1.0
OD2 A:ASP654 3.4 7.6 1.0
ZN A:ZN1 3.7 14.1 1.0
O A:HOH916 4.0 25.1 1.0
OE2 A:GLU682 4.0 9.0 1.0
O A:HOH1180 4.0 16.5 1.0
NE2 A:HIS685 4.1 7.2 1.0
CD2 A:HIS653 4.1 8.2 1.0
OG1 A:THR723 4.1 7.9 1.0
O A:HOH879 4.2 17.3 1.0
CD2 A:HIS685 4.2 8.0 1.0
O A:HIS653 4.3 6.2 1.0
CD2 A:HIS613 4.4 14.0 1.0
CB A:ASP654 4.4 7.3 1.0
O A:THR723 4.4 8.3 1.0
NE2 A:HIS613 4.4 12.2 1.0
NE2 A:HIS653 4.5 6.7 1.0
OD2 A:ASP764 4.6 12.8 1.0
ND1 A:HIS657 4.7 13.1 1.0
CB A:THR723 4.7 8.0 1.0
CE1 A:HIS657 4.8 6.0 1.0
CA A:ASP654 4.8 6.2 1.0
CG A:GLU682 4.9 7.8 1.0
CD A:GLU682 4.9 7.0 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: Sun Aug 10 04:52:13 2025

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