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Zinc 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:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was determined in the Catalytic Domain of Human Phosphodiesterase 5A in Complex with Sildenafil, PDB code: 1tbf:

Zinc binding site 1 out of 1 in 1tbf

Go back to Zinc Binding Sites List in 1tbf
Zinc 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 Zinc with other atoms in the Zn 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:Zn1

b:14.1
occ:1.00
 O A:HOH1175 2.1 13.1 1.0
OD1 A:ASP764 2.1 7.9 1.0
OD2 A:ASP654 2.1 7.6 1.0
NE2 A:HIS653 2.1 6.7 1.0
NE2 A:HIS617 2.1 7.2 1.0
O A:HOH1180 2.2 16.5 1.0
CD2 A:HIS653 3.0 8.2 1.0
CG A:ASP764 3.0 7.7 1.0
CE1 A:HIS617 3.1 6.5 1.0
CG A:ASP654 3.1 6.3 1.0
CD2 A:HIS617 3.2 6.3 1.0
CE1 A:HIS653 3.2 7.3 1.0
OD2 A:ASP764 3.3 12.8 1.0
OD1 A:ASP654 3.6 7.5 1.0
MG A:MG2 3.7 11.3 1.0
O A:HOH1178 4.0 14.0 1.0
CD2 A:HIS613 4.1 14.0 1.0
O A:HOH1181 4.2 15.7 1.0
CG A:HIS653 4.2 7.6 1.0
ND1 A:HIS617 4.3 6.6 1.0
ND1 A:HIS653 4.3 7.5 1.0
CG A:HIS617 4.3 5.3 1.0
NE2 A:HIS613 4.3 12.2 1.0
CB A:ASP764 4.3 6.9 1.0
CB A:ASP654 4.4 7.3 1.0
O A:HOH916 4.4 25.1 1.0
O A:HOH1176 4.7 12.1 1.0
O A:ASP764 4.8 8.0 1.0
CA A:ASP764 4.8 6.4 1.0
OG1 A:THR621 4.9 7.1 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: Mon Jan 25 16:14:03 2021

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