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Zinc in PDB 1udu: Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis):
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis), PDB code: 1udu was solved by B.-J.Sung, J.I.Lee, Y.-S.Heo, J.H.Kim, J.Moon, J.M.Yoon, Y.-L.Hyun, E.Kim, S.J.Eum, T.G.Lee, J.M.Cho, S.-Y.Park, J.-O.Lee, Y.H.Jeon, K.Y.Hwang, S.Ro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.59 / 2.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.352, 48.561, 123.863, 90.00, 117.28, 90.00
R / Rfree (%) 26.3 / 37.4

Other elements in 1udu:

The structure of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) (pdb code 1udu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis), PDB code: 1udu:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1udu

Go back to Zinc Binding Sites List in 1udu
Zinc binding site 1 out of 2 in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:0.0
occ:1.00
OD2 A:ASP654 1.8 31.7 1.0
NE2 A:HIS653 1.9 6.0 1.0
NE2 A:HIS617 2.3 36.4 1.0
CD2 A:HIS653 2.5 29.1 1.0
CD2 A:HIS617 2.7 16.4 1.0
OD2 A:ASP764 3.0 29.1 1.0
CG A:ASP654 3.1 38.3 1.0
CE1 A:HIS653 3.2 47.1 1.0
OD1 A:ASP764 3.2 21.9 1.0
CG A:ASP764 3.4 69.4 1.0
CE1 A:HIS617 3.6 36.0 1.0
CG A:HIS653 3.8 20.1 1.0
OD1 A:ASP654 3.9 19.8 1.0
CB A:ASP654 4.0 20.7 1.0
ND1 A:HIS653 4.0 18.1 1.0
CG A:HIS617 4.1 47.8 1.0
CD2 A:HIS613 4.2 40.8 1.0
MG A:MG1002 4.4 36.6 1.0
ND1 A:HIS617 4.4 85.0 1.0
NE2 A:HIS613 4.5 6.0 1.0
CB A:ASP764 4.7 53.5 1.0
CA A:ASP764 5.0 19.3 1.0

Zinc binding site 2 out of 2 in 1udu

Go back to Zinc Binding Sites List in 1udu
Zinc binding site 2 out of 2 in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Human Phosphodiesterase 5 Complexed with Tadalafil(Cialis) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:0.0
occ:1.00
OD2 B:ASP764 2.3 33.9 1.0
OD1 B:ASP764 2.3 71.0 1.0
OD2 B:ASP654 2.4 22.2 1.0
NE2 B:HIS653 2.5 28.0 1.0
CG B:ASP764 2.5 95.8 1.0
CD2 B:HIS653 2.7 26.4 1.0
NE2 B:HIS617 2.7 30.8 1.0
CD2 B:HIS617 3.3 74.7 1.0
CG B:ASP654 3.5 54.7 1.0
CE1 B:HIS653 3.8 29.2 1.0
CE1 B:HIS617 3.8 20.4 1.0
CB B:ASP764 3.9 0.0 1.0
MG B:MG2002 4.0 16.0 1.0
CG B:HIS653 4.0 34.7 1.0
OD1 B:ASP654 4.1 6.0 1.0
CA B:ASP764 4.4 13.2 1.0
ND1 B:HIS653 4.5 15.6 1.0
CG B:HIS617 4.5 50.5 1.0
NE2 B:HIS613 4.6 13.9 1.0
CD2 B:HIS613 4.6 17.0 1.0
CB B:ASP654 4.7 11.9 1.0
ND1 B:HIS617 4.8 31.1 1.0
O B:ASP764 4.8 70.3 1.0
C B:ASP764 4.9 58.2 1.0

Reference:

B.-J.Sung, K.Y.Hwang, Y.H.Jeon, J.I.Lee, Y.-S.Heo, J.H.Kim, J.Moon, J.M.Yoon, Y.-L.Hyun, E.Kim, S.J.Eum, S.-Y.Park, J.-O.Lee, T.G.Lee, S.Ro, J.M.Cho. Structure of the Catalytic Domain of Human Phosphodiesterase 5 with Bound Drug Molecules Nature V. 425 98 2003.
ISSN: ISSN 0028-0836
PubMed: 12955149
DOI: 10.1038/NATURE01914
Page generated: Wed Oct 16 19:30:08 2024

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