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Zinc in PDB 1udt: Crystal Structure of Human Phosphodiesterase 5 Complexed with Sildenafil(Viagra)

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 5 Complexed with Sildenafil(Viagra)

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 5 Complexed with Sildenafil(Viagra), PDB code: 1udt 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) 19.88 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 60.122, 155.632, 89.896, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 25.1

Other elements in 1udt:

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

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Sildenafil(Viagra) (pdb code 1udt). 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 Crystal Structure of Human Phosphodiesterase 5 Complexed with Sildenafil(Viagra), PDB code: 1udt:

Zinc binding site 1 out of 1 in 1udt

Go back to Zinc Binding Sites List in 1udt
Zinc binding site 1 out of 1 in the Crystal Structure of Human Phosphodiesterase 5 Complexed with Sildenafil(Viagra)


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 Sildenafil(Viagra) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:33.1
occ:1.00
 O A:HOH77 1.9 31.3 1.0
OD2 A:ASP654 2.1 29.8 1.0
NE2 A:HIS653 2.1 25.2 1.0
NE2 A:HIS617 2.2 26.2 1.0
OD1 A:ASP764 2.3 26.9 1.0
O A:HOH78 2.3 30.7 1.0
CD2 A:HIS653 2.9 28.9 1.0
CD2 A:HIS617 3.1 26.5 1.0
CE1 A:HIS617 3.2 20.8 1.0
CG A:ASP764 3.2 29.3 1.0
CG A:ASP654 3.2 26.6 1.0
O A:HOH76 3.2 30.6 1.0
CE1 A:HIS653 3.2 34.0 1.0
OD2 A:ASP764 3.4 25.3 1.0
OD1 A:ASP654 3.7 29.6 1.0
MG A:MG1002 3.8 27.9 1.0
O A:HOH75 4.0 34.4 1.0
CD2 A:HIS613 4.1 26.0 1.0
CG A:HIS653 4.1 23.6 1.0
NE2 A:HIS613 4.2 25.8 1.0
ND1 A:HIS653 4.2 24.5 1.0
ND1 A:HIS617 4.3 29.1 1.0
CG A:HIS617 4.3 29.7 1.0
CB A:ASP654 4.4 26.2 1.0
CB A:ASP764 4.6 29.2 1.0
O A:ASP764 4.7 28.7 1.0
O A:HOH72 4.9 23.9 1.0
OG1 A:THR621 5.0 20.8 1.0
CA A:ASP764 5.0 31.8 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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