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Zinc in PDB 3jwq: Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil

Enzymatic activity of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil

All present enzymatic activity of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil, PDB code: 3jwq was solved by B.Barren, L.Gakhar, H.Muradov, K.K.Boyd, S.Ramaswamy, N.O.Artemyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.08 / 2.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.732, 109.825, 199.668, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 27.5

Other elements in 3jwq:

The structure of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil (pdb code 3jwq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil, PDB code: 3jwq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3jwq

Go back to Zinc Binding Sites List in 3jwq
Zinc binding site 1 out of 4 in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil


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 Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn899

b:28.6
occ:1.00
 OD2 A:ASP654 2.1 18.9 1.0
NE2 A:HIS653 2.1 13.3 1.0
NE2 A:HIS617 2.2 12.3 1.0
O A:HOH6 2.3 25.3 1.0
OD1 A:ASP764 2.3 26.9 1.0
CD2 A:HIS653 3.0 14.1 1.0
CG A:ASP654 3.0 16.6 1.0
CG A:ASP764 3.0 22.5 1.0
CE1 A:HIS617 3.1 13.9 1.0
OD2 A:ASP764 3.2 22.5 1.0
CE1 A:HIS653 3.2 13.0 1.0
CD2 A:HIS617 3.2 14.8 1.0
MG A:MG900 3.3 17.5 1.0
OD1 A:ASP654 3.4 16.9 1.0
CD2 A:HIS613 4.1 23.0 1.0
NE2 A:HIS613 4.2 24.5 1.0
CG A:HIS653 4.2 13.8 1.0
ND1 A:HIS617 4.2 13.7 1.0
ND1 A:HIS653 4.2 11.9 1.0
CB A:ASP654 4.3 15.4 1.0
CG A:HIS617 4.3 14.3 1.0
O A:HOH8 4.4 40.0 1.0
CB A:ASP764 4.5 20.1 1.0
O A:HOH4 4.5 17.1 1.0
CA A:ASP764 5.0 19.5 1.0

Zinc binding site 2 out of 4 in 3jwq

Go back to Zinc Binding Sites List in 3jwq
Zinc binding site 2 out of 4 in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil


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 Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn899

b:34.1
occ:1.00
 OD2 B:ASP654 2.1 18.9 1.0
OD1 B:ASP764 2.2 26.6 1.0
NE2 B:HIS617 2.3 12.5 1.0
NE2 B:HIS653 2.3 13.5 1.0
CG B:ASP764 3.0 22.6 1.0
CD2 B:HIS653 3.1 14.2 1.0
CG B:ASP654 3.1 16.4 1.0
CE1 B:HIS617 3.1 13.8 1.0
OD2 B:ASP764 3.1 22.0 1.0
CD2 B:HIS617 3.3 14.5 1.0
CE1 B:HIS653 3.4 13.0 1.0
OD1 B:ASP654 3.4 17.0 1.0
MG B:MG900 3.7 29.7 1.0
CD2 B:HIS613 4.1 22.9 1.0
NE2 B:HIS613 4.2 24.5 1.0
O B:HOH1 4.3 27.7 1.0
ND1 B:HIS617 4.3 13.7 1.0
CG B:HIS653 4.3 13.7 1.0
ND1 B:HIS653 4.4 11.7 1.0
CG B:HIS617 4.4 14.5 1.0
CB B:ASP654 4.4 15.5 1.0
CB B:ASP764 4.4 20.2 1.0
O B:HOH12 4.8 24.6 1.0
CA B:ASP764 4.9 19.6 1.0

Zinc binding site 3 out of 4 in 3jwq

Go back to Zinc Binding Sites List in 3jwq
Zinc binding site 3 out of 4 in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn899

b:50.8
occ:1.00
 OD2 C:ASP654 2.1 18.8 1.0
NE2 C:HIS653 2.3 13.4 1.0
OD1 C:ASP764 2.3 26.8 1.0
NE2 C:HIS617 2.4 12.6 1.0
CG C:ASP654 3.0 16.7 1.0
CD2 C:HIS653 3.0 14.3 1.0
CG C:ASP764 3.1 22.9 1.0
OD2 C:ASP764 3.2 22.5 1.0
CE1 C:HIS617 3.3 14.0 1.0
OD1 C:ASP654 3.3 16.8 1.0
CE1 C:HIS653 3.4 13.1 1.0
CD2 C:HIS617 3.4 14.8 1.0
MG C:MG900 3.9 28.4 1.0
CD2 C:HIS613 4.0 23.1 1.0
NE2 C:HIS613 4.0 24.5 1.0
O C:HOH3 4.1 4.8 1.0
CG C:HIS653 4.3 13.9 1.0
CB C:ASP654 4.3 15.7 1.0
ND1 C:HIS653 4.4 12.1 1.0
ND1 C:HIS617 4.4 13.8 1.0
O C:HOH14 4.5 2.1 1.0
CG C:HIS617 4.5 14.4 1.0
CB C:ASP764 4.5 20.1 1.0

Zinc binding site 4 out of 4 in 3jwq

Go back to Zinc Binding Sites List in 3jwq
Zinc binding site 4 out of 4 in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn899

b:43.0
occ:1.00
 OD2 D:ASP654 2.0 18.7 1.0
NE2 D:HIS653 2.2 13.4 1.0
NE2 D:HIS617 2.2 12.8 1.0
OD1 D:ASP764 2.3 26.3 1.0
CG D:ASP654 3.0 16.7 1.0
CD2 D:HIS653 3.0 14.3 1.0
CG D:ASP764 3.1 22.6 1.0
CD2 D:HIS617 3.2 14.7 1.0
CE1 D:HIS617 3.2 13.8 1.0
CE1 D:HIS653 3.2 13.1 1.0
OD2 D:ASP764 3.3 22.4 1.0
OD1 D:ASP654 3.5 17.5 1.0
O D:HOH5 3.8 18.4 1.0
CD2 D:HIS613 4.0 23.2 1.0
NE2 D:HIS613 4.2 24.5 1.0
CG D:HIS653 4.2 13.8 1.0
CB D:ASP654 4.2 15.6 1.0
MG D:MG900 4.2 54.2 1.0
ND1 D:HIS617 4.3 13.9 1.0
ND1 D:HIS653 4.3 12.1 1.0
CG D:HIS617 4.3 14.4 1.0
CB D:ASP764 4.5 20.2 1.0
OG1 D:THR621 5.0 20.4 1.0

Reference:

B.Barren, L.Gakhar, H.Muradov, K.K.Boyd, S.Ramaswamy, N.O.Artemyev. Structural Basis of Phosphodiesterase 6 Inhibition By the C-Terminal Region of the Gamma-Subunit Embo J. V. 28 3613 2009.
ISSN: ISSN 0261-4189
PubMed: 19798052
DOI: 10.1038/EMBOJ.2009.284
Page generated: Wed Dec 16 04:28:51 2020

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