Atomistry » Zinc » PDB 3jr4-3k0v » 3jwq
Atomistry »
  Zinc »
    PDB 3jr4-3k0v »
      3jwq »

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: Sat Oct 26 07:32:21 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy