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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with Sildenafil, PDB code: 3jwq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3jwq

Go back to Magnesium Binding Sites List in 3jwq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg900

b:17.5
occ:1.00
OD1 A:ASP654 2.3 16.9 1.0
O A:HOH4 2.3 17.1 1.0
O A:HOH7 2.4 13.2 1.0
O A:HOH8 2.6 40.0 1.0
O A:HOH6 2.9 25.3 1.0
CG A:ASP654 3.3 16.6 1.0
ZN A:ZN899 3.3 28.6 1.0
OD2 A:ASP654 3.4 18.9 1.0
O A:THR723 3.6 17.1 1.0
CD2 A:HIS653 3.8 14.1 1.0
OD2 A:ASP764 3.9 22.5 1.0
OG1 A:THR723 4.0 16.8 1.0
OE2 A:GLU682 4.1 21.0 1.0
NE2 A:HIS653 4.2 13.3 1.0
CB A:THR723 4.2 16.1 1.0
O A:HIS653 4.4 15.3 1.0
C A:THR723 4.5 17.5 1.0
NE2 A:HIS613 4.6 24.5 1.0
NE2 A:HIS685 4.7 17.8 1.0
CB A:ASP654 4.7 15.4 1.0
CD2 A:HIS613 4.7 23.0 1.0
CG A:ASP764 4.8 22.5 1.0
OD1 A:ASP764 4.8 26.9 1.0
CD2 A:HIS685 4.9 16.5 1.0
CD A:GLU682 5.0 21.7 1.0

Magnesium binding site 2 out of 4 in 3jwq

Go back to Magnesium Binding Sites List in 3jwq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg900

b:29.7
occ:1.00
O B:HOH1 1.9 27.7 1.0
O B:HOH12 2.0 24.6 1.0
O B:HOH11 2.2 17.0 1.0
OD1 B:ASP654 2.6 17.0 1.0
O B:THR723 3.5 17.2 1.0
CG B:ASP654 3.6 16.4 1.0
OE2 B:GLU682 3.6 20.7 1.0
ZN B:ZN899 3.7 34.1 1.0
OD2 B:ASP654 3.9 18.9 1.0
OG1 B:THR723 4.0 16.3 1.0
OD2 B:ASP764 4.1 22.0 1.0
CD2 B:HIS653 4.2 14.2 1.0
CB B:THR723 4.2 16.0 1.0
C B:THR723 4.4 17.4 1.0
NE2 B:HIS685 4.5 17.8 1.0
O B:HIS653 4.6 15.3 1.0
CD B:GLU682 4.6 21.9 1.0
CD2 B:HIS685 4.7 16.3 1.0
CG B:GLU682 4.7 18.9 1.0
NE2 B:HIS653 4.7 13.5 1.0
NE2 B:HIS613 4.9 24.5 1.0
CB B:ASP654 5.0 15.5 1.0
CG B:ASP764 5.0 22.6 1.0

Magnesium binding site 3 out of 4 in 3jwq

Go back to Magnesium Binding Sites List in 3jwq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg900

b:28.4
occ:1.00
O C:HOH3 2.0 4.8 1.0
O C:HOH14 2.3 2.1 1.0
O C:HOH13 2.6 4.8 1.0
OD1 C:ASP654 2.9 16.8 1.0
O C:THR723 3.2 16.7 1.0
OE2 C:GLU682 3.3 20.6 1.0
ZN C:ZN899 3.9 50.8 1.0
CG C:ASP654 4.0 16.7 1.0
OG1 C:THR723 4.1 17.1 1.0
C C:THR723 4.1 17.2 1.0
OD2 C:ASP764 4.2 22.5 1.0
CD C:GLU682 4.2 21.6 1.0
CB C:THR723 4.3 16.3 1.0
CG C:GLU682 4.4 19.1 1.0
OD2 C:ASP654 4.4 18.8 1.0
CD2 C:HIS653 4.5 14.3 1.0
NE2 C:HIS685 4.6 17.9 1.0
O C:HIS653 4.7 15.4 1.0
CD2 C:HIS685 4.8 16.8 1.0
CA C:THR723 4.9 16.6 1.0
N C:ASP724 5.0 18.0 1.0

Magnesium binding site 4 out of 4 in 3jwq

Go back to Magnesium Binding Sites List in 3jwq
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg900

b:54.2
occ:1.00
O D:HOH5 2.1 18.4 1.0
OD1 D:ASP654 2.6 17.5 1.0
OE2 D:GLU682 3.3 20.8 1.0
O D:THR723 3.5 16.9 1.0
CG D:ASP654 3.7 16.7 1.0
OG1 D:THR723 3.7 17.1 1.0
O D:HIS653 3.8 15.6 1.0
NE2 D:HIS685 3.9 18.0 1.0
CD2 D:HIS685 4.0 16.8 1.0
CG D:GLU682 4.0 19.0 1.0
CD D:GLU682 4.1 21.6 1.0
CB D:THR723 4.1 16.6 1.0
OD2 D:ASP654 4.1 18.7 1.0
CD2 D:HIS653 4.1 14.3 1.0
ZN D:ZN899 4.2 43.0 1.0
C D:THR723 4.3 17.3 1.0
OD2 D:ASP764 4.6 22.4 1.0
NE2 D:HIS653 4.8 13.4 1.0
C D:HIS653 4.9 15.4 1.0
CA D:THR723 4.9 16.8 1.0
CB D:ASP654 4.9 15.6 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: Mon Dec 14 08:20:54 2020

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