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Magnesium in PDB 3jwr: Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87.

Enzymatic activity of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87.

All present enzymatic activity of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87.:
3.1.4.17; 3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87., PDB code: 3jwr 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) 40.41 / 2.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.257, 125.651, 153.854, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 28

Other elements in 3jwr:

The structure of Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87. also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87. (pdb code 3jwr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87., PDB code: 3jwr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3jwr

Go back to Magnesium Binding Sites List in 3jwr
Magnesium binding site 1 out of 2 in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87.


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 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg900

b:18.6
occ:1.00
OD1 A:ASP654 2.5 24.2 1.0
O A:HOH5 2.5 20.0 1.0
OE2 A:GLU682 3.0 47.1 1.0
OG1 A:THR723 3.4 30.4 1.0
CG A:ASP654 3.6 29.8 1.0
O A:THR723 3.8 40.4 1.0
CD A:GLU682 3.8 48.8 1.0
CG A:GLU682 3.8 46.7 1.0
OD2 A:ASP654 3.9 30.3 1.0
O A:HIS653 3.9 54.1 1.0
CD2 A:HIS685 3.9 42.7 1.0
NE2 A:HIS685 3.9 33.0 1.0
ZN A:ZN899 3.9 44.0 1.0
CB A:THR723 4.1 32.3 1.0
CD2 A:HIS653 4.1 26.6 1.0
C A:THR723 4.4 36.3 1.0
OD1 A:ASP764 4.6 39.3 1.0
CB A:ASP654 4.9 28.1 1.0
C A:HIS653 4.9 38.8 1.0
NE2 A:HIS653 4.9 25.9 1.0
CA A:THR723 4.9 40.2 1.0

Magnesium binding site 2 out of 2 in 3jwr

Go back to Magnesium Binding Sites List in 3jwr
Magnesium binding site 2 out of 2 in the Crystal Structure of Chimeric PDE5/PDE6 Catalytic Domain Complexed with 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87.


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 3-Isobutyl-1-Methylxanthine (Ibmx) and PDE6 Gamma-Subunit Inhibitory Peptide 70-87. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg900

b:21.6
occ:1.00
O B:HOH12 2.4 20.3 1.0
O B:HOH16 2.4 16.8 1.0
O B:HOH15 2.4 37.2 1.0
O B:HOH11 2.5 32.3 1.0
OE2 B:GLU682 2.8 40.6 1.0
OD1 B:ASP654 2.9 27.2 1.0
O B:HOH17 3.4 19.1 1.0
O B:THR723 3.6 28.6 1.0
CD B:GLU682 3.8 44.7 1.0
CG B:ASP654 4.0 28.7 1.0
OG1 B:THR723 4.0 26.4 1.0
CG B:GLU682 4.1 41.1 1.0
ZN B:ZN899 4.2 41.8 1.0
O B:HOH9 4.2 22.2 1.0
OD2 B:ASP654 4.2 29.9 1.0
NE2 B:HIS685 4.2 32.3 1.0
C B:THR723 4.3 38.2 1.0
CD2 B:HIS685 4.4 38.9 1.0
CB B:THR723 4.5 27.2 1.0
O B:HIS653 4.6 36.2 1.0
OD1 B:ASP764 4.7 35.6 1.0
CD2 B:HIS653 4.7 25.5 1.0
CD2 B:HIS657 4.9 39.3 1.0
OE1 B:GLU682 4.9 29.7 1.0
N B:ASP724 5.0 32.3 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 08:20:53 2020

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