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Zinc 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:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3jwr

Go back to Zinc Binding Sites List in 3jwr
Zinc 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 Zinc with other atoms in the Zn 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:Zn899

b:44.0
occ:1.00
 OD2 A:ASP764 2.1 42.0 1.0
OD2 A:ASP654 2.1 30.3 1.0
NE2 A:HIS653 2.3 25.9 1.0
NE2 A:HIS617 2.5 26.1 1.0
CD2 A:HIS653 2.9 26.6 1.0
CG A:ASP764 3.0 41.8 1.0
CG A:ASP654 3.1 29.8 1.0
CE1 A:HIS617 3.3 36.4 1.0
OD1 A:ASP764 3.3 39.3 1.0
CE1 A:HIS653 3.5 30.6 1.0
CD2 A:HIS617 3.5 32.4 1.0
OD1 A:ASP654 3.5 24.2 1.0
O A:HOH4 3.7 24.8 1.0
NE2 A:HIS613 3.9 33.8 1.0
MG A:MG900 3.9 18.6 1.0
CD2 A:HIS613 4.0 41.0 1.0
O A:HOH5 4.1 20.0 1.0
CG A:HIS653 4.2 29.7 1.0
CB A:ASP764 4.4 34.2 1.0
O A:ASP764 4.4 34.6 1.0
CB A:ASP654 4.4 28.1 1.0
ND1 A:HIS653 4.4 23.4 1.0
ND1 A:HIS617 4.5 32.1 1.0
CG A:HIS617 4.6 31.6 1.0
CA A:ASP764 4.9 27.3 1.0
C13 A:IBM901 4.9 58.1 1.0
C A:ASP764 5.0 38.1 1.0

Zinc binding site 2 out of 2 in 3jwr

Go back to Zinc Binding Sites List in 3jwr
Zinc 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 Zinc with other atoms in the Zn 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:Zn899

b:41.8
occ:1.00
 O B:HOH12 2.0 20.3 1.0
OD2 B:ASP764 2.1 38.9 1.0
OD2 B:ASP654 2.1 29.9 1.0
NE2 B:HIS653 2.2 24.3 1.0
NE2 B:HIS617 2.4 32.1 1.0
CD2 B:HIS653 2.8 25.5 1.0
O B:HOH18 3.0 20.8 1.0
CG B:ASP764 3.0 36.9 1.0
O B:HOH16 3.1 16.8 1.0
CG B:ASP654 3.1 28.7 1.0
CE1 B:HIS617 3.2 36.2 1.0
OD1 B:ASP764 3.4 35.6 1.0
CE1 B:HIS653 3.4 28.0 1.0
CD2 B:HIS617 3.4 31.9 1.0
OD1 B:ASP654 3.6 27.2 1.0
NE2 B:HIS613 4.0 37.5 1.0
CD2 B:HIS613 4.0 37.4 1.0
CG B:HIS653 4.1 21.9 1.0
MG B:MG900 4.2 21.6 1.0
O B:HOH15 4.2 37.2 1.0
ND1 B:HIS653 4.3 21.1 1.0
O B:ASP764 4.4 39.6 1.0
CB B:ASP654 4.4 22.9 1.0
CB B:ASP764 4.4 32.9 1.0
ND1 B:HIS617 4.4 28.9 1.0
CG B:HIS617 4.5 29.9 1.0
O B:HOH17 4.6 19.1 1.0
CA B:ASP764 4.8 26.9 1.0
C B:ASP764 5.0 36.8 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 04:28:50 2020

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