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Magnesium in PDB 1rkp: Crystal Structure of PDE5A1-Ibmx

Enzymatic activity of Crystal Structure of PDE5A1-Ibmx

All present enzymatic activity of Crystal Structure of PDE5A1-Ibmx:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE5A1-Ibmx, PDB code: 1rkp was solved by Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.05
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.456, 74.456, 130.132, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 24.3

Other elements in 1rkp:

The structure of Crystal Structure of PDE5A1-Ibmx also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE5A1-Ibmx (pdb code 1rkp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of PDE5A1-Ibmx, PDB code: 1rkp:

Magnesium binding site 1 out of 1 in 1rkp

Go back to Magnesium Binding Sites List in 1rkp
Magnesium binding site 1 out of 1 in the Crystal Structure of PDE5A1-Ibmx


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 PDE5A1-Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:29.8
occ:1.00
OD1 A:ASP654 2.1 21.4 1.0
O A:HOH6 2.3 19.5 1.0
O A:HOH5 2.3 20.0 1.0
O A:HOH3 2.3 23.2 1.0
O A:HOH2 2.4 20.2 1.0
O A:HOH4 2.4 24.4 1.0
CG A:ASP654 3.1 20.7 1.0
OD2 A:ASP654 3.5 20.2 1.0
O A:HOH68 4.0 32.3 1.0
ZN A:ZN501 4.0 34.4 1.0
NE2 A:HIS685 4.1 20.9 1.0
CD2 A:HIS653 4.1 17.6 1.0
O A:HIS653 4.1 20.4 1.0
O A:HOH72 4.2 37.7 1.0
O A:HOH1 4.2 22.1 1.0
OE2 A:GLU682 4.2 28.6 1.0
OG1 A:THR723 4.2 21.2 1.0
CD2 A:HIS685 4.3 21.1 1.0
O A:THR723 4.4 22.9 1.0
CD2 A:HIS657 4.4 23.0 1.0
CB A:ASP654 4.4 19.9 1.0
OD2 A:ASP764 4.6 22.8 1.0
NE2 A:HIS613 4.6 23.9 1.0
CB A:THR723 4.7 22.3 1.0
CD2 A:HIS613 4.7 22.4 1.0
NE2 A:HIS657 4.7 22.8 1.0
CA A:ASP654 4.7 20.0 1.0
NE2 A:HIS653 4.7 17.3 1.0
C A:HIS653 4.9 20.2 1.0

Reference:

Q.Huai, Y.Liu, S.H.Francis, J.D.Corbin, H.Ke. Crystal Structures of Phosphodiesterases 4 and 5 in Complex with Inhibitor Ibmx Suggest A Conformation Determinant of Inhibitor Selectivity J.Biol.Chem. V. 279 13095 2004.
ISSN: ISSN 0021-9258
PubMed: 14668322
DOI: 10.1074/JBC.M311556200
Page generated: Mon Dec 14 06:42:42 2020

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