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Magnesium in PDB 4g2y: Crystal Structure of PDE5A Complexed with Its Inhibitor

Protein crystallography data

The structure of Crystal Structure of PDE5A Complexed with Its Inhibitor, PDB code: 4g2y was solved by J.Ren, T.T.Chen, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.38 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 74.790, 74.790, 132.890, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 21.4

Other elements in 4g2y:

The structure of Crystal Structure of PDE5A Complexed with Its Inhibitor also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE5A Complexed with Its Inhibitor (pdb code 4g2y). 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 PDE5A Complexed with Its Inhibitor, PDB code: 4g2y:

Magnesium binding site 1 out of 1 in 4g2y

Go back to Magnesium Binding Sites List in 4g2y
Magnesium binding site 1 out of 1 in the Crystal Structure of PDE5A Complexed with Its Inhibitor


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 PDE5A Complexed with Its Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg903

b:35.2
occ:1.00
O A:HOH1004 2.1 27.9 1.0
OD1 A:ASP654 2.2 26.2 1.0
O A:HOH1057 2.3 33.7 1.0
O A:HOH1065 2.3 30.8 1.0
O A:HOH1055 2.3 30.5 1.0
O A:HOH1001 2.4 25.7 1.0
CG A:ASP654 3.1 26.4 1.0
OD2 A:ASP654 3.3 24.0 1.0
ZN A:ZN902 3.6 41.6 1.0
O A:HOH1009 3.8 29.4 1.0
C2 A:PEG901 4.2 50.9 1.0
CD2 A:HIS653 4.2 22.3 1.0
OG1 A:THR723 4.3 25.9 1.0
C1 A:PEG901 4.4 39.8 1.0
O A:HIS653 4.4 23.3 1.0
O A:THR723 4.4 31.3 1.0
CD2 A:HIS657 4.4 28.7 1.0
CB A:ASP654 4.5 25.4 1.0
O2 A:PEG901 4.5 55.7 1.0
NE2 A:HIS685 4.5 28.3 1.0
OE2 A:GLU682 4.6 41.9 1.0
NE2 A:HIS613 4.7 27.7 1.0
NE2 A:HIS653 4.7 27.7 1.0
CD2 A:HIS685 4.7 25.6 1.0
CD2 A:HIS613 4.7 28.6 1.0
OD2 A:ASP764 4.7 32.7 1.0
NE2 A:HIS657 4.7 29.5 1.0
O1 A:PEG901 4.8 34.6 1.0
CB A:THR723 4.9 26.6 1.0
CA A:ASP654 4.9 22.3 1.0

Reference:

G.Wang, Z.Liu, T.T.Chen, Z.Wang, H.Yang, M.Zheng, J.Ren, G.Tian, X.Yang, L.Li, J.Li, J.Suo, R.Zhang, X.Jiang, N.K.Terrett, J.Shen, Y.C.Xu, H.Jiang. Design, Synthesis, and Pharmacological Evaluation of Monocyclic Pyrimidinones As Novel Inhibitors of PDE5. J.Med.Chem. V. 55 10540 2012.
ISSN: ISSN 0022-2623
PubMed: 23137303
DOI: 10.1021/JM301159Y
Page generated: Mon Dec 14 15:56:19 2020

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