Magnesium in PDB 3tvx: The Structure of PDE4A with Pentoxifylline at 2.84A Resolution

All present enzymatic activity of The Structure of PDE4A with Pentoxifylline at 2.84A Resolution:
3.1.4.17;

The structure of The Structure of PDE4A with Pentoxifylline at 2.84A Resolution, PDB code: 3tvx was solved by J.Badger, V.Sridhar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.40 / 2.84
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.938, 104.938, 163.652, 90.00, 90.00, 90.00
R / Rfree (%)	22 / 29

The structure of The Structure of PDE4A with Pentoxifylline at 2.84A Resolution also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the The Structure of PDE4A with Pentoxifylline at 2.84A Resolution (pdb code 3tvx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Structure of PDE4A with Pentoxifylline at 2.84A Resolution, PDB code: 3tvx:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Structure of PDE4A with Pentoxifylline at 2.84A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Structure of PDE4A with Pentoxifylline at 2.84A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:88.3 occ:1.00 OD1 A:ASP413 2.4 55.0 1.0 O A:HIS412 3.2 54.7 1.0 CG A:ASP413 3.3 54.2 1.0 OG1 A:THR483 3.4 57.7 1.0 OD2 A:ASP413 3.6 55.0 1.0 CD2 A:HIS412 3.7 54.6 1.0 CB A:THR483 3.9 58.3 1.0 ZN A:ZN900 3.9 64.7 1.0 CD2 A:HIS445 4.1 52.7 1.0 OE2 A:GLU442 4.2 56.3 1.0 O A:THR483 4.2 59.4 1.0 NE2 A:HIS445 4.2 52.5 1.0 C A:HIS412 4.3 54.2 1.0 NE2 A:HIS412 4.4 53.6 1.0 OD2 A:ASP530 4.5 64.6 1.0 CG A:GLU442 4.5 52.4 1.0 CB A:ASP413 4.6 54.0 1.0 CG A:HIS412 4.6 54.9 1.0 C A:THR483 4.7 59.2 1.0 CA A:ASP413 4.7 54.2 1.0 CD A:GLU442 4.8 54.3 1.0 CG2 A:THR483 4.9 57.8 1.0 N A:ASP413 4.9 54.0 1.0 CA A:THR483 5.0 58.3 1.0

Magnesium binding site 2 out of 2 in the The Structure of PDE4A with Pentoxifylline at 2.84A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Structure of PDE4A with Pentoxifylline at 2.84A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:92.7 occ:1.00 OD1 B:ASP413 2.3 53.7 1.0 CG B:ASP413 3.2 52.6 1.0 ZN B:ZN900 3.2 63.5 1.0 OD2 B:ASP413 3.3 54.1 1.0 CD2 B:HIS412 4.0 51.9 1.0 OD2 B:ASP530 4.1 62.9 1.0 O B:HIS412 4.1 52.8 1.0 O B:THR483 4.2 59.6 1.0 OG1 B:THR483 4.3 57.2 1.0 NE2 B:HIS412 4.3 51.8 1.0 CB B:THR483 4.4 57.4 1.0 OE2 B:GLU442 4.5 58.2 1.0 NE2 B:HIS372 4.6 55.1 1.0 CB B:ASP413 4.6 52.3 1.0 NE2 B:HIS445 4.6 48.9 1.0 CD2 B:HIS372 4.7 54.7 1.0 OD1 B:ASP530 4.8 63.2 1.0 CG B:ASP530 4.8 63.5 1.0 CD2 B:HIS445 4.9 49.1 1.0 CD2 B:HIS416 4.9 54.3 1.0 C B:THR483 5.0 58.6 1.0

M.I.Recht, V.Sridhar, J.Badger, L.Hernandez, B.Chie-Leon, V.Nienaber, F.E.Torres. Fragment-Based Screening For Inhibitors of PDE4A Using Enthalpy Arrays and X-Ray Crystallography. J Biomol Screen V. 17 469 2012.
ISSN: ISSN 1087-0571
PubMed: 22223051
DOI: 10.1177/1087057111430987