Zinc 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:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc where determined in the The Structure of PDE4A with Pentoxifylline at 2.84A Resolution, PDB code: 3tvx:
Jump to Zinc binding site number: 1; 2;

Zinc 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 Zinc with other atoms in the Zn 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:Zn900 b:64.7 occ:1.00 OD2 A:ASP413 2.1 55.0 1.0 NE2 A:HIS412 2.2 53.6 1.0 NE2 A:HIS376 2.2 55.6 1.0 OD1 A:ASP530 2.3 63.4 1.0 CD2 A:HIS412 3.0 54.6 1.0 CE1 A:HIS376 3.1 56.1 1.0 CG A:ASP530 3.1 63.1 1.0 CD2 A:HIS376 3.2 56.8 1.0 CE1 A:HIS412 3.2 54.1 1.0 CG A:ASP413 3.2 54.2 1.0 OD2 A:ASP530 3.2 64.6 1.0 OD1 A:ASP413 3.7 55.0 1.0 MG A:MG901 3.9 88.3 1.0 CG A:HIS412 4.1 54.9 1.0 CD2 A:HIS372 4.2 54.8 1.0 ND1 A:HIS376 4.2 56.5 1.0 ND1 A:HIS412 4.2 54.6 1.0 CG A:HIS376 4.3 56.7 1.0 NE2 A:HIS372 4.4 54.7 1.0 CB A:ASP413 4.4 54.0 1.0 CB A:ASP530 4.5 62.3 1.0 CG2 A:VAL380 4.7 58.0 1.0

Zinc 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 Zinc with other atoms in the Zn 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:Zn900 b:63.5 occ:1.00 OD2 B:ASP413 2.1 54.1 1.0 NE2 B:HIS412 2.2 51.8 1.0 NE2 B:HIS376 2.2 55.7 1.0 OD1 B:ASP530 2.3 63.2 1.0 CD2 B:HIS412 2.9 51.9 1.0 CG B:ASP530 3.1 63.5 1.0 CD2 B:HIS376 3.2 56.3 1.0 CG B:ASP413 3.2 52.6 1.0 MG B:MG901 3.2 92.7 1.0 OD2 B:ASP530 3.2 62.9 1.0 CE1 B:HIS412 3.3 52.2 1.0 CE1 B:HIS376 3.3 56.0 1.0 OD1 B:ASP413 3.6 53.7 1.0 CD2 B:HIS372 4.1 54.7 1.0 CG B:HIS412 4.1 51.7 1.0 NE2 B:HIS372 4.2 55.1 1.0 ND1 B:HIS412 4.3 51.8 1.0 CG B:HIS376 4.3 56.6 1.0 ND1 B:HIS376 4.3 55.2 1.0 CB B:ASP413 4.4 52.3 1.0 CB B:ASP530 4.5 63.9 1.0 CG2 B:VAL380 4.8 59.4 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