Zinc in PDB 1ro6: Crystal Structure of PDE4B2B Complexed with Rolipram (R & S)

All present enzymatic activity of Crystal Structure of PDE4B2B Complexed with Rolipram (R & S):
3.1.4.17;

The structure of Crystal Structure of PDE4B2B Complexed with Rolipram (R & S), PDB code: 1ro6 was solved by R.X.Xu, W.J.Rocque, M.H.Lambert, D.E.Vanderwall, R.T.Nolte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.148, 160.891, 108.780, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 24.5

The structure of Crystal Structure of PDE4B2B Complexed with Rolipram (R & S) also contains other interesting chemical elements:

Arsenic	(As)	1 atom
Manganese	(Mn)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of PDE4B2B Complexed with Rolipram (R & S) (pdb code 1ro6). 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 PDE4B2B Complexed with Rolipram (R & S), PDB code: 1ro6:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of PDE4B2B Complexed with Rolipram (R & S)


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 PDE4B2B Complexed with Rolipram (R & S) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn529 b:24.9 occ:1.00 O A:HOH788 1.9 32.9 1.0 NE2 A:HIS274 2.0 19.5 1.0 NE2 A:HIS238 2.0 20.4 1.0 OD2 A:ASP275 2.2 22.5 1.0 OD1 A:ASP392 2.2 25.5 1.0 CD2 A:HIS274 3.0 19.6 1.0 CE1 A:HIS238 3.0 20.1 1.0 CD2 A:HIS238 3.0 19.5 1.0 CE1 A:HIS274 3.0 19.6 1.0 CG A:ASP392 3.1 26.7 1.0 O1 A:ROL601 3.3 34.4 0.5 CG A:ASP275 3.3 21.2 1.0 OD2 A:ASP392 3.4 27.2 1.0 OD1 A:ASP275 3.9 21.7 1.0 MN A:MN530 4.0 79.3 1.0 O A:HOH778 4.1 44.2 1.0 CG A:HIS274 4.1 18.9 1.0 ND1 A:HIS274 4.1 18.8 1.0 ND1 A:HIS238 4.1 20.4 1.0 CG A:HIS238 4.2 20.2 1.0 CD2 A:HIS234 4.2 19.5 1.0 C1 A:ROL601 4.4 35.3 0.5 CB A:ASP275 4.4 20.4 1.0 CB A:ASP392 4.5 25.5 1.0 CG2 A:VAL242 4.5 23.5 1.0 NE2 A:HIS234 4.6 21.1 1.0 H1 A:ROL601 4.7 35.8 0.5 N1 A:ROL601 5.0 35.8 0.5

Zinc binding site 2 out of 2 in the Crystal Structure of PDE4B2B Complexed with Rolipram (R & S)


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 PDE4B2B Complexed with Rolipram (R & S) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn529 b:29.7 occ:1.00 O B:HOH715 1.8 31.2 1.0 NE2 B:HIS238 1.9 25.4 1.0 NE2 B:HIS274 2.1 25.9 1.0 OD2 B:ASP275 2.1 30.2 1.0 OD1 B:ASP392 2.1 30.4 1.0 CE1 B:HIS238 2.9 25.4 1.0 CD2 B:HIS238 2.9 25.6 1.0 CD2 B:HIS274 3.0 25.8 1.0 O1 B:ROL602 3.0 41.6 0.5 CE1 B:HIS274 3.1 26.7 1.0 CG B:ASP392 3.2 31.2 1.0 CG B:ASP275 3.2 28.1 1.0 OD2 B:ASP392 3.6 32.2 1.0 OD1 B:ASP275 3.7 28.6 1.0 O B:HOH695 4.0 33.2 1.0 ND1 B:HIS238 4.0 24.8 1.0 CG B:HIS238 4.1 26.5 1.0 C1 B:ROL602 4.1 42.2 0.5 O B:HOH716 4.1 74.8 1.0 ND1 B:HIS274 4.2 25.4 1.0 CG B:HIS274 4.2 26.1 1.0 CD2 B:HIS234 4.2 28.6 1.0 CB B:ASP275 4.4 27.0 1.0 CB B:ASP392 4.5 29.6 1.0 H1 B:ROL602 4.5 42.4 0.5 CG2 B:VAL242 4.5 28.8 1.0 NE2 B:HIS234 4.6 28.3 1.0 N1 B:ROL602 4.7 42.4 0.5 MN B:MN530 4.8 79.1 1.0 CA B:ASP392 5.0 29.8 1.0

R.X.Xu, W.J.Rocque, M.H.Lambert, D.E.Vanderwall, M.A.Luther, R.T.Nolte. Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B Complexed with Amp, 8-Br-Amp, and Rolipram. J.Mol.Biol. V. 337 355 2004.
ISSN: ISSN 0022-2836
PubMed: 15003452
DOI: 10.1016/J.JMB.2004.01.040