Zinc in PDB 1ror: Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp

All present enzymatic activity of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp:
3.1.4.17;

The structure of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp, PDB code: 1ror 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 (°)	105.111, 159.861, 109.053, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 22.8

The binding sites of Zinc atom in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp (pdb code 1ror). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp, PDB code: 1ror:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:24.7 occ:1.00 NE2 A:HIS238 2.0 19.6 1.0 O2P A:AMP603 2.0 43.7 1.0 NE2 A:HIS274 2.0 15.8 1.0 OD2 A:ASP275 2.2 18.8 1.0 OD1 A:ASP392 2.4 23.1 1.0 O1P A:AMP603 2.6 43.5 1.0 P A:AMP603 2.8 45.1 1.0 CE1 A:HIS238 2.9 19.5 1.0 CE1 A:HIS274 3.0 14.8 1.0 CD2 A:HIS238 3.0 19.8 1.0 CD2 A:HIS274 3.1 15.2 1.0 CG A:ASP392 3.3 24.6 1.0 CG A:ASP275 3.3 18.4 1.0 OD2 A:ASP392 3.5 24.9 1.0 O3P A:AMP603 3.8 44.8 1.0 OD1 A:ASP275 3.8 19.1 1.0 O5' A:AMP603 4.0 43.0 1.0 ND1 A:HIS238 4.1 20.0 1.0 O A:HOH607 4.1 31.3 1.0 ND1 A:HIS274 4.1 15.7 1.0 CG A:HIS238 4.1 20.4 1.0 CG A:HIS274 4.2 15.2 1.0 CD2 A:HIS234 4.3 22.9 1.0 ZN A:ZN602 4.3 46.5 1.0 CB A:ASP275 4.4 18.0 1.0 CG2 A:VAL242 4.6 23.1 1.0 CB A:ASP392 4.6 23.8 1.0 NE2 A:HIS234 4.7 23.0 1.0

Zinc binding site 2 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:46.5 occ:1.00 O A:HOH605 2.3 22.4 1.0 O A:HOH622 2.4 20.0 1.0 O A:HOH623 2.4 22.2 1.0 OD1 A:ASP275 2.4 19.1 1.0 O3P A:AMP603 2.6 44.8 1.0 O1P A:AMP603 2.7 43.5 1.0 P A:AMP603 3.2 45.1 1.0 CG A:ASP275 3.5 18.4 1.0 O A:HOH670 3.5 31.1 1.0 OD2 A:ASP275 3.8 18.8 1.0 O2P A:AMP603 4.1 43.7 1.0 OE2 A:GLU304 4.3 22.2 1.0 NE2 A:HIS307 4.3 18.1 1.0 ZN A:ZN601 4.3 24.7 1.0 O A:HIS274 4.4 17.6 1.0 O A:HOH663 4.4 34.7 1.0 OG1 A:THR345 4.4 20.9 1.0 CD2 A:HIS274 4.4 15.2 1.0 NE2 A:HIS234 4.5 23.0 1.0 O5' A:AMP603 4.5 43.0 1.0 CD2 A:HIS234 4.6 22.9 1.0 CD2 A:HIS278 4.6 16.8 1.0 CD2 A:HIS307 4.6 16.2 1.0 O A:THR345 4.7 24.4 1.0 C5' A:AMP603 4.7 45.0 1.0 CB A:THR345 4.8 22.7 1.0 NE2 A:HIS278 4.8 15.4 1.0 O A:HOH747 4.8 33.4 1.0 NE2 A:HIS274 4.8 15.8 1.0 CB A:ASP275 4.8 18.0 1.0 OD2 A:ASP392 4.9 24.9 1.0 CG A:GLU304 4.9 19.7 1.0 CD A:GLU304 5.0 21.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:28.8 occ:1.00 NE2 B:HIS238 1.9 25.3 1.0 O3P B:AMP703 2.0 42.2 1.0 NE2 B:HIS274 2.1 22.5 1.0 OD2 B:ASP275 2.2 24.9 1.0 OD1 B:ASP392 2.3 26.1 1.0 O2P B:AMP703 2.5 41.4 1.0 P B:AMP703 2.8 43.1 1.0 CE1 B:HIS238 2.9 26.6 1.0 CD2 B:HIS238 3.0 26.4 1.0 CE1 B:HIS274 3.0 22.8 1.0 CD2 B:HIS274 3.1 23.1 1.0 CG B:ASP275 3.2 23.4 1.0 CG B:ASP392 3.3 27.6 1.0 OD2 B:ASP392 3.5 28.7 1.0 OD1 B:ASP275 3.6 23.2 1.0 O1P B:AMP703 3.7 42.5 1.0 O5' B:AMP703 3.9 43.3 1.0 O B:HOH822 4.1 36.3 1.0 ND1 B:HIS238 4.1 25.9 1.0 CG B:HIS238 4.1 26.4 1.0 ND1 B:HIS274 4.2 21.9 1.0 CG B:HIS274 4.2 21.9 1.0 CD2 B:HIS234 4.3 29.9 1.0 ZN B:ZN702 4.3 50.5 1.0 CB B:ASP275 4.4 23.8 1.0 CG2 B:VAL242 4.5 28.5 1.0 CB B:ASP392 4.6 26.9 1.0 NE2 B:HIS234 4.6 31.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structures of the Catalytic Domain of Phosphodiesterase 4B2B Complexed with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:50.5 occ:1.00 O B:HOH704 2.3 17.8 1.0 O B:HOH707 2.4 25.1 1.0 O1P B:AMP703 2.4 42.5 1.0 OD1 B:ASP275 2.5 23.2 1.0 O B:HOH724 2.6 22.3 1.0 O2P B:AMP703 2.7 41.4 1.0 P B:AMP703 3.2 43.1 1.0 O B:HOH706 3.5 37.4 1.0 CG B:ASP275 3.6 23.4 1.0 OD2 B:ASP275 3.9 24.9 1.0 OE2 B:GLU304 4.1 26.0 1.0 O3P B:AMP703 4.1 42.2 1.0 NE2 B:HIS307 4.2 22.9 1.0 ZN B:ZN701 4.3 28.8 1.0 O5' B:AMP703 4.4 43.3 1.0 OG1 B:THR345 4.4 27.4 1.0 O B:HIS274 4.4 24.5 1.0 CD2 B:HIS274 4.5 23.1 1.0 O B:THR345 4.5 26.4 1.0 O B:HOH725 4.5 41.6 1.0 C5' B:AMP703 4.5 45.3 1.0 CD2 B:HIS307 4.6 22.2 1.0 CD2 B:HIS278 4.7 23.9 1.0 NE2 B:HIS234 4.7 31.2 1.0 O B:HOH744 4.8 33.2 1.0 CD2 B:HIS234 4.8 29.9 1.0 CB B:THR345 4.8 26.9 1.0 OD2 B:ASP392 4.8 28.7 1.0 NE2 B:HIS278 4.9 23.5 1.0 CB B:ASP275 4.9 23.8 1.0 NE2 B:HIS274 4.9 22.5 1.0 CD B:GLU304 4.9 24.8 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