Iron in PDB 3qfo: Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp

The structure of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp, PDB code: 3qfo was solved by Y.L.Jiang, J.W.Zhang, W.L.Yu, W.Cheng, C.C.Zhang, C.Z.Zhou, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.654, 74.940, 149.130, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 24.5

The structure of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp (pdb code 3qfo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp, PDB code: 3qfo:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe264 b:23.0 occ:1.00 O A:HOH266 2.1 31.6 1.0 OD2 A:ASP11 2.1 20.9 1.0 O2P A:AMP263 2.1 31.4 1.0 NE2 A:HIS13 2.2 23.2 1.0 NE2 A:HIS166 2.2 22.4 1.0 OD2 A:ASP39 2.4 20.5 1.0 CE1 A:HIS13 3.0 23.0 1.0 CG A:ASP11 3.1 22.3 1.0 CE1 A:HIS166 3.2 23.3 1.0 CD2 A:HIS166 3.2 22.8 1.0 CG A:ASP39 3.3 22.7 1.0 P A:AMP263 3.3 33.5 1.0 CD2 A:HIS13 3.3 22.1 1.0 MN A:MN265 3.3 22.3 1.0 CB A:ASP39 3.5 22.8 1.0 O1P A:AMP263 3.6 34.8 1.0 CB A:ASP11 3.7 20.2 1.0 O5' A:AMP263 4.0 31.0 1.0 C5' A:AMP263 4.0 31.8 1.0 OD1 A:ASP11 4.1 19.2 1.0 ND1 A:HIS13 4.2 21.7 1.0 ND1 A:HIS166 4.3 22.0 1.0 O A:HIS164 4.3 24.1 1.0 CG A:HIS166 4.4 23.0 1.0 CA A:ASP11 4.4 21.5 1.0 O A:HOH272 4.4 43.4 1.0 CG A:HIS13 4.4 22.0 1.0 CE1 A:HIS128 4.4 21.6 1.0 NE2 A:HIS128 4.4 22.4 1.0 OD1 A:ASP39 4.5 23.6 1.0 CD1 A:TRP67 4.5 25.6 1.0 O3P A:AMP263 4.6 36.9 1.0 CA A:HIS164 4.6 22.6 1.0 NE1 A:TRP67 4.7 25.1 1.0 C A:HIS164 4.8 23.5 1.0 ND1 A:HIS164 5.0 18.3 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe264 b:21.2 occ:1.00 O B:HOH267 1.9 22.4 1.0 OD2 B:ASP11 2.1 20.8 1.0 O2P B:AMP263 2.2 42.1 1.0 NE2 B:HIS13 2.2 16.9 1.0 NE2 B:HIS166 2.3 19.5 1.0 OD2 B:ASP39 2.3 16.3 1.0 CE1 B:HIS13 3.1 16.9 1.0 CG B:ASP11 3.2 19.9 1.0 CE1 B:HIS166 3.2 19.4 1.0 CG B:ASP39 3.2 19.3 1.0 P B:AMP263 3.3 43.4 1.0 CD2 B:HIS166 3.3 19.4 1.0 CD2 B:HIS13 3.3 18.3 1.0 MN B:MN265 3.4 20.9 1.0 CB B:ASP39 3.5 20.0 1.0 O1P B:AMP263 3.5 46.3 1.0 CB B:ASP11 3.7 18.8 1.0 O5' B:AMP263 4.0 45.3 1.0 C5' B:AMP263 4.0 45.9 1.0 OD1 B:ASP11 4.2 18.6 1.0 ND1 B:HIS13 4.2 17.0 1.0 O B:HIS164 4.3 22.8 1.0 ND1 B:HIS166 4.3 16.9 1.0 CE1 B:HIS128 4.4 20.4 1.0 CA B:ASP11 4.4 19.7 1.0 CG B:HIS13 4.4 19.0 1.0 OD1 B:ASP39 4.4 19.2 1.0 NE2 B:HIS128 4.4 19.4 1.0 CG B:HIS166 4.4 19.3 1.0 CD1 B:TRP67 4.5 21.4 1.0 O B:HOH393 4.6 48.9 1.0 NE1 B:TRP67 4.6 21.6 1.0 O3P B:AMP263 4.6 46.5 1.0 CA B:HIS164 4.6 21.3 1.0 C B:HIS164 4.8 21.9 1.0 ND1 B:HIS164 5.0 21.6 1.0 CA B:ASP39 5.0 20.6 1.0

Y.L.Jiang, J.W.Zhang, W.L.Yu, W.Cheng, C.C.Zhang, C.Frolet, A.-M.Di-Guilmi, T.Vernet, C.Z.Zhou, Y.Chen. Structural and Enzymatic Characterization of A Streptococcal Atp/Diadenosine Polyphosphate and Phosphodiester Hydrolase SPR1479/Saph To Be Published.