Iron in PDB 3qfm: Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph

The structure of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph, PDB code: 3qfm 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)	30.00 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.559, 75.102, 148.796, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.9

The structure of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph 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 (pdb code 3qfm). 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, PDB code: 3qfm:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe264 b:17.7 occ:1.00 O A:HOH267 1.9 25.3 1.0 OD2 A:ASP11 2.1 17.4 1.0 NE2 A:HIS13 2.2 17.2 1.0 OD2 A:ASP39 2.3 14.9 1.0 NE2 A:HIS166 2.3 17.0 1.0 CE1 A:HIS13 3.1 15.8 1.0 CG A:ASP11 3.1 15.6 1.0 CD2 A:HIS13 3.2 16.2 1.0 CG A:ASP39 3.3 16.2 1.0 CE1 A:HIS166 3.3 17.3 1.0 CD2 A:HIS166 3.3 15.9 1.0 MN A:MN263 3.4 16.7 1.0 CB A:ASP39 3.5 15.1 1.0 CB A:ASP11 3.7 14.2 1.0 O A:HOH275 4.0 27.3 1.0 O A:HIS164 4.1 16.1 1.0 OD1 A:ASP11 4.1 14.2 1.0 ND1 A:HIS13 4.2 16.5 1.0 CG A:HIS13 4.3 15.5 1.0 CA A:ASP11 4.3 15.4 1.0 NE2 A:HIS128 4.4 14.8 1.0 CE1 A:HIS128 4.4 14.8 1.0 ND1 A:HIS166 4.4 15.4 1.0 OD1 A:ASP39 4.4 16.2 1.0 CD2 A:PHE259 4.4 30.2 1.0 CG A:HIS166 4.5 17.0 1.0 CA A:HIS164 4.5 15.8 1.0 C A:HIS164 4.6 16.2 1.0 CD1 A:TRP67 4.6 23.2 1.0 CE2 A:PHE259 4.7 31.2 1.0 NE1 A:TRP67 4.7 25.9 1.0 ND1 A:HIS164 4.9 16.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe264 b:20.9 occ:1.00 O B:HOH265 1.9 22.3 1.0 OD2 B:ASP11 2.1 21.4 1.0 NE2 B:HIS13 2.1 20.7 1.0 NE2 B:HIS166 2.3 20.9 1.0 OD2 B:ASP39 2.3 20.1 1.0 CG B:ASP11 3.1 20.2 1.0 CE1 B:HIS13 3.1 22.1 1.0 CD2 B:HIS13 3.2 19.8 1.0 CE1 B:HIS166 3.2 21.5 1.0 CG B:ASP39 3.2 21.4 1.0 CD2 B:HIS166 3.3 21.5 1.0 MN B:MN263 3.3 21.1 1.0 CB B:ASP39 3.5 20.3 1.0 CB B:ASP11 3.6 17.6 1.0 O B:HOH266 4.0 22.9 1.0 OD1 B:ASP11 4.1 21.5 1.0 O B:HIS164 4.1 20.7 1.0 ND1 B:HIS13 4.2 21.3 1.0 CA B:ASP11 4.3 18.6 1.0 CG B:HIS13 4.3 19.4 1.0 ND1 B:HIS166 4.3 18.7 1.0 CE1 B:HIS128 4.4 18.4 1.0 NE2 B:HIS128 4.4 21.0 1.0 OD1 B:ASP39 4.4 20.2 1.0 CG B:HIS166 4.4 18.3 1.0 CA B:HIS164 4.5 19.2 1.0 CD1 B:TRP67 4.6 24.8 1.0 C B:HIS164 4.7 20.2 1.0 NE1 B:TRP67 4.7 26.2 1.0 ND1 B:HIS164 5.0 21.6 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.