Manganese 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:

Iron

(Fe)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph Im Complex with Amp, PDB code: 3qfo:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn265 b:22.3 occ:1.00 O A:HOH266 2.0 31.6 1.0 O1P A:AMP263 2.1 34.8 1.0 NE2 A:HIS128 2.2 22.4 1.0 OD2 A:ASP39 2.2 20.5 1.0 OD1 A:ASN66 2.2 26.1 1.0 ND1 A:HIS164 2.3 18.3 1.0 CE1 A:HIS164 3.1 18.4 1.0 CD2 A:HIS128 3.1 21.6 1.0 CE1 A:HIS128 3.1 21.6 1.0 CG A:ASN66 3.2 26.1 1.0 CG A:ASP39 3.2 22.7 1.0 P A:AMP263 3.3 33.5 1.0 FE A:FE264 3.3 23.0 1.0 CG A:HIS164 3.4 21.3 1.0 ND2 A:ASN66 3.5 23.5 1.0 O2P A:AMP263 3.6 31.4 1.0 OD1 A:ASP39 3.6 23.6 1.0 CA A:HIS164 3.8 22.6 1.0 CB A:HIS164 3.8 21.9 1.0 OD2 A:ASP11 3.9 20.9 1.0 O5' A:AMP263 4.0 31.0 1.0 O A:HIS164 4.2 24.1 1.0 ND1 A:HIS128 4.2 22.5 1.0 NE2 A:HIS164 4.3 20.0 1.0 CG A:HIS128 4.3 23.5 1.0 CD1 A:TRP67 4.3 25.6 1.0 O A:ASN134 4.3 29.3 1.0 CD2 A:HIS164 4.4 19.1 1.0 N A:ASN66 4.5 25.9 1.0 O3P A:AMP263 4.5 36.9 1.0 CB A:ASP39 4.5 22.8 1.0 C A:HIS164 4.5 23.5 1.0 CB A:ASN66 4.5 26.3 1.0 N A:HIS164 4.7 22.4 1.0 NE1 A:TRP67 4.9 25.1 1.0 C5' A:AMP263 4.9 31.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn265 b:20.9 occ:1.00 O1P B:AMP263 2.0 46.3 1.0 O B:HOH267 2.0 22.4 1.0 OD1 B:ASN66 2.1 21.1 1.0 NE2 B:HIS128 2.1 19.4 1.0 OD2 B:ASP39 2.2 16.3 1.0 ND1 B:HIS164 2.3 21.6 1.0 CE1 B:HIS164 3.1 21.3 1.0 CE1 B:HIS128 3.1 20.4 1.0 CD2 B:HIS128 3.1 18.2 1.0 CG B:ASP39 3.2 19.3 1.0 CG B:ASN66 3.2 22.8 1.0 P B:AMP263 3.2 43.4 1.0 FE B:FE264 3.4 21.2 1.0 CG B:HIS164 3.4 21.6 1.0 OD1 B:ASP39 3.5 19.2 1.0 O2P B:AMP263 3.6 42.1 1.0 ND2 B:ASN66 3.7 22.1 1.0 CA B:HIS164 3.7 21.3 1.0 CB B:HIS164 3.8 21.2 1.0 OD2 B:ASP11 3.9 20.8 1.0 O5' B:AMP263 3.9 45.3 1.0 O B:HIS164 4.2 22.8 1.0 ND1 B:HIS128 4.2 19.4 1.0 CD1 B:TRP67 4.3 21.4 1.0 NE2 B:HIS164 4.3 22.1 1.0 CG B:HIS128 4.3 20.8 1.0 O B:ASN134 4.3 28.1 1.0 O3P B:AMP263 4.4 46.5 1.0 N B:ASN66 4.4 21.8 1.0 CD2 B:HIS164 4.4 22.0 1.0 CB B:ASP39 4.5 20.0 1.0 C B:HIS164 4.5 21.9 1.0 CB B:ASN66 4.5 22.2 1.0 N B:HIS164 4.7 20.7 1.0 NE1 B:TRP67 4.8 21.6 1.0 C5' B:AMP263 4.8 45.9 1.0 CA B:ASN66 5.0 22.6 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.