Manganese in PDB 3qfn: Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph in Complex with Inorganic Phosphate

The structure of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph in Complex with Inorganic Phosphate, PDB code: 3qfn 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 / 2.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.883, 74.935, 149.326, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.4

The structure of Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph in Complex with Inorganic Phosphate 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 in Complex with Inorganic Phosphate (pdb code 3qfn). 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 in Complex with Inorganic Phosphate, PDB code: 3qfn:
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 in Complex with Inorganic Phosphate


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 in Complex with Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn264 b:26.8 occ:1.00 O1 A:PO4263 2.0 35.5 1.0 O A:HOH266 2.1 28.1 1.0 OD1 A:ASN66 2.1 26.8 1.0 NE2 A:HIS128 2.2 20.6 1.0 ND1 A:HIS164 2.3 28.0 1.0 OD2 A:ASP39 2.3 24.0 1.0 CE1 A:HIS164 3.1 28.7 1.0 CG A:ASN66 3.1 27.1 1.0 CD2 A:HIS128 3.1 21.4 1.0 CG A:ASP39 3.2 24.0 1.0 CE1 A:HIS128 3.2 23.2 1.0 P A:PO4263 3.3 37.6 1.0 OD1 A:ASP39 3.4 25.9 1.0 ND2 A:ASN66 3.4 27.6 1.0 CG A:HIS164 3.4 28.6 1.0 FE A:FE265 3.5 26.3 1.0 O2 A:PO4263 3.7 34.9 1.0 O4 A:PO4263 3.8 36.2 1.0 CB A:HIS164 3.9 26.6 1.0 CA A:HIS164 3.9 26.8 1.0 OD2 A:ASP11 4.0 27.8 1.0 CD1 A:TRP67 4.2 25.9 1.0 O A:HIS164 4.2 28.3 1.0 O A:ASN134 4.2 31.6 1.0 NE2 A:HIS164 4.3 29.2 1.0 ND1 A:HIS128 4.3 22.7 1.0 CG A:HIS128 4.3 25.1 1.0 N A:ASN66 4.4 27.6 1.0 CB A:ASN66 4.5 27.9 1.0 CD2 A:HIS164 4.5 29.3 1.0 O3 A:PO4263 4.5 41.0 1.0 CB A:ASP39 4.5 23.1 1.0 C A:HIS164 4.6 27.1 1.0 NE1 A:TRP67 4.6 28.3 1.0 N A:HIS164 5.0 25.7 1.0 CA A:ASN66 5.0 27.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph in Complex with Inorganic Phosphate


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 in Complex with Inorganic Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn264 b:29.1 occ:1.00 O1 B:PO4263 2.1 33.6 1.0 OD2 B:ASP39 2.1 27.2 1.0 NE2 B:HIS128 2.2 30.1 1.0 OD1 B:ASN66 2.2 31.1 1.0 ND1 B:HIS164 2.3 27.9 1.0 O B:HOH266 2.4 30.2 1.0 CE1 B:HIS164 3.0 27.4 1.0 CG B:ASP39 3.0 29.2 1.0 CE1 B:HIS128 3.2 29.8 1.0 CG B:ASN66 3.2 30.2 1.0 CD2 B:HIS128 3.2 29.1 1.0 P B:PO4263 3.2 36.3 1.0 OD1 B:ASP39 3.3 31.3 1.0 CG B:HIS164 3.4 28.6 1.0 FE B:FE265 3.5 28.0 1.0 ND2 B:ASN66 3.5 27.5 1.0 O2 B:PO4263 3.5 30.7 1.0 CA B:HIS164 3.9 27.9 1.0 O4 B:PO4263 3.9 29.9 1.0 OD2 B:ASP11 3.9 26.1 1.0 CB B:HIS164 3.9 27.5 1.0 CD1 B:TRP67 4.2 29.3 1.0 NE2 B:HIS164 4.2 26.5 1.0 O B:HIS164 4.2 28.4 1.0 ND1 B:HIS128 4.3 29.5 1.0 CG B:HIS128 4.3 29.9 1.0 CB B:ASP39 4.3 28.1 1.0 N B:ASN66 4.3 31.4 1.0 O B:ASN134 4.4 34.1 1.0 CD2 B:HIS164 4.4 28.4 1.0 O3 B:PO4263 4.5 40.3 1.0 CB B:ASN66 4.5 30.5 1.0 C B:HIS164 4.6 27.8 1.0 NE1 B:TRP67 4.7 29.5 1.0 N B:HIS164 4.8 27.9 1.0 CA B:ASN66 5.0 31.4 1.0 N B:TRP67 5.0 31.9 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.