Manganese 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:

Iron

(Fe)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Streptococcal Asymmetric AP4A Hydrolase and Phosphodiesterase SPR1479/Saph, PDB code: 3qfm:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn263 b:16.7 occ:1.00 O A:HOH267 2.0 25.3 1.0 OD1 A:ASN66 2.1 16.6 1.0 NE2 A:HIS128 2.2 14.8 1.0 OD2 A:ASP39 2.3 14.9 1.0 ND1 A:HIS164 2.3 16.3 1.0 CE1 A:HIS164 3.1 19.1 1.0 CD2 A:HIS128 3.1 12.2 1.0 O A:HOH275 3.1 27.3 1.0 CG A:ASP39 3.2 16.2 1.0 CE1 A:HIS128 3.2 14.8 1.0 CG A:ASN66 3.2 19.0 1.0 FE A:FE264 3.4 17.7 1.0 CG A:HIS164 3.4 17.5 1.0 OD1 A:ASP39 3.5 16.2 1.0 CA A:HIS164 3.7 15.8 1.0 ND2 A:ASN66 3.8 15.5 1.0 CB A:HIS164 3.8 14.8 1.0 OD2 A:ASP11 3.9 17.4 1.0 O A:HIS164 4.1 16.1 1.0 O A:ASN134 4.2 21.3 1.0 CD1 A:TRP67 4.2 23.2 1.0 CG A:HIS128 4.3 12.0 1.0 NE2 A:HIS164 4.3 20.0 1.0 ND1 A:HIS128 4.3 14.2 1.0 C A:HIS164 4.4 16.2 1.0 N A:ASN66 4.4 18.9 1.0 CD2 A:HIS164 4.4 18.9 1.0 CB A:ASP39 4.5 15.1 1.0 CB A:ASN66 4.5 18.6 1.0 N A:HIS164 4.7 15.9 1.0 NE1 A:TRP67 4.7 25.9 1.0 CA A:ASN66 5.0 18.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn263 b:21.1 occ:1.00 NE2 B:HIS128 2.1 21.0 1.0 O B:HOH265 2.1 22.3 1.0 OD1 B:ASN66 2.2 18.4 1.0 OD2 B:ASP39 2.2 20.1 1.0 ND1 B:HIS164 2.3 21.6 1.0 CE1 B:HIS128 3.1 18.4 1.0 CE1 B:HIS164 3.1 21.5 1.0 O B:HOH266 3.1 22.9 1.0 CD2 B:HIS128 3.2 19.0 1.0 CG B:ASP39 3.2 21.4 1.0 CG B:ASN66 3.3 24.0 1.0 FE B:FE264 3.3 20.9 1.0 CG B:HIS164 3.3 19.7 1.0 OD1 B:ASP39 3.5 20.2 1.0 CA B:HIS164 3.7 19.2 1.0 CB B:HIS164 3.7 20.0 1.0 OD2 B:ASP11 3.8 21.4 1.0 ND2 B:ASN66 3.8 19.9 1.0 O B:HIS164 4.1 20.7 1.0 ND1 B:HIS128 4.2 19.5 1.0 CD1 B:TRP67 4.3 24.8 1.0 NE2 B:HIS164 4.3 21.8 1.0 CG B:HIS128 4.3 19.6 1.0 O B:ASN134 4.3 23.8 1.0 CD2 B:HIS164 4.4 20.4 1.0 C B:HIS164 4.4 20.2 1.0 N B:ASN66 4.4 23.4 1.0 CB B:ASP39 4.4 20.3 1.0 CB B:ASN66 4.5 23.0 1.0 N B:HIS164 4.6 19.1 1.0 NE1 B:TRP67 4.8 26.2 1.0 CG B:ASP11 4.9 20.2 1.0 CA B:ASN66 5.0 24.3 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.