Manganese in PDB 3gve: Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis

The structure of Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis, PDB code: 3gve was solved by Y.Kim, N.Marshall, G.Cobb, A.Joachimiak, Midwest Center For Structuralgenomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.54 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.091, 92.505, 50.316, 90.00, 89.94, 90.00
R / Rfree (%)	15.4 / 16.3

The structure of Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Manganese atom in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis (pdb code 3gve). 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 Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis, PDB code: 3gve:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis


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 Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:9.5 occ:1.00 OD1 A:ASP16 2.2 8.7 1.0 O A:HOH424 2.2 10.0 1.0 NE2 A:HIS18 2.2 9.2 1.0 O A:HOH398 2.2 11.8 1.0 NE2 A:HIS248 2.2 10.7 1.0 OD2 A:ASP61 2.3 8.5 1.0 CE1 A:HIS18 3.1 9.5 1.0 CE1 A:HIS248 3.2 11.3 1.0 CD2 A:HIS248 3.3 10.3 1.0 CG A:ASP16 3.3 7.6 1.0 CG A:ASP61 3.3 7.8 1.0 CD2 A:HIS18 3.3 8.9 1.0 MG A:MG403 3.6 8.7 1.0 CB A:ASP61 3.6 7.7 1.0 CB A:ASP16 3.8 7.5 1.0 O A:HIS246 4.2 8.9 1.0 O4 A:CIT502 4.3 16.5 1.0 ND1 A:HIS18 4.3 9.4 1.0 ND1 A:HIS248 4.3 11.5 1.0 OD2 A:ASP16 4.3 7.6 1.0 CG A:HIS248 4.4 10.1 1.0 CG A:HIS18 4.4 8.7 1.0 O A:HOH652 4.4 18.4 1.0 CD2 A:HIS106 4.4 9.7 1.0 OD1 A:ASP61 4.4 8.8 1.0 O3 A:CIT502 4.5 21.7 1.0 CA A:ASP16 4.6 7.4 1.0 NE2 A:HIS213 4.7 8.8 1.0 O A:HOH716 4.7 38.9 1.0 CE1 A:HIS213 4.8 8.6 1.0 CA A:HIS246 4.8 8.2 1.0 C5 A:CIT502 4.9 17.8 1.0 C A:HIS246 4.9 8.3 1.0 NE2 A:HIS106 5.0 10.9 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis


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 Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:8.2 occ:1.00 O B:HOH396 2.2 11.1 1.0 OD1 B:ASP16 2.2 7.8 1.0 NE2 B:HIS18 2.2 8.2 1.0 OD2 B:ASP61 2.2 8.4 1.0 NE2 B:HIS248 2.4 8.8 1.0 O B:HOH734 2.6 12.9 1.0 CE1 B:HIS18 3.1 8.2 1.0 CG B:ASP61 3.2 7.5 1.0 CE1 B:HIS248 3.3 10.1 1.0 CD2 B:HIS18 3.3 7.6 1.0 CG B:ASP16 3.3 7.0 1.0 CD2 B:HIS248 3.4 9.1 1.0 MG B:MG404 3.5 7.7 1.0 CB B:ASP61 3.6 7.3 1.0 CB B:ASP16 3.8 7.3 1.0 O2 B:CIT501 4.2 15.8 1.0 ND1 B:HIS18 4.2 8.7 1.0 O B:HIS246 4.3 8.2 1.0 OD1 B:ASP61 4.4 7.7 1.0 OD2 B:ASP16 4.4 7.4 1.0 CD2 B:HIS106 4.4 8.9 1.0 O B:HOH629 4.4 15.9 1.0 CG B:HIS18 4.4 7.9 1.0 ND1 B:HIS248 4.4 10.8 1.0 CG B:HIS248 4.5 9.4 1.0 O1 B:CIT501 4.5 19.4 1.0 CA B:ASP16 4.6 7.2 1.0 NE2 B:HIS213 4.7 8.0 1.0 CE1 B:HIS213 4.8 7.6 1.0 C1 B:CIT501 4.9 15.1 1.0 CA B:HIS246 4.9 7.7 1.0 NE2 B:HIS106 5.0 10.1 1.0 C B:HIS246 5.0 7.6 1.0

Y.Kim, N.Marshall, G.Cobb, A.Joachimiak. Crystal Structure of Calcineurin-Like Phosphoesterase From Bacillus Subtilis To Be Published.