Magnesium 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:

Manganese

(Mn)

2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis, PDB code: 3gve:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg403 b:8.7 occ:1.00 OD1 A:ASN105 2.1 11.2 1.0 NE2 A:HIS213 2.3 8.8 1.0 ND1 A:HIS246 2.4 9.0 1.0 OD2 A:ASP61 2.4 8.5 1.0 O A:HOH424 2.4 10.0 1.0 CG A:ASN105 3.1 10.4 1.0 CG A:ASP61 3.1 7.8 1.0 CD2 A:HIS213 3.2 8.0 1.0 CE1 A:HIS246 3.2 9.0 1.0 CE1 A:HIS213 3.3 8.6 1.0 OD1 A:ASP61 3.4 8.8 1.0 CG A:HIS246 3.5 8.4 1.0 O4 A:CIT502 3.5 16.5 1.0 ND2 A:ASN105 3.6 10.9 1.0 MN A:MN402 3.6 9.5 1.0 CA A:HIS246 3.8 8.2 1.0 OD1 A:ASP16 3.8 8.7 1.0 CB A:HIS246 3.9 8.9 1.0 C5 A:CIT502 4.1 17.8 1.0 O3 A:CIT502 4.2 21.7 1.0 O A:HIS246 4.2 8.9 1.0 O A:HOH398 4.2 11.8 1.0 N A:ASN105 4.3 8.4 1.0 CB A:ASP61 4.3 7.7 1.0 CG A:HIS213 4.4 7.5 1.0 NE2 A:HIS246 4.4 9.7 1.0 ND1 A:HIS213 4.4 8.4 1.0 CD2 A:HIS106 4.5 9.7 1.0 CB A:ASN105 4.5 9.2 1.0 C A:HIS246 4.5 8.3 1.0 CD2 A:HIS246 4.6 8.6 1.0 N A:HIS246 4.7 7.6 1.0 CG A:ASP16 4.9 7.6 1.0 CA A:ASN105 5.0 8.2 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg404 b:7.7 occ:1.00 OD1 B:ASN105 2.2 9.4 1.0 NE2 B:HIS213 2.3 8.0 1.0 O B:HOH734 2.3 12.9 1.0 OD2 B:ASP61 2.4 8.4 1.0 ND1 B:HIS246 2.4 8.5 1.0 CG B:ASP61 3.1 7.5 1.0 CD2 B:HIS213 3.2 7.6 1.0 CE1 B:HIS246 3.3 8.2 1.0 CG B:ASN105 3.3 9.1 1.0 CE1 B:HIS213 3.3 7.6 1.0 OD1 B:ASP61 3.5 7.7 1.0 MN B:MN401 3.5 8.2 1.0 CG B:HIS246 3.5 8.2 1.0 O2 B:CIT501 3.6 15.8 1.0 CA B:HIS246 3.7 7.7 1.0 OD1 B:ASP16 3.7 7.8 1.0 ND2 B:ASN105 3.7 10.3 1.0 CB B:HIS246 3.9 8.0 1.0 C1 B:CIT501 4.2 15.1 1.0 O B:HIS246 4.2 8.2 1.0 O B:HOH396 4.2 11.1 1.0 O1 B:CIT501 4.2 19.4 1.0 CB B:ASP61 4.3 7.3 1.0 N B:ASN105 4.4 7.8 1.0 ND1 B:HIS213 4.4 7.5 1.0 CG B:HIS213 4.4 7.2 1.0 C B:HIS246 4.4 7.6 1.0 NE2 B:HIS246 4.5 8.8 1.0 CD2 B:HIS106 4.5 8.9 1.0 CB B:ASN105 4.6 8.6 1.0 CD2 B:HIS246 4.6 8.2 1.0 N B:HIS246 4.6 7.1 1.0 CG B:ASP16 4.8 7.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Calcineurin-Like Phosphoesterase Yfkn From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg405 b:19.3 occ:1.00 O B:HOH384 2.8 9.9 1.0 O4 B:CIT501 2.8 18.3 1.0 OD1 B:ASN109 3.0 12.0 1.0 ND2 B:ASN105 3.1 10.3 1.0 ND1 B:HIS106 3.3 9.1 1.0 CE1 B:HIS106 3.4 9.3 1.0 O B:ASN105 3.6 7.9 1.0 C5 B:CIT501 3.6 21.3 1.0 C B:ASN105 3.7 7.7 1.0 C4 B:CIT501 3.7 15.7 1.0 CG B:HIS106 3.8 8.0 1.0 CB B:ASN105 3.8 8.6 1.0 NE2 B:HIS106 3.8 10.1 1.0 N B:HIS106 3.9 7.9 1.0 CG B:ASN105 3.9 9.1 1.0 CB B:TRP175 3.9 10.5 1.0 CA B:HIS106 4.0 7.7 1.0 OD2 B:ASP176 4.0 11.2 1.0 CG B:ASN109 4.0 9.8 1.0 CD2 B:HIS106 4.0 8.9 1.0 ND2 B:ASN109 4.2 9.0 1.0 CA B:ASN105 4.4 7.6 1.0 CE3 B:TRP175 4.4 10.4 1.0 CB B:HIS106 4.5 8.0 1.0 CG B:TRP175 4.5 11.6 1.0 CD2 B:TRP175 4.6 10.5 1.0 O B:HOH494 4.7 29.0 1.0 O3 B:CIT501 4.8 22.4 1.0 CG B:ASP176 4.9 10.8 1.0

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