Magnesium in PDB 4r7o: Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci

The structure of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci, PDB code: 4r7o was solved by Y.Kim, M.Zhou, S.Shatsman, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.70 / 2.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	209.644, 85.891, 191.539, 90.00, 121.33, 90.00
R / Rfree (%)	15.4 / 20.4

The binding sites of Magnesium atom in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci (pdb code 4r7o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci, PDB code: 4r7o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


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 Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:18.8 occ:1.00 O A:HOH603 2.2 42.1 1.0 O3 A:GOL405 2.3 57.9 1.0 OE1 A:GLU152 2.3 50.3 1.0 OE2 A:GLU70 2.4 29.8 1.0 O2 A:GOL405 2.4 52.9 1.0 OD1 A:ASP72 2.5 47.2 1.0 O A:HOH602 2.6 25.8 1.0 C3 A:GOL405 3.1 55.2 1.0 C2 A:GOL405 3.2 53.2 1.0 CD A:GLU152 3.5 46.4 1.0 CG A:ASP72 3.5 43.9 1.0 CD A:GLU70 3.6 33.2 1.0 C1 A:GOL405 3.8 51.2 1.0 OD2 A:ASP72 3.9 38.8 1.0 O1 A:GOL405 4.0 55.2 1.0 NE2 A:GLN188 4.0 27.1 1.0 OE2 A:GLU152 4.1 47.9 1.0 OE1 A:GLU70 4.1 36.2 1.0 NE2 A:HIS43 4.3 32.4 1.0 CB A:GLU152 4.5 30.9 1.0 CD2 A:HIS85 4.5 38.0 1.0 CG A:GLU152 4.6 38.7 1.0 CD2 A:HIS43 4.7 31.7 1.0 OE1 A:GLN188 4.7 35.0 1.0 CD A:GLN188 4.7 27.0 1.0 NE2 A:HIS85 4.8 39.5 1.0 CG A:GLU70 4.8 27.9 1.0 CB A:ASP72 4.9 34.5 1.0

Magnesium binding site 2 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


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 Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:29.0 occ:1.00 OE2 B:GLU152 2.1 43.8 1.0 O B:HOH597 2.5 64.1 1.0 OE2 B:GLU70 2.5 38.6 1.0 OD1 B:ASP72 2.6 48.5 1.0 O B:HOH598 3.0 45.7 1.0 O B:HOH595 3.1 41.9 1.0 CD B:GLU152 3.3 40.7 1.0 CG B:ASP72 3.5 42.4 1.0 CD B:GLU70 3.7 42.2 1.0 OD2 B:ASP72 3.8 41.6 1.0 OE1 B:GLU152 4.0 43.5 1.0 NE2 B:GLN188 4.0 30.2 1.0 OE1 B:GLU70 4.2 45.0 1.0 CB B:GLU152 4.4 26.9 1.0 NE2 B:HIS43 4.4 36.9 1.0 CG B:GLU152 4.4 30.5 1.0 OE1 B:GLN188 4.5 29.0 1.0 CD B:GLN188 4.6 29.3 1.0 CD2 B:HIS85 4.6 39.9 1.0 CD2 B:HIS43 4.8 30.1 1.0 CG B:GLU70 4.9 35.0 1.0 CB B:ASP72 4.9 32.9 1.0

Magnesium binding site 3 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


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 Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:28.1 occ:1.00 O C:HOH616 2.1 38.8 1.0 OE2 C:GLU152 2.3 49.1 1.0 OE2 C:GLU70 2.4 38.1 1.0 O C:HOH614 2.4 41.2 1.0 OD1 C:ASP72 2.5 33.6 1.0 O C:HOH615 2.7 39.5 1.0 O C:HOH617 3.1 33.9 1.0 CD C:GLU70 3.4 36.9 1.0 CD C:GLU152 3.5 41.6 1.0 CG C:ASP72 3.6 32.2 1.0 OE1 C:GLU70 3.8 43.8 1.0 OD2 C:ASP72 3.9 36.0 1.0 NE2 C:GLN188 4.1 34.8 1.0 OE1 C:GLU152 4.1 35.8 1.0 NE2 C:HIS43 4.2 37.9 1.0 CD2 C:HIS85 4.4 42.5 1.0 CB C:GLU152 4.5 29.0 1.0 OE1 C:GLN188 4.5 38.6 1.0 CD2 C:HIS43 4.6 32.2 1.0 CG C:GLU152 4.6 34.1 1.0 CD C:GLN188 4.6 30.4 1.0 NE2 C:HIS85 4.7 41.2 1.0 CG C:GLU70 4.7 26.8 1.0 CB C:ASP72 4.9 28.8 1.0

Magnesium binding site 4 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:34.0 occ:1.00 OE2 D:GLU152 2.2 49.4 1.0 OE2 D:GLU70 2.4 36.0 1.0 O D:HOH515 2.4 44.3 1.0 OD1 D:ASP72 2.5 40.4 1.0 O D:HOH589 2.6 34.5 1.0 O D:HOH592 2.9 35.1 1.0 CD D:GLU152 3.5 48.8 1.0 CD D:GLU70 3.6 32.9 1.0 CG D:ASP72 3.6 35.3 1.0 O D:HOH591 3.8 30.7 1.0 OD2 D:ASP72 3.9 33.4 1.0 OE1 D:GLU70 4.0 36.4 1.0 NE2 D:GLN188 4.1 36.2 1.0 NE2 D:HIS43 4.1 42.5 1.0 OE1 D:GLU152 4.2 52.9 1.0 CB D:GLU152 4.3 33.5 1.0 CG D:GLU152 4.5 40.0 1.0 OE1 D:GLN188 4.6 46.7 1.0 CD2 D:HIS43 4.6 37.3 1.0 CD D:GLN188 4.7 41.0 1.0 CD2 D:HIS85 4.7 39.9 1.0 CG D:GLU70 4.8 28.6 1.0 CB D:ASP72 4.9 25.1 1.0 O D:HOH558 5.0 32.2 1.0

Magnesium binding site 5 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:29.2 occ:1.00 OE2 E:GLU152 2.3 49.1 1.0 OE2 E:GLU70 2.3 40.4 1.0 OD1 E:ASP72 2.4 41.0 1.0 O E:HOH612 2.4 38.4 1.0 O E:HOH577 2.6 31.9 1.0 O E:HOH613 2.6 54.7 1.0 CG E:ASP72 3.3 38.4 1.0 CD E:GLU70 3.4 39.3 1.0 CD E:GLU152 3.5 42.0 1.0 OD2 E:ASP72 3.5 44.0 1.0 O E:HOH611 3.6 37.2 1.0 OE1 E:GLU70 3.9 45.7 1.0 OE1 E:GLU152 4.1 48.8 1.0 NE2 E:HIS43 4.2 40.2 1.0 CD2 E:HIS85 4.3 32.5 1.0 NE2 E:GLN188 4.4 26.4 1.0 CB E:GLU152 4.6 26.2 1.0 CG E:GLU152 4.6 31.9 1.0 OE1 E:GLN188 4.6 35.7 1.0 CD2 E:HIS43 4.6 38.1 1.0 CG E:GLU70 4.7 32.4 1.0 CB E:ASP72 4.8 21.4 1.0 NE2 E:HIS85 4.8 35.5 1.0 CD E:GLN188 4.8 31.5 1.0 NE E:ARG44 5.0 36.2 1.0

Magnesium binding site 6 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:51.5 occ:1.00 O E:ASP90 2.1 31.1 1.0 O E:HOH505 2.2 25.1 1.0 O E:HOH574 2.3 28.3 1.0 O E:THR93 2.5 27.5 1.0 O A:TRP224 2.5 30.4 1.0 C E:ASP90 3.3 27.8 1.0 C A:TRP224 3.6 21.2 1.0 O A:HOH503 3.6 30.4 1.0 C E:THR93 3.7 26.9 1.0 CA A:SER225 3.8 27.3 1.0 C A:SER225 3.9 31.2 1.0 O E:ARG91 4.0 29.6 1.0 O A:SER225 4.1 34.3 1.0 CA E:ASP90 4.1 26.2 1.0 C E:ARG91 4.2 22.1 1.0 N A:SER225 4.2 20.7 1.0 O A:HOH520 4.2 22.8 1.0 N E:THR93 4.2 24.9 1.0 O A:HOH577 4.3 34.7 1.0 N E:ARG91 4.3 23.6 1.0 CA E:ARG91 4.4 20.3 1.0 N A:GLY226 4.5 27.1 1.0 O E:GLY95 4.5 29.4 1.0 CA E:THR93 4.6 23.4 1.0 N E:ASN94 4.6 29.6 1.0 CA E:ASN94 4.6 30.9 1.0 N E:THR92 4.7 20.1 1.0 CD1 A:TRP224 4.7 30.0 1.0 CA A:TRP224 4.8 19.0 1.0 CB E:ASP90 4.9 30.4 1.0 O E:VAL89 4.9 26.0 1.0 O A:GLU223 4.9 29.2 1.0

Magnesium binding site 7 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg401 b:36.3 occ:1.00 OE1 F:GLU152 2.1 54.5 1.0 O F:HOH578 2.1 40.1 1.0 OE2 F:GLU70 2.3 42.7 1.0 O F:HOH583 2.3 45.2 1.0 O F:HOH577 2.6 34.8 1.0 OD1 F:ASP72 2.7 40.9 1.0 CD F:GLU152 3.3 52.8 1.0 O F:HOH582 3.4 58.7 1.0 CD F:GLU70 3.5 42.2 1.0 CG F:ASP72 3.7 41.0 1.0 OD2 F:ASP72 4.0 38.8 1.0 OE1 F:GLU70 4.0 43.2 1.0 NE2 F:GLN188 4.0 44.5 1.0 OE2 F:GLU152 4.1 55.3 1.0 NE2 F:HIS43 4.2 47.0 1.0 CB F:GLU152 4.2 31.1 1.0 OE1 F:GLN188 4.2 35.7 1.0 CG F:GLU152 4.4 48.4 1.0 CD F:GLN188 4.5 37.9 1.0 CD2 F:HIS43 4.5 41.7 1.0 CG F:GLU70 4.7 36.6 1.0 CD2 F:HIS85 4.7 43.5 1.0 NE2 F:HIS85 4.9 45.0 1.0

Magnesium binding site 8 out of 8 in the Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg401 b:44.9 occ:1.00 O G:HOH520 2.3 50.0 1.0 O G:HOH522 2.4 55.1 1.0 OD1 G:ASP72 2.4 64.6 1.0 OE2 G:GLU70 2.4 58.5 1.0 O G:HOH521 2.5 46.4 1.0 OE2 G:GLU152 2.5 70.3 1.0 CG G:ASP72 3.5 62.8 1.0 CD G:GLU70 3.5 51.9 1.0 O G:HOH519 3.6 51.2 1.0 CD G:GLU152 3.7 69.6 1.0 OE1 G:GLU70 3.8 52.8 1.0 OD2 G:ASP72 3.8 59.1 1.0 NE2 G:GLN188 3.9 49.9 1.0 NE2 G:HIS43 4.2 55.1 1.0 CD2 G:HIS85 4.4 56.9 1.0 OE1 G:GLU152 4.4 74.7 1.0 CB G:GLU152 4.6 44.8 1.0 CD2 G:HIS43 4.7 54.2 1.0 OE1 G:GLN188 4.7 50.0 1.0 CD G:GLN188 4.7 50.5 1.0 NE2 G:HIS85 4.8 56.5 1.0 CG G:GLU152 4.8 55.5 1.0 CG G:GLU70 4.8 42.8 1.0 CB G:ASP72 4.8 57.2 1.0

Y.Kim, M.Zhou, S.Shatsman, W.F.Anderson, A.Joachimiak. Crystal Structure of Putative Glycerophosphoryl Diester Phosphodiesterasefrom Bacillus Anthraci To Be Published.