Magnesium in PDB 3d19: Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus

The structure of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19 was solved by J.B.Bonanno, Y.Patskovsky, J.Freeman, K.T.Bain, S.Chang, S.Ozyurt, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo, New York Sgx Researchcenter For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.825, 136.378, 87.060, 90.00, 102.84, 90.00
R / Rfree (%)	20.6 / 26.8

The structure of Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus also contains other interesting chemical elements:

Iron

(Fe)

6 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus (pdb code 3d19). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:31.0 occ:1.00 O A:HOH327 1.9 42.1 1.0 OE2 A:GLU128 2.0 49.5 1.0 OE1 A:GLU259 2.2 40.0 1.0 NE2 A:HIS165 2.2 37.2 1.0 NE2 A:HIS124 2.3 27.7 1.0 CD A:GLU128 2.9 45.8 1.0 FE A:FE302 3.0 41.7 1.0 CD A:GLU259 3.0 37.5 1.0 CE1 A:HIS165 3.0 38.3 1.0 OE2 A:GLU259 3.1 38.5 1.0 CE1 A:HIS124 3.3 31.8 1.0 OE1 A:GLU128 3.3 47.1 1.0 CD2 A:HIS124 3.3 28.7 1.0 CD2 A:HIS165 3.4 34.8 1.0 CG2 A:ILE161 3.9 29.7 1.0 CG A:GLU128 4.1 38.5 1.0 ND1 A:HIS165 4.2 38.9 1.0 CG A:HIS165 4.4 35.4 1.0 ND1 A:HIS124 4.4 34.4 1.0 CG A:GLU259 4.5 36.1 1.0 CG A:HIS124 4.5 35.3 1.0 NE2 A:HIS255 4.8 35.2 1.0 CG1 A:VAL256 4.8 35.7 1.0 CD2 A:HIS255 4.9 37.4 1.0 NE2 A:HIS37 4.9 39.0 1.0 CB A:GLU259 4.9 35.0 1.0

Magnesium binding site 2 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:37.2 occ:1.00 OE2 B:GLU128 2.0 35.6 1.0 OE1 B:GLU259 2.1 26.8 1.0 NE2 B:HIS124 2.1 33.6 1.0 NE2 B:HIS165 2.3 28.5 1.0 O B:HOH341 2.7 43.8 1.0 FE B:FE302 3.0 42.1 1.0 CD B:GLU128 3.1 34.1 1.0 CD2 B:HIS124 3.1 32.2 1.0 CD B:GLU259 3.1 30.4 1.0 CE1 B:HIS165 3.1 30.1 1.0 CE1 B:HIS124 3.2 32.4 1.0 CD2 B:HIS165 3.3 32.6 1.0 OE1 B:GLU128 3.4 36.0 1.0 OE2 B:GLU259 3.4 31.6 1.0 CG2 B:ILE161 4.0 29.1 1.0 CG B:HIS124 4.2 34.2 1.0 ND1 B:HIS124 4.3 29.1 1.0 CG1 B:ILE161 4.3 31.3 1.0 ND1 B:HIS165 4.3 31.0 1.0 CG B:GLU128 4.4 32.9 1.0 CG B:HIS165 4.4 32.5 1.0 NE2 B:HIS255 4.5 38.8 1.0 CG B:GLU259 4.5 32.0 1.0 CD2 B:HIS255 4.7 38.6 1.0 CB B:GLU259 4.9 33.1 1.0 NE2 B:HIS37 4.9 30.4 1.0 CB B:ILE161 4.9 31.0 1.0

Magnesium binding site 3 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:35.3 occ:1.00 OE2 C:GLU128 2.0 33.5 1.0 NE2 C:HIS124 2.2 37.0 1.0 OE1 C:GLU259 2.3 30.6 1.0 NE2 C:HIS165 2.4 28.1 1.0 O C:HOH312 2.4 40.5 1.0 CD C:GLU128 3.0 32.6 1.0 FE C:FE302 3.0 38.7 1.0 CD C:GLU259 3.1 30.4 1.0 CE1 C:HIS124 3.1 35.2 1.0 OE2 C:GLU259 3.2 33.4 1.0 CD2 C:HIS124 3.2 35.4 1.0 CE1 C:HIS165 3.3 27.0 1.0 OE1 C:GLU128 3.3 33.2 1.0 CD2 C:HIS165 3.4 25.6 1.0 CG2 C:ILE161 3.9 35.8 1.0 ND1 C:HIS124 4.3 35.6 1.0 CG C:GLU128 4.3 31.2 1.0 CG C:HIS124 4.3 35.8 1.0 NE2 C:HIS255 4.3 28.5 1.0 ND1 C:HIS165 4.4 24.6 1.0 CG C:GLU259 4.5 33.7 1.0 CG C:HIS165 4.5 28.1 1.0 CD2 C:HIS255 4.6 30.8 1.0 CG1 C:VAL256 4.8 30.5 1.0 NE2 C:HIS37 4.8 37.2 1.0 CB C:GLU259 4.8 32.6 1.0

Magnesium binding site 4 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:35.9 occ:1.00 NE2 D:HIS124 2.1 45.3 1.0 OE2 D:GLU128 2.2 49.5 1.0 O D:HOH310 2.3 39.7 1.0 OE1 D:GLU259 2.3 38.7 1.0 NE2 D:HIS165 2.4 46.3 1.0 CE1 D:HIS124 3.0 44.7 1.0 FE D:FE302 3.0 47.0 1.0 CD2 D:HIS124 3.1 45.3 1.0 CD D:GLU128 3.2 48.7 1.0 CD2 D:HIS165 3.3 44.6 1.0 CD D:GLU259 3.4 39.5 1.0 CE1 D:HIS165 3.4 45.5 1.0 OE1 D:GLU128 3.5 53.3 1.0 OE2 D:GLU259 3.8 38.3 1.0 CG2 D:ILE161 4.1 34.8 1.0 ND1 D:HIS124 4.1 45.0 1.0 CG D:HIS124 4.2 42.2 1.0 CG D:HIS165 4.5 40.5 1.0 ND1 D:HIS165 4.5 43.1 1.0 CG D:GLU128 4.5 45.5 1.0 NE2 D:HIS255 4.6 41.7 1.0 CD2 D:HIS255 4.7 43.1 1.0 CG1 D:ILE161 4.7 36.6 1.0 CG D:GLU259 4.7 37.9 1.0 CG1 D:VAL256 4.8 36.6 1.0 NE2 D:HIS37 5.0 42.0 1.0 CB D:GLU259 5.0 35.7 1.0

Magnesium binding site 5 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg301 b:40.2 occ:1.00 OE1 E:GLU259 1.8 58.0 1.0 OE2 E:GLU128 1.9 44.6 1.0 O E:HOH308 2.2 43.6 1.0 NE2 E:HIS165 2.4 42.6 1.0 NE2 E:HIS124 2.6 39.8 1.0 CD E:GLU259 2.8 55.1 1.0 FE E:FE302 2.9 53.8 1.0 CD E:GLU128 2.9 44.5 1.0 CE1 E:HIS165 3.1 44.0 1.0 OE2 E:GLU259 3.1 55.5 1.0 OE1 E:GLU128 3.3 45.0 1.0 CD2 E:HIS124 3.4 41.0 1.0 CD2 E:HIS165 3.5 41.7 1.0 CE1 E:HIS124 3.6 44.3 1.0 CG2 E:ILE161 4.0 39.7 1.0 CG E:GLU259 4.2 52.5 1.0 NE2 E:HIS255 4.2 50.1 1.0 CG E:GLU128 4.2 45.3 1.0 ND1 E:HIS165 4.3 43.4 1.0 CD2 E:HIS255 4.4 51.4 1.0 CG E:HIS165 4.5 44.0 1.0 CB E:GLU259 4.6 51.1 1.0 CG E:HIS124 4.6 43.4 1.0 ND1 E:HIS124 4.7 45.1 1.0 CG1 E:VAL256 4.9 47.7 1.0 CG1 E:ILE161 4.9 42.0 1.0 NE2 E:HIS37 4.9 43.9 1.0

Magnesium binding site 6 out of 6 in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus


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 A Conserved Metalloprotein From Bacillus Cereus within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg301 b:36.4 occ:1.00 O F:HOH316 1.9 52.0 1.0 OE2 F:GLU128 2.0 43.2 1.0 OE1 F:GLU259 2.1 43.7 1.0 NE2 F:HIS165 2.2 43.1 1.0 NE2 F:HIS124 2.4 38.1 1.0 CD F:GLU259 3.0 39.0 1.0 CE1 F:HIS165 3.0 44.0 1.0 CD F:GLU128 3.1 42.8 1.0 FE F:FE302 3.1 45.1 1.0 CE1 F:HIS124 3.3 38.2 1.0 OE2 F:GLU259 3.3 36.8 1.0 CD2 F:HIS165 3.3 42.0 1.0 CD2 F:HIS124 3.4 38.1 1.0 OE1 F:GLU128 3.5 44.3 1.0 CG2 F:ILE161 3.6 36.0 1.0 ND1 F:HIS165 4.2 39.5 1.0 CG F:GLU259 4.4 41.3 1.0 CG F:HIS165 4.4 38.2 1.0 ND1 F:HIS124 4.4 40.7 1.0 CG F:GLU128 4.4 42.0 1.0 CG F:HIS124 4.5 41.3 1.0 NE2 F:HIS255 4.7 43.1 1.0 CB F:GLU259 4.7 41.2 1.0 CD2 F:HIS255 4.8 42.6 1.0 CD1 F:ILE161 4.9 34.4 1.0 NE2 F:HIS37 5.0 38.7 1.0 CB F:ILE161 5.0 38.0 1.0 CG1 F:VAL256 5.0 36.8 1.0

J.B.Bonanno, Y.Patskovsky, J.Freeman, K.T.Bain, S.Chang, S.Ozyurt, D.Smith, S.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus. To Be Published.