Iron 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:

Magnesium

(Mg)

6 atoms

The binding sites of Iron 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 Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of A Conserved Metalloprotein From Bacillus Cereus, PDB code: 3d19:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:41.7 occ:1.00 OE2 A:GLU259 2.1 38.5 1.0 OE1 A:GLU128 2.1 47.1 1.0 NE2 A:HIS37 2.3 39.0 1.0 NE2 A:HIS255 2.3 35.2 1.0 O A:HOH327 2.4 42.1 1.0 CD A:GLU128 3.0 45.8 1.0 MG A:MG301 3.0 31.0 1.0 CD A:GLU259 3.1 37.5 1.0 CE1 A:HIS37 3.2 40.8 1.0 CD2 A:HIS255 3.2 37.4 1.0 OE2 A:GLU128 3.2 49.5 1.0 CD2 A:HIS37 3.3 37.4 1.0 CE1 A:HIS255 3.3 41.1 1.0 OE1 A:GLU259 3.5 40.0 1.0 CG2 A:ILE33 3.6 27.8 1.0 ND1 A:HIS37 4.3 40.4 1.0 CG A:HIS255 4.4 35.6 1.0 CG A:HIS37 4.4 37.6 1.0 CG A:GLU128 4.4 38.5 1.0 CG A:GLU259 4.4 36.1 1.0 ND1 A:HIS255 4.4 37.7 1.0 CD1 A:ILE33 4.6 26.1 1.0 NE2 A:HIS124 4.7 27.7 1.0 CD2 A:HIS124 4.9 28.7 1.0 CB A:ILE33 4.9 31.1 1.0 CB A:GLU128 4.9 36.8 1.0 NE2 A:HIS165 4.9 37.2 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:42.1 occ:1.00 OE2 B:GLU259 2.1 31.6 1.0 OE1 B:GLU128 2.1 36.0 1.0 NE2 B:HIS37 2.2 30.4 1.0 NE2 B:HIS255 2.3 38.8 1.0 O B:HOH341 2.6 43.8 1.0 MG B:MG301 3.0 37.2 1.0 CD B:GLU128 3.0 34.1 1.0 CD B:GLU259 3.0 30.4 1.0 CE1 B:HIS37 3.1 33.1 1.0 OE2 B:GLU128 3.2 35.6 1.0 CE1 B:HIS255 3.2 37.0 1.0 OE1 B:GLU259 3.3 26.8 1.0 CD2 B:HIS37 3.3 33.4 1.0 CD2 B:HIS255 3.3 38.6 1.0 CG2 B:ILE33 3.4 32.7 1.0 ND1 B:HIS37 4.3 32.6 1.0 ND1 B:HIS255 4.4 38.2 1.0 CG B:GLU259 4.4 32.0 1.0 CG B:HIS37 4.4 34.5 1.0 CG B:HIS255 4.4 39.1 1.0 CG B:GLU128 4.4 32.9 1.0 NE2 B:HIS124 4.5 33.6 1.0 CD2 B:HIS124 4.6 32.2 1.0 CB B:ILE33 4.8 30.5 1.0 NE2 B:HIS165 4.9 28.5 1.0 CB B:GLU128 4.9 34.4 1.0 CD1 B:ILE33 4.9 25.1 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:38.7 occ:1.00 OE1 C:GLU128 2.1 33.2 1.0 NE2 C:HIS37 2.1 37.2 1.0 OE2 C:GLU259 2.2 33.4 1.0 O C:HOH312 2.3 40.5 1.0 NE2 C:HIS255 2.3 28.5 1.0 CD C:GLU128 3.0 32.6 1.0 MG C:MG301 3.0 35.3 1.0 CE1 C:HIS37 3.1 34.8 1.0 CE1 C:HIS255 3.2 30.1 1.0 OE2 C:GLU128 3.2 33.5 1.0 CD2 C:HIS37 3.2 34.6 1.0 CD C:GLU259 3.2 30.4 1.0 CD2 C:HIS255 3.4 30.8 1.0 CG2 C:ILE33 3.5 30.4 1.0 OE1 C:GLU259 3.6 30.6 1.0 ND1 C:HIS37 4.2 33.0 1.0 CG C:HIS37 4.3 33.7 1.0 ND1 C:HIS255 4.3 27.4 1.0 CG C:GLU128 4.4 31.2 1.0 NE2 C:HIS124 4.4 37.0 1.0 CG C:HIS255 4.5 30.9 1.0 CD1 C:ILE33 4.5 28.7 1.0 CG C:GLU259 4.6 33.7 1.0 CD2 C:HIS124 4.6 35.4 1.0 CB C:GLU128 4.8 33.5 1.0 CB C:ILE33 4.8 33.0 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:47.0 occ:1.00 OE1 D:GLU128 2.1 53.3 1.0 O D:HOH310 2.2 39.7 1.0 OE2 D:GLU259 2.2 38.3 1.0 NE2 D:HIS255 2.2 41.7 1.0 NE2 D:HIS37 2.3 42.0 1.0 CD D:GLU259 3.0 39.5 1.0 MG D:MG301 3.0 35.9 1.0 CE1 D:HIS37 3.1 43.6 1.0 CD D:GLU128 3.1 48.7 1.0 OE1 D:GLU259 3.1 38.7 1.0 CD2 D:HIS255 3.1 43.1 1.0 OE2 D:GLU128 3.3 49.5 1.0 CE1 D:HIS255 3.3 39.8 1.0 CD2 D:HIS37 3.4 42.5 1.0 CG2 D:ILE33 3.6 38.8 1.0 ND1 D:HIS37 4.3 43.6 1.0 CG D:HIS255 4.3 39.5 1.0 ND1 D:HIS255 4.4 40.6 1.0 CG D:GLU128 4.5 45.5 1.0 CG D:HIS37 4.5 44.4 1.0 CG D:GLU259 4.5 37.9 1.0 NE2 D:HIS124 4.5 45.3 1.0 CD2 D:HIS124 4.7 45.3 1.0 CD1 D:ILE33 4.8 39.0 1.0 CB D:GLU128 4.8 43.5 1.0 CB D:ILE33 4.8 40.9 1.0 CG2 D:THR125 5.0 40.2 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:53.8 occ:1.00 OE1 E:GLU128 2.0 45.0 1.0 OE2 E:GLU259 2.1 55.5 1.0 NE2 E:HIS255 2.2 50.1 1.0 NE2 E:HIS37 2.3 43.9 1.0 O E:HOH308 2.6 43.6 1.0 CD E:GLU128 2.8 44.5 1.0 MG E:MG301 2.9 40.2 1.0 OE2 E:GLU128 3.0 44.6 1.0 CD E:GLU259 3.1 55.1 1.0 CE1 E:HIS37 3.1 42.4 1.0 CE1 E:HIS255 3.1 50.9 1.0 CD2 E:HIS255 3.2 51.4 1.0 OE1 E:GLU259 3.3 58.0 1.0 CD2 E:HIS37 3.4 44.4 1.0 CG2 E:ILE33 3.5 46.9 1.0 CG E:GLU128 4.3 45.3 1.0 ND1 E:HIS255 4.3 51.4 1.0 ND1 E:HIS37 4.3 43.6 1.0 CG E:HIS255 4.4 50.9 1.0 CG E:GLU259 4.5 52.5 1.0 CG E:HIS37 4.5 45.3 1.0 NE2 E:HIS124 4.6 39.8 1.0 CD2 E:HIS124 4.7 41.0 1.0 CB E:GLU128 4.7 45.5 1.0 CB E:ILE33 4.9 47.9 1.0 CD1 E:ILE33 5.0 42.5 1.0 NE2 E:HIS165 5.0 42.6 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe302 b:45.1 occ:1.00 NE2 F:HIS37 2.1 38.7 1.0 OE2 F:GLU259 2.2 36.8 1.0 OE1 F:GLU128 2.2 44.3 1.0 O F:HOH316 2.3 52.0 1.0 NE2 F:HIS255 2.4 43.1 1.0 CE1 F:HIS37 2.8 38.8 1.0 CD F:GLU128 3.0 42.8 1.0 MG F:MG301 3.1 36.4 1.0 CD F:GLU259 3.2 39.0 1.0 OE2 F:GLU128 3.2 43.2 1.0 CD2 F:HIS37 3.2 37.4 1.0 CD2 F:HIS255 3.4 42.6 1.0 OE1 F:GLU259 3.4 43.7 1.0 CE1 F:HIS255 3.4 43.3 1.0 CG2 F:ILE33 3.6 41.9 1.0 ND1 F:HIS37 4.0 40.0 1.0 CG F:HIS37 4.3 39.8 1.0 CG F:GLU128 4.5 42.0 1.0 NE2 F:HIS124 4.5 38.1 1.0 ND1 F:HIS255 4.5 39.3 1.0 CG F:HIS255 4.5 40.4 1.0 CG F:GLU259 4.6 41.3 1.0 CD2 F:HIS124 4.6 38.1 1.0 CD1 F:ILE33 4.7 42.6 1.0 CB F:ILE33 4.8 43.3 1.0 CB F:GLU128 4.9 42.5 1.0 CG2 F:THR125 5.0 38.9 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.