Iron in PDB 3qb9: Mycobacterium Tuberculosis Bacterioferritin, Bfra

The structure of Mycobacterium Tuberculosis Bacterioferritin, Bfra, PDB code: 3qb9 was solved by L.M.Mcmath, C.W.Goulding, Tb Structural Genomics Consortium (Tbsgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.32 / 2.11
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	124.343, 124.343, 174.976, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 23.6

The structure of Mycobacterium Tuberculosis Bacterioferritin, Bfra also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iron atom in the Mycobacterium Tuberculosis Bacterioferritin, Bfra (pdb code 3qb9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 15 binding sites of Iron where determined in the Mycobacterium Tuberculosis Bacterioferritin, Bfra, PDB code: 3qb9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:67.8 occ:0.50 OE2 A:GLU51 2.4 59.3 1.0 OE2 A:GLU94 2.5 77.3 1.0 OE2 A:GLU127 2.6 54.5 1.0 ND1 A:HIS130 3.0 46.2 1.0 CD A:GLU127 3.3 59.3 1.0 OE1 A:GLU127 3.4 68.8 1.0 CD A:GLU94 3.5 63.6 1.0 CD A:GLU51 3.6 50.2 1.0 OE1 A:GLU47 3.6 59.8 1.0 CG A:HIS130 3.7 42.8 1.0 CB A:HIS130 3.7 31.4 1.0 OE1 A:GLU94 3.8 65.3 1.0 O A:HOH503 3.9 40.8 1.0 CE1 A:HIS130 4.0 44.1 1.0 FE A:FE201 4.1 53.9 0.5 OE1 A:GLU51 4.3 54.5 1.0 CE2 A:TYR25 4.3 32.9 1.0 OH A:TYR25 4.5 41.2 1.0 CG A:GLU127 4.6 44.5 1.0 CG A:GLU51 4.7 41.7 1.0 CA A:GLU127 4.7 30.5 1.0 CD2 A:HIS130 4.8 45.8 1.0 CD A:GLU47 4.8 63.5 1.0 CG A:GLU94 4.9 41.6 1.0 O A:ASP126 4.9 25.6 1.0 CZ A:TYR25 4.9 40.3 1.0 NE2 A:HIS130 4.9 40.5 1.0 O A:HOH509 4.9 44.7 1.0

Iron binding site 2 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:53.9 occ:0.50 OE1 A:GLU51 2.2 54.5 1.0 O A:HOH509 2.2 44.7 1.0 ND1 A:HIS54 2.5 51.8 1.0 OE1 A:GLU18 2.7 41.5 1.0 OE2 A:GLU127 2.7 54.5 1.0 CD A:GLU51 3.0 50.2 1.0 OE2 A:GLU18 3.0 38.3 1.0 OE2 A:GLU51 3.1 59.3 1.0 O A:HOH503 3.1 40.8 1.0 CD A:GLU18 3.2 37.8 1.0 CE1 A:HIS54 3.3 52.4 1.0 CD A:GLU127 3.5 59.3 1.0 CG A:HIS54 3.6 46.9 1.0 CB A:HIS54 4.0 32.0 1.0 OE1 A:GLU127 4.0 68.8 1.0 FE A:FE202 4.1 67.8 0.5 CG2 A:ILE123 4.3 19.8 1.0 CG A:GLU127 4.3 44.5 1.0 CG A:GLU51 4.4 41.7 1.0 O A:HOH508 4.4 39.1 1.0 NE2 A:HIS54 4.5 51.7 1.0 CA A:GLU51 4.5 30.2 1.0 CD2 A:HIS54 4.6 48.9 1.0 CG A:GLU18 4.7 36.5 1.0 CB A:GLU51 4.8 40.7 1.0

Iron binding site 3 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:0.8 occ:1.00 FE C:HEM301 0.0 0.8 1.0 NC C:HEM301 2.1 95.0 1.0 NA C:HEM301 2.1 0.1 1.0 NB C:HEM301 2.1 90.7 1.0 ND C:HEM301 2.1 0.7 1.0 SD C:MET52 2.6 52.0 1.0 SD D:MET52 2.6 44.2 1.0 CE D:MET52 3.0 49.4 1.0 C1A C:HEM301 3.1 0.8 1.0 C4D C:HEM301 3.1 0.5 1.0 C1C C:HEM301 3.1 87.0 1.0 C4B C:HEM301 3.1 86.6 1.0 C4C C:HEM301 3.1 91.5 1.0 C4A C:HEM301 3.1 0.7 1.0 C1D C:HEM301 3.1 1.0 1.0 C1B C:HEM301 3.2 89.1 1.0 CHA C:HEM301 3.4 0.6 1.0 CHC C:HEM301 3.4 84.6 1.0 CE C:MET52 3.5 70.5 1.0 CHD C:HEM301 3.5 95.0 1.0 CHB C:HEM301 3.5 98.5 1.0 CG C:MET52 3.7 47.8 1.0 CG D:MET52 3.8 37.9 1.0 C2A C:HEM301 4.3 0.2 1.0 C3D C:HEM301 4.3 0.5 1.0 C2C C:HEM301 4.3 80.5 1.0 C3A C:HEM301 4.3 0.9 1.0 C2D C:HEM301 4.3 0.2 1.0 C3B C:HEM301 4.3 80.1 1.0 C3C C:HEM301 4.3 81.5 1.0 C2B C:HEM301 4.3 78.4 1.0 CB C:MET52 4.5 41.6 1.0 CB D:MET52 4.7 36.6 1.0

Iron binding site 4 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:64.6 occ:0.50 OE1 B:GLU51 2.2 58.9 1.0 OE2 B:GLU127 2.4 79.8 1.0 OE1 B:GLU18 2.5 47.2 1.0 O B:HOH521 2.5 45.4 1.0 ND1 B:HIS54 2.7 49.9 1.0 OE2 B:GLU18 2.9 59.4 1.0 CD B:GLU51 3.1 59.1 1.0 CD B:GLU18 3.1 46.7 1.0 OE2 B:GLU51 3.2 68.5 1.0 CD B:GLU127 3.6 74.1 1.0 CE1 B:HIS54 3.6 55.0 1.0 CG B:HIS54 3.7 49.8 1.0 FE B:FE202 3.8 73.5 0.5 CB B:HIS54 4.0 40.2 1.0 OE1 B:GLU127 4.3 78.5 1.0 CG2 B:ILE123 4.3 32.3 1.0 O B:HOH504 4.4 43.3 1.0 CG B:GLU51 4.5 52.8 1.0 CG B:GLU127 4.6 60.9 1.0 CG B:GLU18 4.6 38.3 1.0 CA B:GLU51 4.6 35.0 1.0 NE2 B:GLN14 4.7 32.0 1.0 NE2 B:HIS54 4.7 57.3 1.0 CD2 B:HIS54 4.8 49.6 1.0 CB B:GLU51 4.9 45.0 1.0

Iron binding site 5 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe301 b:0.1 occ:1.00 FE E:HEM301 0.0 0.1 1.0 NA E:HEM301 2.1 0.3 1.0 NC E:HEM301 2.1 0.9 1.0 NB E:HEM301 2.1 0.6 1.0 ND E:HEM301 2.1 1.0 1.0 SD E:MET52 2.4 46.3 1.0 SD F:MET52 2.7 41.1 1.0 C4A E:HEM301 3.1 0.2 1.0 C1A E:HEM301 3.1 0.2 1.0 CE F:MET52 3.1 60.2 1.0 C4D E:HEM301 3.1 0.9 1.0 C1B E:HEM301 3.1 96.0 1.0 C4C E:HEM301 3.1 0.9 1.0 C1D E:HEM301 3.1 0.3 1.0 C4B E:HEM301 3.1 99.2 1.0 C1C E:HEM301 3.1 0.8 1.0 CHA E:HEM301 3.4 0.3 1.0 CHB E:HEM301 3.5 0.2 1.0 CHD E:HEM301 3.5 0.6 1.0 CHC E:HEM301 3.5 0.6 1.0 CE E:MET52 3.6 57.8 1.0 CG E:MET52 3.8 44.5 1.0 CB E:MET52 4.2 40.0 1.0 C3A E:HEM301 4.3 0.0 1.0 C2A E:HEM301 4.3 0.4 1.0 CG F:MET52 4.3 25.8 1.0 C3D E:HEM301 4.3 0.2 1.0 C2D E:HEM301 4.3 0.7 1.0 C2B E:HEM301 4.3 82.6 1.0 C3B E:HEM301 4.3 87.4 1.0 C3C E:HEM301 4.3 0.2 1.0 C2C E:HEM301 4.3 0.7 1.0 CZ F:PHE49 4.8 65.6 1.0 CE1 F:PHE49 4.9 73.5 1.0

Iron binding site 6 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:73.5 occ:0.50 OE2 B:GLU51 2.5 68.5 1.0 OE2 B:GLU127 2.6 79.8 1.0 OE1 B:GLU127 2.7 78.5 1.0 CD B:GLU127 2.9 74.1 1.0 OE2 B:GLU94 3.0 71.2 1.0 CD B:GLU51 3.6 59.1 1.0 ND1 B:HIS130 3.7 58.4 1.0 FE B:FE201 3.8 64.6 0.5 CD B:GLU94 3.8 64.6 1.0 OE1 B:GLU94 4.0 71.5 1.0 O B:HOH521 4.0 45.4 1.0 OE1 B:GLU51 4.1 58.9 1.0 CB B:HIS130 4.1 40.8 1.0 OE1 B:GLU47 4.2 64.6 1.0 CG B:GLU127 4.2 60.9 1.0 CG B:HIS130 4.3 53.6 1.0 O B:HOH519 4.3 55.4 1.0 CA B:GLU127 4.3 39.7 1.0 O B:ASP126 4.6 43.8 1.0 CE1 B:HIS130 4.7 57.0 1.0 CB B:GLU127 4.7 47.0 1.0 N B:GLU127 4.8 36.3 1.0 CG B:GLU51 4.8 52.8 1.0 C B:ASP126 4.8 39.0 1.0 CE2 B:TYR25 4.9 31.8 1.0 OH B:TYR25 4.9 50.4 1.0 CE1 B:HIS54 4.9 55.0 1.0 ND1 B:HIS54 5.0 49.9 1.0

Iron binding site 7 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:0.3 occ:1.00 FE B:HEM301 0.0 0.3 1.0 NC B:HEM301 2.1 97.1 1.0 NB B:HEM301 2.1 93.6 1.0 NA B:HEM301 2.1 0.4 1.0 ND B:HEM301 2.2 0.5 1.0 SD A:MET52 2.4 40.2 1.0 SD B:MET52 2.6 44.5 1.0 C4D B:HEM301 3.1 0.5 1.0 C4B B:HEM301 3.1 88.5 1.0 C1C B:HEM301 3.1 91.3 1.0 C1A B:HEM301 3.1 0.1 1.0 CE A:MET52 3.1 43.9 1.0 C1D B:HEM301 3.1 0.4 1.0 C4C B:HEM301 3.1 93.8 1.0 C4A B:HEM301 3.2 0.1 1.0 C1B B:HEM301 3.2 88.3 1.0 CE B:MET52 3.2 33.9 1.0 CHA B:HEM301 3.4 0.3 1.0 CHC B:HEM301 3.4 88.8 1.0 CHD B:HEM301 3.5 96.8 1.0 CHB B:HEM301 3.5 96.1 1.0 CG A:MET52 3.8 32.6 1.0 CG B:MET52 3.9 37.2 1.0 C3D B:HEM301 4.3 0.4 1.0 C2D B:HEM301 4.3 0.8 1.0 C2C B:HEM301 4.3 87.3 1.0 C3B B:HEM301 4.3 78.2 1.0 C3C B:HEM301 4.3 84.1 1.0 C2A B:HEM301 4.3 0.8 1.0 C3A B:HEM301 4.4 0.1 1.0 C2B B:HEM301 4.4 73.5 1.0 CB A:MET52 4.7 33.6 1.0 CB B:MET52 4.7 36.0 1.0 CE1 A:PHE49 4.8 68.5 1.0

Iron binding site 8 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:63.8 occ:0.50 ND1 C:HIS54 2.3 49.7 1.0 OE1 C:GLU18 2.4 50.4 1.0 O C:HOH520 2.5 47.9 1.0 OE1 C:GLU51 2.5 59.8 1.0 OE2 C:GLU51 2.5 46.7 1.0 OE2 C:GLU127 2.7 52.4 1.0 CD C:GLU51 2.8 52.3 1.0 OE2 C:GLU18 2.9 59.6 1.0 CD C:GLU18 3.0 55.1 1.0 CE1 C:HIS54 3.1 55.1 1.0 CG C:HIS54 3.4 51.6 1.0 CB C:HIS54 3.7 46.8 1.0 CD C:GLU127 3.8 54.2 1.0 FE C:FE202 4.0 68.3 0.5 CG C:GLU51 4.2 49.1 1.0 CA C:GLU51 4.3 34.8 1.0 NE2 C:HIS54 4.3 57.8 1.0 CD2 C:HIS54 4.4 54.4 1.0 O C:HOH505 4.4 42.7 1.0 CG C:GLU18 4.5 40.6 1.0 O C:HOH511 4.5 54.8 1.0 CG2 C:ILE123 4.5 28.8 1.0 CB C:GLU51 4.6 36.5 1.0 OE1 C:GLU127 4.6 64.4 1.0 CG C:GLU127 4.7 41.5 1.0 NE2 C:GLN14 5.0 35.3 1.0 N C:GLU51 5.0 35.0 1.0

Iron binding site 9 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:68.3 occ:0.50 OE2 C:GLU94 2.7 71.2 1.0 OE2 C:GLU51 2.7 46.7 1.0 OE2 C:GLU127 2.8 52.4 1.0 OE1 C:GLU127 2.8 64.4 1.0 O C:HOH511 2.9 54.8 1.0 CD C:GLU127 3.2 54.2 1.0 CD C:GLU51 3.2 52.3 1.0 ND1 C:HIS130 3.2 57.2 1.0 OE1 C:GLU51 3.4 59.8 1.0 CD C:GLU94 3.6 60.0 1.0 OE1 C:GLU94 3.7 63.0 1.0 O C:HOH520 3.8 47.9 1.0 OE1 C:GLU47 3.9 67.5 1.0 FE C:FE201 4.0 63.8 0.5 CE2 C:TYR25 4.0 43.6 1.0 CE1 C:HIS130 4.0 53.7 1.0 CG C:HIS130 4.1 48.3 1.0 CG C:GLU51 4.2 49.1 1.0 CB C:HIS130 4.2 42.8 1.0 OH C:TYR25 4.3 44.4 1.0 CG C:GLU127 4.6 41.5 1.0 CZ C:TYR25 4.7 45.7 1.0 CA C:GLU127 4.9 34.2 1.0 CG C:GLU94 5.0 46.7 1.0

Iron binding site 10 out of 15 in the Mycobacterium Tuberculosis Bacterioferritin, Bfra


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Mycobacterium Tuberculosis Bacterioferritin, Bfra within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:53.9 occ:0.50 OE1 D:GLU18 2.4 56.0 1.0 OE2 D:GLU127 2.5 67.8 1.0 OE1 D:GLU51 2.5 58.3 1.0 ND1 D:HIS54 2.7 52.3 1.0 OE2 D:GLU51 2.8 48.7 1.0 CD D:GLU51 2.9 50.2 1.0 CD D:GLU18 3.2 50.0 1.0 OE2 D:GLU18 3.2 54.4 1.0 O D:HOH506 3.2 60.3 1.0 CD D:GLU127 3.4 62.3 1.0 CE1 D:HIS54 3.5 54.9 1.0 CG D:HIS54 3.7 50.6 1.0 OE1 D:GLU127 3.9 66.7 1.0 CB D:HIS54 4.0 42.2 1.0 FE D:FE202 4.3 75.3 0.5 CG D:GLU51 4.3 43.0 1.0 CG2 D:ILE123 4.5 23.2 1.0 CG D:GLU127 4.5 54.7 1.0 CA D:GLU51 4.5 29.1 1.0 CG D:GLU18 4.6 45.6 1.0 NE2 D:HIS54 4.7 57.5 1.0 CB D:GLU51 4.8 36.1 1.0 CD2 D:HIS54 4.8 52.5 1.0 NE2 D:GLN14 4.9 35.6 1.0

L.M.Mcmath, C.W.Goulding. Mycobacterium Tuberculosis Bacterioferritin, Bfra To Be Published.