Iron in PDB 5zur: Achromobacter DH1F Bacterioferritin

The structure of Achromobacter DH1F Bacterioferritin, PDB code: 5zur was solved by A.Dwivedy, B.Jha, K.H.Singh, M.Ahmed, A.Ashraf, D.Kumar, B.K.Biswal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.70 / 1.95
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	158.665, 158.665, 118.061, 90.00, 90.00, 90.00
R / Rfree (%)	14.2 / 18.7

The structure of Achromobacter DH1F Bacterioferritin also contains other interesting chemical elements:

Barium	(Ba)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Iron atom in the Achromobacter DH1F Bacterioferritin (pdb code 5zur). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Achromobacter DH1F Bacterioferritin, PDB code: 5zur:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Achromobacter DH1F Bacterioferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Achromobacter DH1F Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:14.9 occ:0.40 FE A:HEM201 0.0 14.9 0.4 ND A:HEM201 1.9 17.8 0.5 NA A:HEM201 2.0 16.9 0.5 NC A:HEM201 2.1 16.8 0.5 NB A:HEM201 2.1 16.4 0.5 SD A:MET52 2.3 14.2 1.0 C4D A:HEM201 2.9 18.7 0.5 C1D A:HEM201 3.0 18.3 0.5 C1A A:HEM201 3.0 17.6 0.5 C4B A:HEM201 3.1 16.1 0.4 C4C A:HEM201 3.1 16.7 0.5 C1C A:HEM201 3.1 16.2 0.4 C1B A:HEM201 3.1 15.7 0.5 C4A A:HEM201 3.1 16.8 0.5 CE A:MET52 3.3 12.6 1.0 CHA A:HEM201 3.4 17.6 0.5 CHD A:HEM201 3.4 17.8 0.5 CHC A:HEM201 3.5 16.2 0.5 CG A:MET52 3.5 12.1 1.0 CHB A:HEM201 3.6 16.4 0.5 C3D A:HEM201 4.2 20.4 0.5 C2D A:HEM201 4.2 19.8 0.5 C2A A:HEM201 4.2 17.8 0.5 CB A:MET52 4.3 12.8 1.0 C3C A:HEM201 4.3 16.8 0.5 C2C A:HEM201 4.3 16.3 0.5 C3A A:HEM201 4.3 17.6 0.5 C3B A:HEM201 4.3 15.8 0.5 C2B A:HEM201 4.3 15.9 0.5

Iron binding site 2 out of 6 in the Achromobacter DH1F Bacterioferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Achromobacter DH1F Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:14.9 occ:1.00 ND1 A:HIS54 2.0 14.0 1.0 O A:HOH423 2.0 23.2 1.0 OE1 A:GLU51 2.0 18.2 1.0 OE1 A:GLU18 2.2 25.0 1.0 OE2 A:GLU18 2.4 17.5 1.0 CD A:GLU18 2.6 19.6 1.0 CE1 A:HIS54 2.9 13.9 1.0 CD A:GLU51 2.9 17.7 1.0 OE2 A:GLU51 3.1 20.3 1.0 CG A:HIS54 3.1 14.8 1.0 O A:HOH301 3.2 38.8 1.0 CB A:HIS54 3.6 12.3 1.0 O A:HOH410 3.8 20.6 1.0 O A:HOH380 3.9 21.1 1.0 NE2 A:HIS54 4.1 16.2 1.0 O A:HOH416 4.1 32.3 1.0 CG A:GLU18 4.2 14.3 1.0 CD2 A:HIS54 4.2 14.8 1.0 CG A:GLU51 4.2 14.2 1.0 O A:HOH371 4.3 23.4 1.0 CA A:GLU51 4.3 11.8 1.0 CG2 A:ILE123 4.4 10.1 1.0 CB A:GLU51 4.6 12.5 1.0 NE2 A:GLN14 4.7 11.3 1.0 OG1 A:THR127 4.7 13.2 1.0 O A:GLY50 4.9 12.8 1.0 CB A:GLU18 5.0 12.1 1.0

Iron binding site 3 out of 6 in the Achromobacter DH1F Bacterioferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Achromobacter DH1F Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:16.2 occ:1.00 OE1 B:GLU51 2.0 18.5 1.0 ND1 B:HIS54 2.0 14.0 1.0 O B:HOH433 2.1 26.6 1.0 OE1 B:GLU18 2.1 25.9 1.0 OE2 B:GLU18 2.5 21.8 1.0 CD B:GLU18 2.6 21.6 1.0 CD B:GLU51 2.9 16.1 1.0 CE1 B:HIS54 2.9 14.6 1.0 OE2 B:GLU51 3.1 20.1 1.0 CG B:HIS54 3.1 13.9 1.0 O B:HOH303 3.3 17.6 1.0 CB B:HIS54 3.5 12.1 1.0 O B:HOH369 3.8 19.9 1.0 O B:HOH401 3.9 24.0 1.0 O B:HOH424 4.0 33.0 1.0 O B:HOH449 4.0 28.3 1.0 NE2 B:HIS54 4.1 15.1 1.0 CG B:GLU18 4.1 16.4 1.0 CG B:GLU51 4.2 14.5 1.0 CD2 B:HIS54 4.2 13.2 1.0 O B:HOH382 4.2 22.6 1.0 CA B:GLU51 4.3 12.9 1.0 CG2 B:ILE123 4.4 11.2 1.0 CB B:GLU51 4.5 12.8 1.0 OG1 B:THR127 4.7 13.0 1.0 NE2 B:GLN14 4.8 12.1 1.0 CB B:GLU18 4.9 13.3 1.0 O B:GLY50 5.0 12.8 1.0 N B:GLU51 5.0 12.4 1.0

Iron binding site 4 out of 6 in the Achromobacter DH1F Bacterioferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Achromobacter DH1F Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:14.1 occ:0.40 FE B:HEM202 0.0 14.1 0.4 ND B:HEM202 1.9 18.3 0.5 NA B:HEM202 2.0 16.7 0.5 NC B:HEM202 2.1 17.0 0.5 NB B:HEM202 2.1 16.3 0.5 SD B:MET52 2.4 15.5 1.0 C1D B:HEM202 2.9 18.4 0.5 C4D B:HEM202 2.9 18.3 0.5 C1A B:HEM202 3.0 17.5 0.5 C4B B:HEM202 3.1 16.6 0.5 C4C B:HEM202 3.1 18.0 0.5 C4A B:HEM202 3.1 16.7 0.5 C1B B:HEM202 3.1 15.8 0.5 C1C B:HEM202 3.1 16.2 0.5 CE B:MET52 3.3 14.2 1.0 CHD B:HEM202 3.4 18.1 0.5 CHA B:HEM202 3.4 16.8 0.5 CG B:MET52 3.5 13.2 1.0 CHC B:HEM202 3.5 17.0 0.5 CHB B:HEM202 3.5 16.0 0.5 C3D B:HEM202 4.2 19.5 0.5 C2D B:HEM202 4.2 19.1 0.5 CB B:MET52 4.2 13.6 1.0 C2A B:HEM202 4.2 17.6 0.5 C3A B:HEM202 4.3 17.3 0.5 C3C B:HEM202 4.3 17.0 0.5 C2B B:HEM202 4.3 16.5 0.5 C2C B:HEM202 4.3 16.8 0.5 C3B B:HEM202 4.3 17.1 0.5

Iron binding site 5 out of 6 in the Achromobacter DH1F Bacterioferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Achromobacter DH1F Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:17.4 occ:0.40 FE C:HEM202 0.0 17.4 0.4 ND C:HEM202 1.9 21.6 0.5 NA C:HEM202 2.0 22.4 0.5 NC C:HEM202 2.1 20.1 0.5 NB C:HEM202 2.1 20.6 0.5 SD C:MET52 2.4 15.3 1.0 C1D C:HEM202 2.9 22.0 0.5 C4D C:HEM202 2.9 23.5 0.5 C1A C:HEM202 3.0 22.9 0.5 C4C C:HEM202 3.1 19.6 0.5 C4B C:HEM202 3.1 19.7 0.5 C1B C:HEM202 3.1 21.5 0.5 C4A C:HEM202 3.1 22.4 0.5 C1C C:HEM202 3.1 19.9 0.5 CE C:MET52 3.3 13.4 1.0 CHA C:HEM202 3.4 21.5 0.5 CHD C:HEM202 3.4 20.6 0.5 CG C:MET52 3.5 12.9 1.0 CHC C:HEM202 3.5 20.3 0.5 CHB C:HEM202 3.5 21.9 0.5 C2D C:HEM202 4.2 23.9 0.5 C3D C:HEM202 4.2 24.6 0.5 C2A C:HEM202 4.2 24.1 0.5 CB C:MET52 4.2 13.5 1.0 C3A C:HEM202 4.3 23.5 0.5 C3C C:HEM202 4.3 20.2 0.5 C2C C:HEM202 4.3 19.8 0.5 C2B C:HEM202 4.3 20.5 0.5 C3B C:HEM202 4.3 20.3 0.5

Iron binding site 6 out of 6 in the Achromobacter DH1F Bacterioferritin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Achromobacter DH1F Bacterioferritin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe203 b:16.3 occ:1.00 ND1 C:HIS54 2.0 14.4 1.0 OE1 C:GLU51 2.0 20.4 1.0 O C:HOH412 2.1 25.3 1.0 OE1 C:GLU18 2.3 26.5 1.0 OE2 C:GLU18 2.5 20.0 1.0 CD C:GLU18 2.7 19.4 1.0 CE1 C:HIS54 2.9 15.1 1.0 CD C:GLU51 2.9 18.9 1.0 OE2 C:GLU51 3.1 20.8 1.0 CG C:HIS54 3.1 14.8 1.0 O C:HOH301 3.3 18.5 1.0 CB C:HIS54 3.5 12.4 1.0 O C:HOH397 3.7 23.8 1.0 O C:HOH444 3.9 32.0 1.0 O C:HOH405 3.9 18.5 1.0 NE2 C:HIS54 4.0 14.7 1.0 CD2 C:HIS54 4.2 14.3 1.0 CG C:GLU18 4.2 16.6 1.0 O C:HOH432 4.2 37.8 1.0 O C:HOH378 4.2 24.5 1.0 CG C:GLU51 4.2 16.4 1.0 CA C:GLU51 4.3 12.9 1.0 CG2 C:ILE123 4.4 11.6 1.0 CB C:GLU51 4.6 13.8 1.0 OG1 C:THR127 4.7 12.7 1.0 NE2 C:GLN14 4.8 13.4 1.0 O C:GLY50 4.9 14.5 1.0 CB C:GLU18 5.0 13.3 1.0

A.Dwivedy, B.Jha, K.H.Singh, M.Ahmad, A.Ashraf, D.Kumar, B.K.Biswal. Serendipitous Crystallization and Structure Determination of Bacterioferritin From Achromobacter. Acta Crystallogr F Struct V. 74 558 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 30198888
DOI: 10.1107/S2053230X18009809