Iron in PDB 6jsb: Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum

The structure of Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum, PDB code: 6jsb was solved by N.Muraki, S.Aono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.09 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	235.170, 33.730, 126.620, 90.00, 121.14, 90.00
R / Rfree (%)	17.7 / 19.8

The structure of Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum (pdb code 6jsb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum, PDB code: 6jsb:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum


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 Heme Binding Protein Htab From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:18.0 occ:0.44 FE A:HEM301 0.0 18.0 0.4 FE A:HEM301 0.5 17.5 0.6 NA A:HEM301 1.8 19.6 0.6 ND A:HEM301 1.9 18.9 0.4 NC A:HEM301 2.1 18.2 0.4 ND A:HEM301 2.1 16.8 0.6 NB A:HEM301 2.1 15.4 0.6 NA A:HEM301 2.1 16.6 0.4 NB A:HEM301 2.2 19.1 0.4 NC A:HEM301 2.3 19.2 0.6 OH A:TYR56 2.5 17.9 1.0 C1A A:HEM301 2.8 19.4 0.6 C4D A:HEM301 2.9 19.5 0.4 C4A A:HEM301 2.9 18.3 0.6 C1D A:HEM301 3.0 18.9 0.4 C4D A:HEM301 3.0 18.0 0.6 C4C A:HEM301 3.0 17.1 0.4 CZ A:PHE209 3.0 23.0 1.0 C1B A:HEM301 3.0 18.2 0.6 C1A A:HEM301 3.0 17.6 0.4 C1C A:HEM301 3.1 19.2 0.4 C4A A:HEM301 3.1 18.6 0.4 C1D A:HEM301 3.1 19.0 0.6 C4B A:HEM301 3.1 19.2 0.6 C4B A:HEM301 3.2 18.6 0.4 C1B A:HEM301 3.2 17.6 0.4 CZ A:TYR56 3.2 17.6 1.0 C1C A:HEM301 3.2 18.6 0.6 CE1 A:PHE209 3.2 23.2 1.0 CHA A:HEM301 3.3 20.8 0.6 C4C A:HEM301 3.3 17.6 0.6 CHA A:HEM301 3.3 20.8 0.4 CHD A:HEM301 3.4 18.4 0.4 CHB A:HEM301 3.4 17.2 0.6 CE2 A:PHE209 3.4 21.1 1.0 CHC A:HEM301 3.5 19.7 0.4 CHC A:HEM301 3.6 19.2 0.6 CHB A:HEM301 3.6 17.6 0.4 CHD A:HEM301 3.6 17.7 0.6 CD1 A:PHE209 3.9 23.4 1.0 CE1 A:TYR56 3.9 18.9 1.0 CE2 A:TYR56 4.0 15.8 1.0 CD2 A:PHE209 4.0 19.5 1.0 C2A A:HEM301 4.1 20.9 0.6 C3A A:HEM301 4.1 21.5 0.6 C3D A:HEM301 4.1 20.7 0.4 C2D A:HEM301 4.2 21.5 0.4 CG A:PHE209 4.2 19.8 1.0 C3C A:HEM301 4.2 20.6 0.4 C3D A:HEM301 4.3 16.0 0.6 NE2 A:HIS113 4.3 20.3 1.0 C2A A:HEM301 4.3 16.2 0.4 C2C A:HEM301 4.3 19.8 0.4 C2B A:HEM301 4.3 20.0 0.6 C2D A:HEM301 4.3 17.0 0.6 C3A A:HEM301 4.3 16.9 0.4 C3B A:HEM301 4.3 19.9 0.6 C3B A:HEM301 4.4 17.6 0.4 C2B A:HEM301 4.4 16.6 0.4 C2C A:HEM301 4.5 16.5 0.6 C3C A:HEM301 4.5 16.9 0.6 CD2 A:HIS113 4.9 20.4 1.0 CD1 A:LEU130 5.0 14.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum


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 Heme Binding Protein Htab From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:17.5 occ:0.56 FE A:HEM301 0.0 17.5 0.6 FE A:HEM301 0.5 18.0 0.4 NB A:HEM301 1.9 19.1 0.4 NC A:HEM301 2.0 19.2 0.6 NB A:HEM301 2.1 15.4 0.6 ND A:HEM301 2.1 16.8 0.6 NC A:HEM301 2.1 18.2 0.4 NA A:HEM301 2.1 16.6 0.4 OH A:TYR56 2.1 17.9 1.0 NA A:HEM301 2.1 19.6 0.6 ND A:HEM301 2.3 18.9 0.4 C4B A:HEM301 2.9 18.6 0.4 C1B A:HEM301 2.9 17.6 0.4 CZ A:TYR56 3.0 17.6 1.0 C1C A:HEM301 3.0 18.6 0.6 C1C A:HEM301 3.0 19.2 0.4 C4C A:HEM301 3.0 17.6 0.6 C4B A:HEM301 3.0 19.2 0.6 C4A A:HEM301 3.0 18.6 0.4 C1D A:HEM301 3.0 19.0 0.6 C4D A:HEM301 3.1 18.0 0.6 C1B A:HEM301 3.1 18.2 0.6 C1A A:HEM301 3.1 19.4 0.6 C4C A:HEM301 3.1 17.1 0.4 C1A A:HEM301 3.2 17.6 0.4 C4A A:HEM301 3.2 18.3 0.6 C4D A:HEM301 3.2 19.5 0.4 CHC A:HEM301 3.3 19.7 0.4 C1D A:HEM301 3.3 18.9 0.4 CZ A:PHE209 3.4 23.0 1.0 CHC A:HEM301 3.4 19.2 0.6 CHB A:HEM301 3.4 17.6 0.4 CHD A:HEM301 3.4 17.7 0.6 CHA A:HEM301 3.5 20.8 0.6 CHA A:HEM301 3.6 20.8 0.4 CHB A:HEM301 3.6 17.2 0.6 CE2 A:PHE209 3.6 21.1 1.0 CHD A:HEM301 3.6 18.4 0.4 CE1 A:PHE209 3.7 23.2 1.0 CE2 A:TYR56 3.7 15.8 1.0 CE1 A:TYR56 3.7 18.9 1.0 NE2 A:HIS113 4.0 20.3 1.0 C3B A:HEM301 4.1 17.6 0.4 CD2 A:PHE209 4.1 19.5 1.0 C2B A:HEM301 4.2 16.6 0.4 C2C A:HEM301 4.2 16.5 0.6 CD1 A:PHE209 4.2 23.4 1.0 C3C A:HEM301 4.2 16.9 0.6 C2C A:HEM301 4.2 19.8 0.4 C2D A:HEM301 4.3 17.0 0.6 C3B A:HEM301 4.3 19.9 0.6 C3A A:HEM301 4.3 16.9 0.4 C3C A:HEM301 4.3 20.6 0.4 C3D A:HEM301 4.3 16.0 0.6 C2B A:HEM301 4.3 20.0 0.6 C2A A:HEM301 4.4 16.2 0.4 C2A A:HEM301 4.4 20.9 0.6 CG A:PHE209 4.4 19.8 1.0 C3A A:HEM301 4.5 21.5 0.6 C3D A:HEM301 4.5 20.7 0.4 C2D A:HEM301 4.5 21.5 0.4 CD1 A:LEU130 4.5 14.4 1.0 CD2 A:HIS113 4.6 20.4 1.0 CE1 A:HIS113 4.9 20.3 1.0 CD2 A:TYR56 4.9 15.1 1.0 CD1 A:TYR56 5.0 17.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum


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 Heme Binding Protein Htab From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:17.5 occ:0.54 FE B:HEM300 0.0 17.5 0.5 FE B:HEM300 0.3 18.9 0.5 NB B:HEM300 1.9 18.0 0.5 NB B:HEM300 2.0 17.3 0.5 NC B:HEM300 2.0 19.0 0.5 NC B:HEM300 2.0 17.5 0.5 NA B:HEM300 2.1 20.9 0.5 NA B:HEM300 2.1 14.1 0.5 ND B:HEM300 2.1 21.4 0.5 ND B:HEM300 2.1 16.2 0.5 OH B:TYR56 2.1 18.6 1.0 CZ B:TYR56 3.0 18.7 1.0 C4B B:HEM300 3.0 17.6 0.5 C1C B:HEM300 3.0 18.0 0.5 C1B B:HEM300 3.0 16.8 0.5 C4B B:HEM300 3.0 17.8 0.5 C1C B:HEM300 3.0 17.0 0.5 C4A B:HEM300 3.1 18.4 0.5 C1B B:HEM300 3.1 19.5 0.5 C1D B:HEM300 3.1 18.9 0.5 C4C B:HEM300 3.1 20.1 0.5 C4C B:HEM300 3.1 16.6 0.5 C1A B:HEM300 3.1 21.6 0.5 C1A B:HEM300 3.1 15.9 0.5 C4D B:HEM300 3.1 16.5 0.5 C4A B:HEM300 3.1 19.9 0.5 C4D B:HEM300 3.1 21.4 0.5 C1D B:HEM300 3.2 19.0 0.5 CZ B:PHE209 3.3 20.4 1.0 CHC B:HEM300 3.3 17.4 0.5 CHC B:HEM300 3.4 16.6 0.5 CHB B:HEM300 3.4 17.6 0.5 CHD B:HEM300 3.5 17.0 0.5 CHB B:HEM300 3.5 21.2 0.5 CHA B:HEM300 3.5 17.6 0.5 CHA B:HEM300 3.5 18.9 0.5 CHD B:HEM300 3.5 19.6 0.5 CE1 B:PHE209 3.6 20.6 1.0 CE2 B:TYR56 3.7 15.8 1.0 CE2 B:PHE209 3.7 22.1 1.0 CE1 B:TYR56 3.8 19.2 1.0 NE2 B:HIS113 4.0 19.3 1.0 CD1 B:PHE209 4.1 18.1 1.0 C3B B:HEM300 4.2 18.6 0.5 C2B B:HEM300 4.2 16.8 0.5 CD2 B:PHE209 4.2 23.3 1.0 C2C B:HEM300 4.2 18.2 0.5 C3B B:HEM300 4.2 18.4 0.5 C2B B:HEM300 4.3 20.0 0.5 C2C B:HEM300 4.3 18.5 0.5 C3C B:HEM300 4.3 19.5 0.5 C3A B:HEM300 4.3 17.1 0.5 C2D B:HEM300 4.3 16.8 0.5 C3C B:HEM300 4.3 16.9 0.5 C3D B:HEM300 4.3 16.3 0.5 C2A B:HEM300 4.3 15.8 0.5 C2A B:HEM300 4.3 23.4 0.5 C3A B:HEM300 4.3 22.4 0.5 C3D B:HEM300 4.4 23.5 0.5 C2D B:HEM300 4.4 22.6 0.5 CG B:PHE209 4.5 19.3 1.0 CD2 B:HIS113 4.6 19.7 1.0 CD1 B:LEU130 4.6 15.2 1.0 CE1 B:HIS113 4.8 18.0 1.0 CD2 B:TYR56 4.9 16.5 1.0 CD1 B:TYR56 5.0 18.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Heme Binding Protein Htab From Corynebacterium Glutamicum


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 Heme Binding Protein Htab From Corynebacterium Glutamicum within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe300 b:18.9 occ:0.46 FE B:HEM300 0.0 18.9 0.5 FE B:HEM300 0.3 17.5 0.5 ND B:HEM300 1.9 21.4 0.5 NA B:HEM300 1.9 20.9 0.5 NC B:HEM300 2.0 17.5 0.5 ND B:HEM300 2.1 16.2 0.5 NA B:HEM300 2.1 14.1 0.5 NB B:HEM300 2.1 17.3 0.5 NB B:HEM300 2.1 18.0 0.5 NC B:HEM300 2.2 19.0 0.5 OH B:TYR56 2.4 18.6 1.0 C1A B:HEM300 2.9 21.6 0.5 C4D B:HEM300 3.0 21.4 0.5 C4A B:HEM300 3.0 19.9 0.5 C1D B:HEM300 3.0 19.0 0.5 C4D B:HEM300 3.0 16.5 0.5 C1A B:HEM300 3.0 15.9 0.5 CZ B:PHE209 3.0 20.4 1.0 C4C B:HEM300 3.0 20.1 0.5 C1B B:HEM300 3.1 19.5 0.5 C1C B:HEM300 3.1 18.0 0.5 C4A B:HEM300 3.1 18.4 0.5 C4B B:HEM300 3.1 17.8 0.5 C1D B:HEM300 3.1 18.9 0.5 C4B B:HEM300 3.1 17.6 0.5 C1B B:HEM300 3.1 16.8 0.5 C1C B:HEM300 3.2 17.0 0.5 CZ B:TYR56 3.2 18.7 1.0 C4C B:HEM300 3.2 16.6 0.5 CHA B:HEM300 3.3 17.6 0.5 CE2 B:PHE209 3.3 22.1 1.0 CHA B:HEM300 3.4 18.9 0.5 CE1 B:PHE209 3.4 20.6 1.0 CHB B:HEM300 3.4 21.2 0.5 CHD B:HEM300 3.4 19.6 0.5 CHC B:HEM300 3.5 17.4 0.5 CHC B:HEM300 3.5 16.6 0.5 CHB B:HEM300 3.5 17.6 0.5 CHD B:HEM300 3.5 17.0 0.5 CE2 B:TYR56 3.9 15.8 1.0 CE1 B:TYR56 3.9 19.2 1.0 CD2 B:PHE209 3.9 23.3 1.0 CD1 B:PHE209 3.9 18.1 1.0 C2A B:HEM300 4.2 23.4 0.5 C3D B:HEM300 4.2 23.5 0.5 C3A B:HEM300 4.2 22.4 0.5 C2D B:HEM300 4.2 22.6 0.5 CG B:PHE209 4.2 19.3 1.0 NE2 B:HIS113 4.2 19.3 1.0 C2A B:HEM300 4.2 15.8 0.5 C3D B:HEM300 4.3 16.3 0.5 C3A B:HEM300 4.3 17.1 0.5 C3C B:HEM300 4.3 19.5 0.5 C2D B:HEM300 4.3 16.8 0.5 C2B B:HEM300 4.3 20.0 0.5 C2C B:HEM300 4.3 18.2 0.5 C3B B:HEM300 4.3 18.4 0.5 C3B B:HEM300 4.3 18.6 0.5 C2B B:HEM300 4.3 16.8 0.5 C2C B:HEM300 4.4 18.5 0.5 C3C B:HEM300 4.4 16.9 0.5 CD2 B:HIS113 4.8 19.7 1.0 CD1 B:LEU130 4.9 15.2 1.0

N.Muraki, C.Kitatsuji, Y.Okamoto, T.Uchida, K.Ishimori, S.Aono. Structural Basis For the Heme Transfer Reaction in Heme Uptake Machinery From Corynebacteria. Chem.Commun.(Camb.) V. 55 13864 2019.
ISSN: ESSN 1364-548X
PubMed: 31670736
DOI: 10.1039/C9CC07369H