Iron in PDB 7dih: Crystal Structure of Thermoglobin Y29F Mutant in Complex with Imidazole

The structure of Crystal Structure of Thermoglobin Y29F Mutant in Complex with Imidazole, PDB code: 7dih 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)	38.02 / 1.50
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	59.771, 35.823, 138.084, 90, 95.2, 90
R / Rfree (%)	19.9 / 22.3

The binding sites of Iron atom in the Crystal Structure of Thermoglobin Y29F Mutant in Complex with Imidazole (pdb code 7dih). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Thermoglobin Y29F Mutant in Complex with Imidazole, PDB code: 7dih:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Thermoglobin Y29F Mutant in Complex with Imidazole


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 Thermoglobin Y29F Mutant in Complex with Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:21.3 occ:1.00 FE A:HEM201 0.0 21.3 1.0 NA A:HEM201 2.0 19.5 1.0 NC A:HEM201 2.0 18.1 1.0 ND A:HEM201 2.0 19.5 1.0 NB A:HEM201 2.0 19.9 1.0 N3 A:IMD202 2.1 21.8 1.0 NE2 A:HIS82 2.2 22.9 1.0 C4C A:HEM201 3.0 20.8 1.0 C1A A:HEM201 3.0 20.6 1.0 C4A A:HEM201 3.0 21.1 1.0 C1D A:HEM201 3.0 23.9 1.0 C4D A:HEM201 3.0 24.4 1.0 C1C A:HEM201 3.0 19.5 1.0 C1B A:HEM201 3.0 22.2 1.0 C2 A:IMD202 3.0 22.7 1.0 C4B A:HEM201 3.1 19.6 1.0 CD2 A:HIS82 3.1 21.8 1.0 C4 A:IMD202 3.2 21.2 1.0 CE1 A:HIS82 3.2 22.8 1.0 CHD A:HEM201 3.4 22.1 1.0 CHB A:HEM201 3.4 23.6 1.0 CHA A:HEM201 3.4 24.2 1.0 CHC A:HEM201 3.4 20.6 1.0 N1 A:IMD202 4.2 23.0 1.0 C2A A:HEM201 4.2 24.8 1.0 C3A A:HEM201 4.2 22.0 1.0 C3C A:HEM201 4.2 21.1 1.0 C2D A:HEM201 4.2 21.7 1.0 C3D A:HEM201 4.2 23.6 1.0 C2C A:HEM201 4.2 21.4 1.0 CG A:HIS82 4.2 24.3 1.0 C2B A:HEM201 4.2 19.8 1.0 ND1 A:HIS82 4.2 21.1 1.0 C3B A:HEM201 4.3 19.4 1.0 C5 A:IMD202 4.3 22.4 1.0 CG2 A:ILE78 4.7 28.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Thermoglobin Y29F Mutant in Complex with Imidazole


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 Thermoglobin Y29F Mutant in Complex with Imidazole within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:23.2 occ:1.00 FE B:HEM201 0.0 23.2 1.0 NC B:HEM201 2.0 20.5 1.0 NA B:HEM201 2.0 21.6 1.0 ND B:HEM201 2.0 21.4 1.0 NB B:HEM201 2.0 21.9 1.0 NE2 B:HIS82 2.2 23.2 1.0 N3 B:IMD202 2.2 26.2 1.0 C4C B:HEM201 3.0 21.7 1.0 C1C B:HEM201 3.0 21.4 1.0 C4A B:HEM201 3.0 23.9 1.0 C4D B:HEM201 3.0 24.6 1.0 C1A B:HEM201 3.0 25.1 1.0 C1B B:HEM201 3.0 22.4 1.0 C1D B:HEM201 3.0 22.2 1.0 C4B B:HEM201 3.1 21.9 1.0 C2 B:IMD202 3.1 26.8 1.0 CE1 B:HIS82 3.1 22.9 1.0 CD2 B:HIS82 3.1 21.0 1.0 C4 B:IMD202 3.2 27.9 1.0 CHA B:HEM201 3.4 25.8 1.0 CHB B:HEM201 3.4 23.4 1.0 CHC B:HEM201 3.4 21.9 1.0 CHD B:HEM201 3.4 21.5 1.0 C2C B:HEM201 4.2 23.0 1.0 ND1 B:HIS82 4.2 22.2 1.0 C3C B:HEM201 4.2 21.8 1.0 C2A B:HEM201 4.2 27.3 1.0 C3A B:HEM201 4.2 28.7 1.0 CG B:HIS82 4.2 23.6 1.0 C3D B:HEM201 4.2 26.3 1.0 C2D B:HEM201 4.2 23.5 1.0 N1 B:IMD202 4.3 28.5 1.0 C2B B:HEM201 4.3 21.4 1.0 C3B B:HEM201 4.3 21.8 1.0 C5 B:IMD202 4.4 26.4 1.0 CG2 B:ILE78 4.8 25.3 1.0

N.Muraki, K.Takeda, D.Nam, M.Muraki, S.Aono. Structural Characterization of Y29F Mutant of Thermoglobin From A Hyperthermophilic Bacterium Aquifex Aeolicus Chem Lett. 2021.
ISSN: ESSN 1348-0715
DOI: 10.1246/CL.200879