Iron in PDB 2fmy: Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form)

The structure of Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form), PDB code: 2fmy was solved by Y.Higuchi, H.Komori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.33 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.654, 93.930, 91.901, 90.00, 104.73, 90.00
R / Rfree (%)	20.7 / 24.7

The binding sites of Iron atom in the Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form) (pdb code 2fmy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form), PDB code: 2fmy:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe300 b:33.4 occ:1.00 FE A:HEM300 0.0 33.4 1.0 N3 A:IMD301 2.0 33.5 1.0 ND A:HEM300 2.0 34.6 1.0 NA A:HEM300 2.1 35.5 1.0 NC A:HEM300 2.1 34.5 1.0 NB A:HEM300 2.1 35.2 1.0 NE2 A:HIS82 2.2 37.5 1.0 C4 A:IMD301 3.0 34.9 1.0 C2 A:IMD301 3.0 34.6 1.0 C4D A:HEM300 3.0 34.2 1.0 C1D A:HEM300 3.0 34.9 1.0 C1A A:HEM300 3.1 36.2 1.0 C4C A:HEM300 3.1 34.2 1.0 CE1 A:HIS82 3.1 38.5 1.0 C1C A:HEM300 3.1 33.5 1.0 C4A A:HEM300 3.1 35.9 1.0 C4B A:HEM300 3.1 34.4 1.0 C1B A:HEM300 3.1 35.5 1.0 CD2 A:HIS82 3.2 39.7 1.0 CHA A:HEM300 3.4 35.0 1.0 CHD A:HEM300 3.4 33.3 1.0 CHC A:HEM300 3.5 33.5 1.0 CHB A:HEM300 3.5 35.6 1.0 N1 A:IMD301 4.2 34.9 1.0 C5 A:IMD301 4.2 35.1 1.0 ND1 A:HIS82 4.2 39.9 1.0 C3D A:HEM300 4.3 33.5 1.0 C2D A:HEM300 4.3 34.5 1.0 C3C A:HEM300 4.3 33.5 1.0 CG A:HIS82 4.3 40.5 1.0 C2A A:HEM300 4.3 38.4 1.0 C2C A:HEM300 4.3 33.7 1.0 C3A A:HEM300 4.3 37.3 1.0 C3B A:HEM300 4.3 34.7 1.0 C2B A:HEM300 4.3 35.7 1.0 SG A:CYS80 4.6 41.0 1.0 O A:HOH4025 4.9 39.6 1.0

Iron binding site 2 out of 4 in the Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1300 b:36.0 occ:1.00 FE B:HEM1300 0.0 36.0 1.0 N3 B:IMD1301 1.9 32.8 1.0 NE2 B:HIS1082 1.9 40.9 1.0 NC B:HEM1300 2.0 35.2 1.0 ND B:HEM1300 2.1 34.7 1.0 NB B:HEM1300 2.1 35.6 1.0 NA B:HEM1300 2.1 36.2 1.0 CE1 B:HIS1082 2.8 41.4 1.0 C4 B:IMD1301 2.9 32.2 1.0 C2 B:IMD1301 3.0 33.0 1.0 CD2 B:HIS1082 3.0 42.1 1.0 C4C B:HEM1300 3.0 34.7 1.0 C1C B:HEM1300 3.0 35.2 1.0 C1D B:HEM1300 3.0 35.1 1.0 C4D B:HEM1300 3.1 35.0 1.0 C4B B:HEM1300 3.1 37.1 1.0 C1A B:HEM1300 3.1 36.8 1.0 C1B B:HEM1300 3.1 36.7 1.0 C4A B:HEM1300 3.1 36.6 1.0 CHD B:HEM1300 3.4 34.3 1.0 CHC B:HEM1300 3.4 35.4 1.0 CHA B:HEM1300 3.4 36.2 1.0 CHB B:HEM1300 3.5 36.7 1.0 ND1 B:HIS1082 4.0 41.9 1.0 C5 B:IMD1301 4.0 33.5 1.0 N1 B:IMD1301 4.1 32.0 1.0 CG B:HIS1082 4.1 41.2 1.0 C3C B:HEM1300 4.2 34.8 1.0 C2C B:HEM1300 4.2 34.5 1.0 C2D B:HEM1300 4.3 35.1 1.0 C3D B:HEM1300 4.3 35.0 1.0 C3B B:HEM1300 4.3 37.7 1.0 C2A B:HEM1300 4.3 37.8 1.0 C2B B:HEM1300 4.3 37.2 1.0 C3A B:HEM1300 4.3 37.2 1.0 SG B:CYS1080 4.6 38.0 1.0 O B:HOH4128 4.9 41.2 1.0

Iron binding site 3 out of 4 in the Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe2300 b:32.3 occ:1.00 FE C:HEM2300 0.0 32.3 1.0 N3 C:IMD2301 1.9 32.1 1.0 NE2 C:HIS2082 1.9 37.9 1.0 NC C:HEM2300 2.1 32.0 1.0 NA C:HEM2300 2.1 32.2 1.0 NB C:HEM2300 2.1 32.2 1.0 ND C:HEM2300 2.1 32.3 1.0 C2 C:IMD2301 2.9 32.8 1.0 CE1 C:HIS2082 2.9 37.1 1.0 C4 C:IMD2301 2.9 32.3 1.0 CD2 C:HIS2082 3.0 38.3 1.0 C1C C:HEM2300 3.1 32.5 1.0 C1A C:HEM2300 3.1 32.5 1.0 C4D C:HEM2300 3.1 31.3 1.0 C4B C:HEM2300 3.1 33.2 1.0 C4A C:HEM2300 3.1 33.1 1.0 C4C C:HEM2300 3.1 32.1 1.0 C1B C:HEM2300 3.1 33.2 1.0 C1D C:HEM2300 3.1 31.2 1.0 CHA C:HEM2300 3.4 31.4 1.0 CHC C:HEM2300 3.4 31.9 1.0 CHB C:HEM2300 3.5 33.0 1.0 CHD C:HEM2300 3.5 30.6 1.0 ND1 C:HIS2082 4.0 37.8 1.0 N1 C:IMD2301 4.0 31.6 1.0 C5 C:IMD2301 4.1 32.8 1.0 CG C:HIS2082 4.1 37.6 1.0 C2C C:HEM2300 4.3 31.7 1.0 C2A C:HEM2300 4.3 33.5 1.0 C3C C:HEM2300 4.3 31.6 1.0 C3D C:HEM2300 4.3 30.9 1.0 C3A C:HEM2300 4.3 33.2 1.0 C3B C:HEM2300 4.3 33.2 1.0 C2B C:HEM2300 4.3 33.1 1.0 C2D C:HEM2300 4.3 30.7 1.0 SG C:CYS2080 4.7 40.5 1.0 O C:HOH4012 4.7 28.4 1.0

Iron binding site 4 out of 4 in the Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Co-Dependent Transcription Factor Cooa From Carboxydothermus Hydrogenoformans (Imidazole-Bound Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe3300 b:44.8 occ:1.00 FE D:HEM3300 0.0 44.8 1.0 N3 D:IMD3301 1.9 43.6 1.0 NE2 D:HIS3082 1.9 44.9 1.0 NC D:HEM3300 2.0 45.6 1.0 NB D:HEM3300 2.0 46.3 1.0 NA D:HEM3300 2.1 45.8 1.0 ND D:HEM3300 2.1 45.2 1.0 CE1 D:HIS3082 2.9 43.8 1.0 C2 D:IMD3301 2.9 43.0 1.0 C4 D:IMD3301 2.9 42.7 1.0 CD2 D:HIS3082 3.0 44.2 1.0 C1C D:HEM3300 3.0 45.9 1.0 C4C D:HEM3300 3.0 45.3 1.0 C4B D:HEM3300 3.1 46.5 1.0 C1B D:HEM3300 3.1 46.5 1.0 C1D D:HEM3300 3.1 44.8 1.0 C4A D:HEM3300 3.1 46.5 1.0 C1A D:HEM3300 3.1 46.8 1.0 C4D D:HEM3300 3.1 45.3 1.0 CHC D:HEM3300 3.4 46.1 1.0 CHD D:HEM3300 3.4 44.9 1.0 CHB D:HEM3300 3.4 46.8 1.0 CHA D:HEM3300 3.5 45.9 1.0 ND1 D:HIS3082 4.0 43.6 1.0 N1 D:IMD3301 4.0 42.6 1.0 C5 D:IMD3301 4.1 43.1 1.0 CG D:HIS3082 4.1 42.9 1.0 C2C D:HEM3300 4.3 45.0 1.0 C3C D:HEM3300 4.3 44.7 1.0 C3B D:HEM3300 4.3 47.3 1.0 C2B D:HEM3300 4.3 47.3 1.0 C3A D:HEM3300 4.3 47.0 1.0 C2D D:HEM3300 4.3 44.8 1.0 C2A D:HEM3300 4.3 47.6 1.0 C3D D:HEM3300 4.3 44.8 1.0 SG D:CYS3080 4.7 38.8 1.0 O D:HOH4162 5.0 49.8 1.0

H.Komori, S.Inagaki, S.Yoshioka, S.Aono, Y.Higuchi. Crystal Structure of Co-Sensing Transcription Activator Cooa Bound to Exogenous Ligand Imidazole J.Mol.Biol. V. 367 864 2007.
ISSN: ISSN 0022-2836
PubMed: 17292914
DOI: 10.1016/J.JMB.2007.01.043