Iron in PDB 7eyr: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo, PDB code: 7eyr was solved by H.Tao, T.Mori, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.57 / 2.12
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.57, 72.704, 78.985, 82.08, 84.95, 70.13
R / Rfree (%)	19.6 / 25.1

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo (pdb code 7eyr). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo, PDB code: 7eyr:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe301 b:51.1 occ:1.00 O C:HOH419 2.1 22.5 1.0 NE2 C:HIS205 2.3 28.1 1.0 OD1 C:ASP130 2.3 22.7 1.0 NE2 C:HIS128 2.4 28.9 1.0 CE1 C:HIS205 3.0 28.1 1.0 CG C:ASP130 3.2 24.2 1.0 CD2 C:HIS128 3.3 30.0 1.0 CE1 C:HIS128 3.3 28.7 1.0 CD2 C:HIS205 3.4 23.6 1.0 OD2 C:ASP130 3.4 21.7 1.0 ND1 C:HIS205 4.2 24.4 1.0 CG C:HIS205 4.4 30.9 1.0 ND1 C:HIS128 4.4 28.8 1.0 CG C:HIS128 4.5 26.5 1.0 O C:HOH426 4.5 26.0 1.0 CB C:ASP130 4.6 23.4 1.0 CA C:ASP130 5.0 22.8 1.0

Iron binding site 2 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:44.4 occ:1.00 OD1 A:ASP130 2.2 14.4 1.0 O A:HOH439 2.3 13.4 1.0 NE2 A:HIS205 2.3 17.0 1.0 NE2 A:HIS128 2.4 21.0 1.0 CG A:ASP130 3.1 18.6 1.0 CE1 A:HIS205 3.1 14.5 1.0 CD2 A:HIS128 3.3 16.6 1.0 CE1 A:HIS128 3.3 13.6 1.0 OD2 A:ASP130 3.3 15.7 1.0 CD2 A:HIS205 3.4 17.2 1.0 O A:HOH549 4.0 25.2 1.0 ND1 A:HIS205 4.3 18.2 1.0 ND1 A:HIS128 4.4 16.8 1.0 CG A:HIS128 4.4 17.9 1.0 CG A:HIS205 4.4 17.6 1.0 O A:HOH436 4.5 24.9 1.0 CB A:ASP130 4.5 13.3 1.0 CA A:ASP130 4.9 13.6 1.0 OE1 A:GLN125 4.9 20.6 1.0 CD1 A:LEU199 5.0 21.3 1.0

Iron binding site 3 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:47.7 occ:1.00 NE2 B:HIS205 2.3 20.9 1.0 OD1 B:ASP130 2.4 17.9 1.0 NE2 B:HIS128 2.4 22.8 1.0 O B:HOH428 2.4 18.5 1.0 CE1 B:HIS205 3.1 22.3 1.0 CD2 B:HIS205 3.3 22.6 1.0 CG B:ASP130 3.3 20.6 1.0 CD2 B:HIS128 3.3 28.2 1.0 CE1 B:HIS128 3.4 26.7 1.0 OD2 B:ASP130 3.5 15.1 1.0 ND1 B:HIS205 4.2 21.3 1.0 CG B:HIS205 4.4 22.9 1.0 CG B:HIS128 4.5 27.9 1.0 ND1 B:HIS128 4.5 29.3 1.0 CB B:ASP130 4.7 15.6 1.0 O B:HOH407 4.8 25.1 1.0 CD1 B:LEU199 4.9 25.2 1.0 OE1 B:GLN125 5.0 27.0 1.0

Iron binding site 4 out of 4 in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf Apo within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:45.9 occ:1.00 O D:HOH412 2.2 18.7 1.0 NE2 D:HIS205 2.2 21.0 1.0 OD1 D:ASP130 2.4 21.1 1.0 NE2 D:HIS128 2.5 22.5 1.0 CE1 D:HIS205 3.1 23.6 1.0 CG D:ASP130 3.2 21.5 1.0 CD2 D:HIS205 3.3 24.4 1.0 OD2 D:ASP130 3.3 18.3 1.0 CE1 D:HIS128 3.3 22.8 1.0 CD2 D:HIS128 3.6 25.9 1.0 ND1 D:HIS205 4.3 20.1 1.0 CG D:HIS205 4.4 23.8 1.0 O D:HOH410 4.4 28.2 1.0 ND1 D:HIS128 4.5 22.2 1.0 CB D:ASP130 4.6 16.4 1.0 CG D:HIS128 4.6 25.9 1.0 O D:HOH453 4.7 34.6 1.0 CD1 D:LEU199 5.0 26.8 1.0 CA D:ASP130 5.0 17.7 1.0

H.Tao, T.Mori, H.Chen, S.Lyu, A.Nonoyama, S.Lee, I.Abe. Molecular Insights Into the Unusually Promiscuous and Catalytically Versatile Fe(II)/ Alpha-Ketoglutarate-Dependent Oxygenase Sptf. Nat Commun V. 13 95 2022.
ISSN: ESSN 2041-1723
PubMed: 35013177
DOI: 10.1038/S41467-021-27636-3