Iron in PDB 7eyw: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf with Terretonin C

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf with Terretonin C, PDB code: 7eyw 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)	48.24 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.651, 72.281, 78.455, 81.93, 84.88, 70.35
R / Rfree (%)	20.6 / 25.6

The binding sites of Iron atom in the Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf with Terretonin C (pdb code 7eyw). 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 with Terretonin C, PDB code: 7eyw:
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 with Terretonin C


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 with Terretonin C within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe302 b:30.0 occ:1.00 O2' C:OGA301 2.0 33.4 1.0 O C:HOH434 2.0 21.8 1.0 NE2 C:HIS205 2.2 23.7 1.0 O1 C:OGA301 2.2 27.7 1.0 NE2 C:HIS128 2.3 26.0 1.0 OD1 C:ASP130 2.3 17.1 1.0 C2 C:OGA301 2.7 34.3 1.0 C1 C:OGA301 2.8 36.3 1.0 CE1 C:HIS205 2.9 26.5 1.0 CG C:ASP130 3.2 22.5 1.0 CE1 C:HIS128 3.2 23.5 1.0 CD2 C:HIS205 3.2 28.4 1.0 CD2 C:HIS128 3.3 26.8 1.0 OD2 C:ASP130 3.3 18.6 1.0 N1 C:OGA301 3.9 39.2 1.0 O2 C:OGA301 4.0 40.8 1.0 ND1 C:HIS205 4.1 28.7 1.0 CG C:HIS205 4.3 29.2 1.0 ND1 C:HIS128 4.3 28.7 1.0 CG C:HIS128 4.4 24.2 1.0 O C:HOH444 4.4 35.7 1.0 CD2 C:LEU199 4.5 33.2 1.0 CB C:ASP130 4.6 21.8 1.0 C4 C:OGA301 4.6 33.6 1.0 OE1 C:GLN125 4.8 34.1 1.0 CA C:ASP130 4.9 22.7 1.0

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


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 with Terretonin C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:34.7 occ:1.00 O A:HOH418 2.1 24.9 1.0 NE2 A:HIS205 2.1 34.4 1.0 NE2 A:HIS128 2.2 32.0 1.0 O2' A:OGA301 2.2 40.7 1.0 O1 A:OGA301 2.3 35.8 1.0 OD1 A:ASP130 2.4 25.2 1.0 C2 A:OGA301 2.8 41.1 1.0 CE1 A:HIS205 2.8 33.1 1.0 C1 A:OGA301 2.9 43.0 1.0 CE1 A:HIS128 3.0 31.8 1.0 CD2 A:HIS205 3.2 28.9 1.0 CG A:ASP130 3.2 30.0 1.0 CD2 A:HIS128 3.2 34.4 1.0 OD2 A:ASP130 3.4 25.7 1.0 ND1 A:HIS205 4.0 34.1 1.0 N1 A:OGA301 4.0 39.0 1.0 O2 A:OGA301 4.1 46.8 1.0 CG A:HIS205 4.1 37.5 1.0 ND1 A:HIS128 4.2 34.6 1.0 CG A:HIS128 4.3 32.5 1.0 O A:HOH420 4.6 33.6 1.0 CB A:ASP130 4.6 27.6 1.0 C4 A:OGA301 4.7 41.3 1.0 OE1 A:GLN125 4.9 41.8 1.0 CA A:ASP130 5.0 26.6 1.0

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


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 with Terretonin C within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:42.7 occ:1.00 O2' B:OGA301 2.0 49.6 1.0 O2 B:OGA301 2.2 39.9 1.0 NE2 B:HIS205 2.2 29.1 1.0 OD1 B:ASP130 2.3 24.3 1.0 O B:HOH472 2.3 30.8 1.0 NE2 B:HIS128 2.5 38.2 1.0 C2 B:OGA301 2.7 42.1 1.0 C1 B:OGA301 2.8 46.6 1.0 CE1 B:HIS205 3.1 30.6 1.0 CG B:ASP130 3.2 32.3 1.0 CD2 B:HIS205 3.3 29.8 1.0 OAY B:0IP303 3.3 44.8 0.7 CE1 B:HIS128 3.4 31.8 1.0 OD2 B:ASP130 3.4 25.8 1.0 CD2 B:HIS128 3.4 31.9 1.0 OAX B:0IP303 3.7 45.3 0.7 N1 B:OGA301 3.9 46.3 1.0 O1 B:OGA301 4.0 56.7 1.0 ND1 B:HIS205 4.2 28.6 1.0 CAH B:0IP303 4.3 42.0 0.7 CG B:HIS205 4.3 27.6 1.0 ND1 B:HIS128 4.5 35.6 1.0 CAG B:0IP303 4.5 43.4 0.7 CG B:HIS128 4.6 33.2 1.0 CB B:ASP130 4.6 25.6 1.0 C4 B:OGA301 4.6 42.1 1.0 CD1 B:LEU199 4.9 34.0 1.0 OBE B:0IP303 4.9 35.6 0.7 CA B:ASP130 5.0 26.2 1.0

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


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 with Terretonin C within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:43.5 occ:1.00 O2' D:OGA301 2.0 41.2 1.0 NE2 D:HIS205 2.3 27.9 1.0 O2 D:OGA301 2.3 41.9 1.0 O D:HOH432 2.4 32.8 1.0 OD1 D:ASP130 2.4 22.8 1.0 NE2 D:HIS128 2.5 34.7 1.0 C2 D:OGA301 2.8 41.0 1.0 C1 D:OGA301 2.9 40.7 1.0 CE1 D:HIS205 3.2 29.7 1.0 CD2 D:HIS205 3.2 32.9 1.0 CG D:ASP130 3.3 34.0 1.0 CE1 D:HIS128 3.3 31.1 1.0 OD2 D:ASP130 3.4 30.7 1.0 CD2 D:HIS128 3.5 31.7 1.0 N1 D:OGA301 4.0 44.0 1.0 O1 D:OGA301 4.1 41.8 1.0 O D:HOH456 4.2 35.5 1.0 ND1 D:HIS205 4.3 28.9 1.0 CG D:HIS205 4.3 31.9 1.0 ND1 D:HIS128 4.4 35.1 1.0 CG D:HIS128 4.6 36.6 1.0 CB D:ASP130 4.7 31.2 1.0 C4 D:OGA301 4.7 39.2 1.0 O D:HOH474 4.8 36.3 1.0 OE1 D:GLN125 4.9 35.8 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