Iron in PDB 7eyt: Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf with Andilesin C and Nog

The structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Sptf with Andilesin C and Nog, PDB code: 7eyt 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)	48.42 / 2.10
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.054, 72.557, 78.826, 81.74, 84.19, 70.23
R / Rfree (%)	23.6 / 28.6

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


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 Andilesin C and Nog within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe303 b:37.8 occ:0.80 O C:HOH449 2.1 25.7 1.0 O2 C:OGA301 2.1 35.4 1.0 O2' C:OGA301 2.2 23.7 1.0 OD1 C:ASP128 2.4 23.4 1.0 NE2 C:HIS203 2.5 26.0 1.0 NE2 C:HIS126 2.7 23.0 1.0 C1 C:OGA301 2.8 32.2 1.0 C2 C:OGA301 2.9 25.1 1.0 CE1 C:HIS203 3.3 24.1 1.0 CG C:ASP128 3.3 24.2 1.0 CD2 C:HIS203 3.5 24.2 1.0 CE1 C:HIS126 3.5 26.4 1.0 OD2 C:ASP128 3.5 24.7 1.0 CD2 C:HIS126 3.7 23.9 1.0 O C:HOH441 3.9 27.0 1.0 O1 C:OGA301 4.0 31.1 1.0 N1 C:OGA301 4.1 29.4 1.0 CAR C:0I3302 4.2 25.3 0.7 CAQ C:0I3302 4.2 25.1 0.7 O C:HOH431 4.4 32.8 1.0 ND1 C:HIS203 4.5 25.2 1.0 CBB C:0I3302 4.5 25.4 0.7 CG C:HIS203 4.6 27.1 1.0 ND1 C:HIS126 4.7 27.9 1.0 OAJ C:0I3302 4.7 27.9 0.7 CB C:ASP128 4.7 20.7 1.0 CAP C:0I3302 4.7 27.0 0.7 CG C:HIS126 4.8 27.5 1.0 CAX C:0I3302 4.8 31.6 0.7 C4 C:OGA301 4.9 28.1 1.0 CAW C:0I3302 4.9 28.3 0.7

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


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 Andilesin C and Nog within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:42.9 occ:0.80 O A:HOH447 2.2 17.6 1.0 O A:HOH493 2.4 22.6 1.0 OD1 A:ASP128 2.4 23.5 1.0 NE2 A:HIS203 2.4 23.5 1.0 NE2 A:HIS126 2.7 24.4 1.0 CG A:ASP128 3.2 22.4 1.0 CE1 A:HIS203 3.3 23.7 1.0 OD2 A:ASP128 3.3 20.4 1.0 CD2 A:HIS203 3.4 24.0 1.0 CE1 A:HIS126 3.6 27.5 1.0 CD2 A:HIS126 3.7 25.3 1.0 O A:HOH444 3.7 33.7 1.0 O A:HOH445 4.2 25.9 1.0 ND1 A:HIS203 4.4 20.6 1.0 CG A:HIS203 4.5 22.6 1.0 CB A:ASP128 4.7 19.3 1.0 ND1 A:HIS126 4.7 27.3 1.0 CG A:HIS126 4.8 26.1 1.0

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


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 Andilesin C and Nog within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:51.1 occ:0.80 O B:HOH491 2.1 27.7 1.0 O B:HOH431 2.3 23.5 1.0 OD1 B:ASP130 2.5 27.1 1.0 NE2 B:HIS205 2.5 25.2 1.0 NE2 B:HIS128 2.5 28.3 1.0 CE1 B:HIS205 3.3 25.4 1.0 CE1 B:HIS128 3.4 29.8 1.0 CG B:ASP130 3.4 27.2 1.0 CD2 B:HIS205 3.5 26.0 1.0 CD2 B:HIS128 3.5 30.9 1.0 OD2 B:ASP130 3.6 23.0 1.0 O B:HOH496 4.0 34.4 1.0 O B:HOH475 4.3 33.4 1.0 ND1 B:HIS205 4.5 27.6 1.0 ND1 B:HIS128 4.5 30.1 1.0 CG B:HIS205 4.6 31.0 1.0 CG B:HIS128 4.6 32.2 1.0 CB B:ASP130 4.8 24.3 1.0 OE1 B:GLN125 4.9 30.1 1.0

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


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 Andilesin C and Nog within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:37.3 occ:0.80 O D:HOH429 2.1 16.7 1.0 O D:HOH489 2.2 26.5 1.0 OD1 D:ASP130 2.3 21.0 1.0 NE2 D:HIS205 2.3 21.0 1.0 O D:HOH488 2.4 28.0 1.0 NE2 D:HIS128 2.6 22.9 1.0 CE1 D:HIS205 3.1 20.6 1.0 CG D:ASP130 3.2 19.1 1.0 OD2 D:ASP130 3.4 17.9 1.0 CD2 D:HIS205 3.4 23.0 1.0 CE1 D:HIS128 3.5 20.2 1.0 CD2 D:HIS128 3.7 19.8 1.0 ND1 D:HIS205 4.3 20.8 1.0 CG D:HIS205 4.5 21.8 1.0 CB D:ASP130 4.6 19.4 1.0 ND1 D:HIS128 4.6 21.6 1.0 CG D:HIS128 4.8 21.7 1.0 CA D:ASP130 5.0 16.6 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