Iron in PDB 7vbq: Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij

The structure of Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij, PDB code: 7vbq was solved by X.Li, T.Awakawa, T.Mori, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.42 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.933, 75.335, 133.611, 90, 90, 90
R / Rfree (%)	17.1 / 21.4

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

Iron binding site 1 out of 3 in the Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:31.8 occ:1.00 OD1 A:ASP138 2.2 18.7 1.0 NE2 A:HIS213 2.3 18.0 1.0 O2' A:OGA301 2.3 32.6 1.0 O1 A:OGA301 2.4 36.5 1.0 NE2 A:HIS136 2.5 16.4 1.0 CE1 A:HIS213 3.0 18.2 1.0 C2 A:OGA301 3.1 33.6 1.0 C1 A:OGA301 3.1 37.1 1.0 CG A:ASP138 3.1 19.5 1.0 OD2 A:ASP138 3.3 23.5 1.0 CD2 A:HIS213 3.4 17.2 1.0 CE1 A:HIS136 3.4 23.4 1.0 CD2 A:HIS136 3.4 19.6 1.0 ND1 A:HIS213 4.2 18.7 1.0 N1 A:OGA301 4.3 34.9 1.0 O2 A:OGA301 4.3 40.6 1.0 CG A:HIS213 4.4 18.9 1.0 ND1 A:HIS136 4.5 21.1 1.0 CG A:HIS136 4.5 18.3 1.0 CB A:ASP138 4.5 19.8 1.0 OE1 A:GLN133 4.8 30.2 1.0 O A:HOH566 4.8 45.9 1.0 CA A:ASP138 4.9 16.5 1.0 C4 A:OGA301 5.0 31.8 1.0

Iron binding site 2 out of 3 in the Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:47.0 occ:1.00 OE2 A:GLU50 2.5 27.8 1.0 OE1 A:GLU50 2.7 29.6 1.0 CD A:GLU50 2.9 30.6 1.0 O A:HOH515 3.0 40.9 1.0 CG A:GLU50 4.4 23.8 1.0 O A:HOH528 4.5 35.3 1.0 O A:HOH521 4.7 30.6 1.0

Iron binding site 3 out of 3 in the Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Heterodimer Structure of Fe(II)/(Alpha)Ketoglutarate-Dependent Dioxygenase Tlxij within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:25.1 occ:1.00 O B:HOH599 2.2 38.5 1.0 OD1 B:ASP124 2.3 16.1 1.0 NE2 B:HIS122 2.4 19.6 1.0 O B:HOH437 2.4 19.6 1.0 NE2 B:HIS200 2.4 16.3 1.0 O B:HOH414 2.5 19.6 1.0 CG B:ASP124 3.2 21.0 1.0 CE1 B:HIS200 3.3 18.5 1.0 CE1 B:HIS122 3.3 19.9 1.0 CD2 B:HIS122 3.3 19.6 1.0 CD2 B:HIS200 3.4 19.1 1.0 OD2 B:ASP124 3.5 18.7 1.0 O B:HOH499 3.6 33.7 1.0 O B:HOH562 4.2 32.6 1.0 O B:HOH486 4.3 37.9 1.0 OH B:TYR194 4.4 15.8 1.0 ND1 B:HIS200 4.4 16.5 1.0 O B:HOH507 4.4 16.2 1.0 ND1 B:HIS122 4.4 18.9 1.0 OE1 B:GLU119 4.5 21.0 1.0 CG B:HIS200 4.5 18.8 1.0 CG B:HIS122 4.5 19.4 1.0 CB B:ASP124 4.7 14.9 1.0 OE2 B:GLU119 5.0 27.1 1.0

X.Li, T.Awakawa, T.Mori, M.Ling, D.Hu, B.Wu, I.Abe. Heterodimeric Non-Heme Iron Enzymes in Fungal Meroterpenoid Biosynthesis. J.Am.Chem.Soc. V. 143 21425 2021.
ISSN: ESSN 1520-5126
PubMed: 34881885
DOI: 10.1021/JACS.1C11548