Iron in PDB 6f2a: Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine

The structure of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine, PDB code: 6f2a was solved by T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha, K.Bastard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.16 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.940, 67.020, 110.750, 107.48, 102.76, 93.74
R / Rfree (%)	20.3 / 23.1

The structure of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine (pdb code 6f2a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine, PDB code: 6f2a:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:0.6 occ:1.00 OE1 A:GLU180 2.5 54.6 1.0 NE2 A:HIS178 2.5 38.6 1.0 N A:LYS402 2.6 47.1 1.0 CD A:GLU180 3.1 51.4 1.0 OE2 A:GLU180 3.1 48.3 1.0 O A:HOH645 3.2 51.7 1.0 NE2 A:HIS314 3.3 48.2 1.0 CD2 A:HIS178 3.4 39.3 1.0 NH1 A:ARG332 3.4 40.5 1.0 CB A:LYS402 3.4 50.3 1.0 CA A:LYS402 3.4 48.3 1.0 CE1 A:HIS178 3.5 38.1 1.0 OXT A:LYS402 3.7 59.4 1.0 CG A:LYS402 3.9 54.5 1.0 C A:LYS402 4.0 56.1 1.0 CE1 A:HIS314 4.2 47.8 1.0 CD2 A:HIS314 4.3 47.8 1.0 O A:HOH501 4.5 39.1 1.0 CG A:GLU180 4.5 37.4 1.0 CG A:HIS178 4.5 37.5 1.0 ND1 A:HIS178 4.6 39.2 1.0 CZ A:ARG332 4.7 54.3 1.0 CB A:GLU180 4.9 30.0 1.0 CA A:GLU180 4.9 29.9 1.0 CD2 A:LEU175 4.9 44.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:0.7 occ:1.00 OE1 B:GLU180 2.3 54.7 1.0 NE2 B:HIS178 2.4 54.0 1.0 N B:LYS402 2.8 57.7 1.0 NE2 B:HIS314 2.9 58.0 1.0 O B:HOH601 3.0 63.8 1.0 CD B:GLU180 3.2 66.3 1.0 CD2 B:HIS178 3.3 53.4 1.0 CE1 B:HIS178 3.4 54.4 1.0 OE2 B:GLU180 3.4 63.2 1.0 NH1 B:ARG332 3.5 55.9 1.0 CE1 B:HIS314 3.8 56.2 1.0 CA B:LYS402 3.8 60.7 1.0 CD2 B:HIS314 3.8 58.6 1.0 CB B:LYS402 3.9 64.2 1.0 O B:LYS402 4.1 76.8 1.0 CG B:LYS402 4.2 74.4 1.0 CG B:HIS178 4.5 52.3 1.0 C B:LYS402 4.5 67.3 1.0 ND1 B:HIS178 4.5 54.7 1.0 O B:HOH504 4.5 52.2 1.0 CG B:GLU180 4.5 53.2 1.0 CD2 B:LEU175 4.8 64.1 1.0 CZ B:ARG332 4.8 67.5 1.0 CB B:GLU180 4.9 40.5 1.0 CA B:GLU180 5.0 39.5 1.0 CG B:HIS314 5.0 54.6 1.0 ND1 B:HIS314 5.0 56.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:99.1 occ:1.00 NE2 C:HIS178 2.2 41.3 1.0 OE1 C:GLU180 2.5 52.6 1.0 N C:LYS402 2.9 49.9 1.0 NE2 C:HIS314 3.0 50.5 1.0 CD2 C:HIS178 3.1 41.8 1.0 CE1 C:HIS178 3.1 41.4 1.0 O C:HOH612 3.2 53.9 1.0 CD C:GLU180 3.3 55.3 1.0 OE2 C:GLU180 3.5 56.0 1.0 CB C:LYS402 3.6 51.7 1.0 NH1 C:ARG332 3.7 50.0 1.0 CA C:LYS402 3.7 49.8 1.0 CG C:LYS402 3.9 54.6 1.0 CD2 C:HIS314 3.9 50.3 1.0 CE1 C:HIS314 3.9 49.4 1.0 CG C:HIS178 4.2 40.3 1.0 O C:LYS402 4.2 51.8 1.0 ND1 C:HIS178 4.2 42.1 1.0 O C:HOH502 4.5 40.9 1.0 C C:LYS402 4.5 52.6 1.0 CG C:GLU180 4.7 44.8 1.0 CD2 C:LEU175 4.7 44.3 1.0 CA C:GLU180 4.9 33.5 1.0 CB C:GLU180 5.0 34.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:0.3 occ:1.00 OE1 D:GLU180 2.4 59.8 1.0 NE2 D:HIS178 2.5 51.2 1.0 N D:LYS402 2.7 60.6 1.0 O D:HOH575 2.7 62.1 1.0 NE2 D:HIS314 3.0 56.7 1.0 CD D:GLU180 3.3 66.5 1.0 NH1 D:ARG332 3.4 54.6 1.0 CE1 D:HIS178 3.4 51.6 1.0 CD2 D:HIS178 3.5 50.3 1.0 OE2 D:GLU180 3.5 68.2 1.0 CA D:LYS402 3.8 63.8 1.0 CD2 D:HIS314 3.9 57.3 1.0 OXT D:LYS402 3.9 73.3 1.0 CE1 D:HIS314 4.0 55.3 1.0 CB D:LYS402 4.0 67.1 1.0 CG D:LYS402 4.3 69.5 1.0 C D:LYS402 4.3 66.8 1.0 ND1 D:HIS178 4.6 52.2 1.0 CG D:HIS178 4.6 49.7 1.0 O D:HOH501 4.6 49.3 1.0 CD2 D:LEU175 4.6 58.2 1.0 CG D:GLU180 4.7 53.2 1.0 CZ D:ARG332 4.7 60.9 1.0

K.Bastard, T.Isabet, E.A.Stura, P.Legrand, A.Zaparucha. Structural Studies Based on Two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity Within the Clavaminate Synthase-Like Family. Sci Rep V. 8 16587 2018.
ISSN: ESSN 2045-2322
PubMed: 30410048
DOI: 10.1038/S41598-018-34795-9