Iron in PDB 6f6j: Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine

The structure of Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine, PDB code: 6f6j 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)	40.00 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	56.950, 67.390, 110.650, 107.55, 102.87, 93.58
R / Rfree (%)	19.4 / 22.5

The binding sites of Iron atom in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine (pdb code 6f6j). 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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine, PDB code: 6f6j:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:76.5 occ:0.80 NE2 A:HIS178 2.3 38.7 1.0 NE2 A:HIS314 2.4 48.0 1.0 OB A:CUW403 2.4 83.2 1.0 OE1 A:GLU180 2.5 64.8 1.0 O A:HOH655 2.7 46.1 0.5 O1 A:SIN402 2.8 58.9 0.5 O2 A:SIN402 2.9 55.0 0.5 C1 A:SIN402 3.0 55.7 0.5 CE1 A:HIS178 3.2 39.0 1.0 CD2 A:HIS314 3.3 47.8 1.0 CD2 A:HIS178 3.3 39.3 1.0 CE1 A:HIS314 3.4 47.4 1.0 CD A:GLU180 3.6 60.6 1.0 CB A:CUW403 3.8 84.6 1.0 NH1 A:ARG332 3.9 43.8 1.0 OE2 A:GLU180 4.0 57.4 1.0 C2 A:SIN402 4.1 52.6 0.5 ND1 A:HIS178 4.3 40.4 1.0 CG A:HIS314 4.4 44.3 1.0 CG A:CUW403 4.4 85.2 1.0 CG A:HIS178 4.4 39.0 1.0 ND1 A:HIS314 4.5 47.5 1.0 O A:CUW403 4.8 81.0 1.0 O A:HOH702 4.8 53.3 0.5 CA A:CUW403 4.8 84.4 1.0 CD2 A:LEU175 4.8 48.0 1.0 N A:CUW403 4.8 84.2 1.0 CG A:GLU180 4.9 41.2 1.0 CB A:GLU180 5.0 30.9 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:0.0 occ:1.00 NE2 B:HIS178 2.3 55.7 1.0 OE1 B:GLU180 2.3 51.6 1.0 O2 B:SIN402 2.5 81.9 1.0 NE2 B:HIS314 2.8 56.1 1.0 O1 B:SIN402 3.1 76.1 1.0 C1 B:SIN402 3.2 79.1 1.0 CD B:GLU180 3.2 62.0 1.0 CD2 B:HIS178 3.3 55.6 1.0 CE1 B:HIS178 3.3 56.6 1.0 OB B:CUW403 3.5 81.2 1.0 OE2 B:GLU180 3.5 58.8 1.0 CE1 B:HIS314 3.6 54.4 1.0 CD2 B:HIS314 3.7 56.7 1.0 NH1 B:ARG332 3.7 47.0 1.0 CB B:CUW403 3.8 82.3 1.0 CG B:CUW403 4.3 80.9 1.0 CG B:HIS178 4.4 55.0 1.0 ND1 B:HIS178 4.4 57.8 1.0 O B:HOH536 4.4 55.9 1.0 OXT B:CUW403 4.5 79.2 1.0 CG B:GLU180 4.6 51.5 1.0 C2 B:SIN402 4.7 77.2 1.0 ND1 B:HIS314 4.8 54.4 1.0 CG B:HIS314 4.8 52.7 1.0 CB B:GLU180 4.8 41.5 1.0 CD2 B:LEU175 4.8 62.6 1.0 CA B:GLU180 4.8 40.3 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:78.9 occ:0.80 NE2 C:HIS178 2.0 42.1 1.0 O3 C:SIN402 2.4 67.9 0.5 NE2 C:HIS314 2.7 47.4 1.0 OE1 C:GLU180 2.7 50.8 1.0 CE1 C:HIS178 2.9 42.5 1.0 C4 C:SIN402 3.0 67.3 0.5 OB C:CUW403 3.0 74.4 1.0 O4 C:SIN402 3.0 65.0 0.5 CD2 C:HIS178 3.1 42.4 1.0 N C:CUW403 3.4 64.7 1.0 O C:HOH709 3.4 79.0 0.5 CD2 C:HIS314 3.5 47.0 1.0 CE1 C:HIS314 3.7 46.2 1.0 CD C:GLU180 3.7 62.4 1.0 CB C:CUW403 3.9 71.8 1.0 NH1 C:ARG332 4.0 45.0 1.0 OE2 C:GLU180 4.0 63.3 1.0 OG C:SER168 4.0 79.7 1.0 CG C:CUW403 4.1 71.3 1.0 ND1 C:HIS178 4.1 43.5 1.0 O4 C:SIN402 4.1 51.4 0.5 CG C:HIS178 4.2 41.1 1.0 CA C:CUW403 4.2 68.6 1.0 C3 C:SIN402 4.4 68.3 0.5 C3 C:SIN402 4.4 49.4 0.5 CD2 C:LEU175 4.5 50.4 1.0 C4 C:SIN402 4.6 48.9 0.5 CG C:HIS314 4.6 42.7 1.0 ND1 C:HIS314 4.7 45.7 1.0 OXT C:CUW403 4.9 66.1 1.0 C2 C:SIN402 4.9 69.8 0.5 C C:CUW403 5.0 67.7 1.0 CG C:GLU180 5.0 47.9 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-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 Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO1 with Fe(II)/Succinate/(3S)-3-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:0.9 occ:1.00 O2 D:SIN402 2.1 83.9 1.0 NE2 D:HIS178 2.2 54.2 1.0 OE1 D:GLU180 2.4 63.2 1.0 NE2 D:HIS314 2.6 59.4 1.0 O D:HOH595 2.9 65.3 1.0 C1 D:SIN402 3.2 83.8 1.0 CE1 D:HIS178 3.2 54.9 1.0 N D:CUW403 3.3 61.7 1.0 CD2 D:HIS178 3.3 53.8 1.0 CD D:GLU180 3.4 71.4 1.0 OB D:CUW403 3.5 71.8 1.0 CD2 D:HIS314 3.5 59.8 1.0 CE1 D:HIS314 3.6 57.8 1.0 O1 D:SIN402 3.7 86.3 1.0 OE2 D:GLU180 3.7 68.5 1.0 NH1 D:ARG332 3.8 51.0 1.0 CB D:CUW403 4.2 67.5 1.0 CA D:CUW403 4.2 64.8 1.0 C2 D:SIN402 4.3 79.7 1.0 ND1 D:HIS178 4.4 55.5 1.0 CG D:CUW403 4.4 63.0 1.0 CG D:HIS178 4.4 52.6 1.0 O D:CUW403 4.5 62.5 1.0 CG D:HIS314 4.6 56.0 1.0 ND1 D:HIS314 4.7 58.0 1.0 O D:HOH502 4.7 47.1 1.0 CG D:GLU180 4.7 54.9 1.0 CD2 D:LEU175 4.8 63.0 1.0 C D:CUW403 4.9 65.1 1.0 CB D:GLU180 4.9 42.6 1.0 CA D:GLU180 5.0 41.7 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