Iron in PDB 6exh: Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine

The structure of Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine, PDB code: 6exh was solved by T.Isabet, E.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)	38.07 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.740, 99.230, 165.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.6

The binding sites of Iron atom in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine (pdb code 6exh). 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 KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine, PDB code: 6exh:
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 KDO5 with Fe(II)/Succinate/(4R)-4-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 Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:75.6 occ:1.00 NE2 A:HIS312 2.1 64.5 1.0 OE2 A:GLU178 2.2 70.8 1.0 NE2 A:HIS176 2.2 61.0 1.0 O4 A:SIN403 2.4 0.9 1.0 O3 A:SIN403 2.8 96.8 1.0 C4 A:SIN403 2.8 0.6 1.0 CE1 A:HIS176 3.0 61.4 1.0 CE1 A:HIS312 3.0 63.0 1.0 CD A:GLU178 3.1 80.7 1.0 CD2 A:HIS312 3.1 64.6 1.0 OE1 A:GLU178 3.3 93.3 1.0 CD2 A:HIS176 3.4 60.9 1.0 ND1 A:HIS312 4.1 63.0 1.0 ND1 A:HIS176 4.2 62.3 1.0 CG A:HIS312 4.2 61.4 1.0 NZ A:LYO402 4.2 72.7 0.5 C3 A:SIN403 4.2 0.1 1.0 CE A:LYO402 4.2 72.2 0.5 O A:HOH639 4.3 47.6 0.5 CG A:HIS176 4.3 59.9 1.0 CG A:GLU178 4.4 62.8 1.0 C2 A:SIN403 4.6 0.0 1.0 NH1 A:ARG338 4.8 71.2 1.0 CB A:GLU178 4.8 50.9 1.0 O A:HOH546 4.8 70.2 1.0 OG A:LYO402 4.8 71.0 0.5 CA A:GLU178 4.8 51.2 1.0 CZ A:PHE191 4.8 64.9 1.0 CD2 A:LEU173 5.0 99.7 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-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 Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:79.4 occ:1.00 O3 B:SIN403 2.1 0.7 1.0 NE2 B:HIS312 2.1 73.3 1.0 NE2 B:HIS176 2.3 80.8 1.0 OE2 B:GLU178 2.4 57.7 1.0 CE1 B:HIS176 2.4 80.4 1.0 C4 B:SIN403 2.7 0.8 1.0 O4 B:SIN403 2.8 0.1 1.0 CE1 B:HIS312 3.1 72.0 1.0 CD2 B:HIS312 3.1 74.0 1.0 CD B:GLU178 3.2 74.7 1.0 OE1 B:GLU178 3.4 94.4 1.0 CD2 B:HIS176 3.5 81.4 1.0 ND1 B:HIS176 3.7 81.2 1.0 CB B:LYO402 4.0 78.7 0.5 OG B:LYO402 4.0 82.6 0.5 C3 B:SIN403 4.2 0.5 1.0 CG B:HIS176 4.2 78.7 1.0 ND1 B:HIS312 4.2 72.9 1.0 CG B:HIS312 4.2 72.5 1.0 O B:LYO402 4.3 75.3 0.5 CG B:LYO402 4.4 81.1 0.5 CG B:GLU178 4.5 63.5 1.0 CD B:LYO402 4.5 80.5 0.5 O B:HOH562 4.6 61.5 0.5 CB B:GLU178 4.8 60.1 1.0 CD2 B:LEU173 4.8 99.0 1.0 CA B:GLU178 4.9 60.0 1.0 NH1 B:ARG338 5.0 85.8 1.0 CA B:LYO402 5.0 78.3 0.5

Iron binding site 3 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-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 Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe401 b:89.6 occ:1.00 NE2 C:HIS312 1.9 71.5 1.0 OE1 C:GLU178 2.3 74.5 1.0 NE2 C:HIS176 2.4 85.0 1.0 CE1 C:HIS176 2.5 84.8 1.0 O C:HOH565 2.7 65.7 1.0 CD2 C:HIS312 2.8 72.4 1.0 CE1 C:HIS312 2.9 70.8 1.0 CD C:GLU178 3.4 92.1 1.0 CD2 C:HIS176 3.8 86.0 1.0 ND1 C:HIS176 3.8 86.3 1.0 OE2 C:GLU178 3.9 96.7 1.0 OG C:LYO402 3.9 0.8 1.0 CG C:HIS312 3.9 70.7 1.0 ND1 C:HIS312 4.0 71.6 1.0 CG C:HIS176 4.4 83.8 1.0 CG C:GLU178 4.7 72.0 1.0 CG C:LYO402 4.7 0.5 1.0 CB C:LYO402 4.8 1.0 1.0 CZ C:PHE191 4.8 75.7 1.0 CD C:LYO402 4.8 0.7 1.0 CB C:GLU178 4.8 63.8 1.0 NH1 C:ARG338 4.9 91.0 1.0 CA C:GLU178 5.0 64.6 1.0 O C:HIS176 5.0 75.3 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-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 Complex Fe(II)/Alpha-Ketoglutarate Dependent Dioxygenase KDO5 with Fe(II)/Succinate/(4R)-4-Hydroxy-L-Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe401 b:85.0 occ:1.00 NE2 D:HIS312 2.0 76.2 1.0 O1 D:SIN402 2.0 58.4 0.5 NE2 D:HIS176 2.2 70.5 1.0 OE2 D:GLU178 2.6 91.7 1.0 O D:HOH572 2.7 0.8 0.5 C1 D:SIN402 2.8 59.8 0.5 CE1 D:HIS312 2.9 73.9 1.0 OE1 D:GLU178 3.0 0.3 1.0 O2 D:SIN402 3.0 57.6 0.5 CD D:GLU178 3.0 0.6 1.0 CD2 D:HIS312 3.0 76.8 1.0 CE1 D:HIS176 3.0 71.3 1.0 CD2 D:HIS176 3.2 69.5 1.0 ND1 D:HIS312 4.0 73.3 1.0 CG D:HIS312 4.1 73.2 1.0 C2 D:SIN402 4.1 62.6 0.5 ND1 D:HIS176 4.1 71.8 1.0 CG D:HIS176 4.2 68.6 1.0 CG D:GLU178 4.3 74.3 1.0 CB D:LYO404 4.3 0.4 1.0 C3 D:SIN402 4.4 63.4 0.5 OG D:LYO404 4.5 0.2 1.0 CD D:LYO404 4.6 0.1 1.0 CB D:GLU178 4.7 63.4 1.0 CG D:LYO404 4.7 0.9 1.0 OXT D:LYO404 4.7 0.3 1.0 CA D:GLU178 4.8 63.0 1.0 CZ D:PHE191 4.8 74.6 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