Iron in PDB 7jsd: Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine

The structure of Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine, PDB code: 7jsd was solved by E.N.Kissman, M.E.Neugebauer, M.C.Y.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.08 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.626, 93.53, 91.339, 90, 107.56, 90
R / Rfree (%)	18 / 22.9

The binding sites of Iron atom in the Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine (pdb code 7jsd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine, PDB code: 7jsd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:31.6 occ:1.00 O2 A:AKG402 2.1 37.4 1.0 OD1 A:ASP144 2.1 36.8 1.0 O5 A:AKG402 2.2 35.2 1.0 NE2 A:HIS142 2.2 25.5 1.0 NE2 A:HIS209 2.2 30.3 1.0 C1 A:AKG402 2.8 36.4 1.0 C2 A:AKG402 2.8 39.0 1.0 CG A:ASP144 3.1 41.8 1.0 CD2 A:HIS209 3.1 26.2 1.0 CD2 A:HIS142 3.1 25.6 1.0 CE1 A:HIS142 3.2 26.4 1.0 CE1 A:HIS209 3.3 27.1 1.0 OD2 A:ASP144 3.4 58.1 1.0 O1 A:AKG402 4.0 40.8 1.0 CG A:HIS142 4.3 34.0 1.0 CG A:HIS209 4.3 23.9 1.0 C3 A:AKG402 4.3 30.8 1.0 ND1 A:HIS142 4.3 25.9 1.0 ND1 A:HIS209 4.4 24.1 1.0 CB A:ASP144 4.4 36.1 1.0 CG A:LYS401 4.5 41.8 1.0 CA A:LYS401 4.7 44.0 1.0 CD2 A:LEU202 4.8 24.5 1.0 CB A:SER204 4.9 32.7 1.0 C4 A:AKG402 4.9 35.6 1.0 N A:ASP144 4.9 31.9 1.0

Iron binding site 2 out of 4 in the Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe403 b:45.1 occ:1.00 OD1 B:ASP144 2.1 39.8 1.0 O1 B:AKG402 2.1 44.1 1.0 NE2 B:HIS209 2.2 28.4 1.0 NE2 B:HIS142 2.3 30.3 1.0 O5 B:AKG402 2.3 38.3 1.0 C1 B:AKG402 2.7 50.6 1.0 C2 B:AKG402 2.8 46.4 1.0 CG B:ASP144 2.9 43.5 1.0 CE1 B:HIS209 3.1 26.9 1.0 CD2 B:HIS142 3.1 29.0 1.0 OD2 B:ASP144 3.1 60.0 1.0 CD2 B:HIS209 3.2 25.7 1.0 CE1 B:HIS142 3.3 33.7 1.0 O2 B:AKG402 3.9 45.6 1.0 ND1 B:HIS209 4.2 28.4 1.0 C3 B:AKG402 4.3 41.4 1.0 CG B:HIS142 4.3 31.5 1.0 CG B:HIS209 4.3 30.0 1.0 CB B:ASP144 4.3 28.3 1.0 ND1 B:HIS142 4.4 27.9 1.0 CG B:LYS401 4.4 47.6 1.0 CB B:SER204 4.7 32.9 1.0 CA B:LYS401 4.7 41.9 1.0 N B:ASP144 4.7 31.3 1.0 CD2 B:LEU202 4.8 21.6 1.0 CB B:LYS401 4.8 47.4 1.0 CA B:ASP144 4.9 34.6 1.0 C B:TRP143 4.9 29.4 1.0

Iron binding site 3 out of 4 in the Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:50.1 occ:1.00 O1 C:AKG402 2.1 56.8 1.0 OD1 C:ASP144 2.1 46.5 1.0 O5 C:AKG402 2.1 36.3 1.0 NE2 C:HIS142 2.2 36.4 1.0 NE2 C:HIS209 2.2 36.9 1.0 C1 C:AKG402 2.7 50.3 1.0 C2 C:AKG402 2.8 42.7 1.0 CG C:ASP144 3.0 43.0 1.0 CD2 C:HIS142 3.1 34.1 1.0 CD2 C:HIS209 3.2 34.2 1.0 CE1 C:HIS209 3.2 33.3 1.0 CE1 C:HIS142 3.2 32.6 1.0 OD2 C:ASP144 3.3 60.8 1.0 O2 C:AKG402 4.0 54.1 1.0 CG C:HIS142 4.3 31.5 1.0 C3 C:AKG402 4.3 34.9 1.0 ND1 C:HIS209 4.3 37.3 1.0 ND1 C:HIS142 4.3 37.2 1.0 CG C:HIS209 4.3 35.3 1.0 CB C:ASP144 4.4 31.9 1.0 CG C:LYS401 4.6 57.7 1.0 CA C:LYS401 4.7 52.5 1.0 C4 C:AKG402 4.9 37.6 1.0 CE1 C:HIS139 4.9 49.0 1.0 N C:ASP144 4.9 45.0 1.0 CD2 C:LEU202 5.0 31.1 1.0 CB C:SER204 5.0 36.4 1.0

Iron binding site 4 out of 4 in the Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Hydroxylase Homolog of Besd with Fe(II), Alpha-Ketoglutarate, and Lysine within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe502 b:41.6 occ:1.00 OD2 D:ASP144 2.1 47.3 1.0 O5 D:AKG501 2.2 41.1 1.0 O2 D:AKG501 2.2 57.3 1.0 NE2 D:HIS209 2.2 32.5 1.0 NE2 D:HIS142 2.2 27.1 1.0 C2 D:AKG501 2.8 45.1 1.0 C1 D:AKG501 2.8 54.6 1.0 CG D:ASP144 2.9 40.8 1.0 CE1 D:HIS209 3.1 30.9 1.0 OD1 D:ASP144 3.1 43.8 1.0 CD2 D:HIS142 3.2 23.1 1.0 CE1 D:HIS142 3.2 33.9 1.0 CD2 D:HIS209 3.2 30.1 1.0 O1 D:AKG501 4.1 54.9 1.0 ND1 D:HIS209 4.2 25.9 1.0 C3 D:AKG501 4.3 36.7 1.0 ND1 D:HIS142 4.3 27.7 1.0 CG D:HIS142 4.3 31.0 1.0 CG D:HIS209 4.3 32.0 1.0 CB D:ASP144 4.4 33.2 1.0 CB D:SER204 4.8 34.2 1.0 C4 D:AKG501 4.9 40.2 1.0

M.E.Neugebauer, E.N.Kissman, J.A.Marchand, J.G.Pelton, N.A.Sambold, D.C.Millar, M.C.Y.Chang. Converting A Radical Hydroxylase Into A Halogenase Through Library Screening and Structure-Guided Engineering To Be Published.