Iron in PDB 6nie: Besd with Fe(II), Chloride, and Alpha-Ketoglutarate

The structure of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate, PDB code: 6nie was solved by 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)	70.03 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	61.358, 68.916, 79.702, 115.36, 91.57, 112.95
R / Rfree (%)	17.7 / 21.6

The structure of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate (pdb code 6nie). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate, PDB code: 6nie:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:33.4 occ:1.00 O1 A:AKG304 2.2 30.1 1.0 O5 A:AKG304 2.2 30.7 1.0 NE2 A:HIS204 2.2 20.2 1.0 NE2 A:HIS137 2.2 16.4 1.0 CL A:CL303 2.4 22.1 1.0 C2 A:AKG304 2.9 31.0 1.0 C1 A:AKG304 2.9 30.5 1.0 CD2 A:HIS137 3.1 20.9 1.0 CD2 A:HIS204 3.1 19.1 1.0 CE1 A:HIS204 3.2 20.4 1.0 CE1 A:HIS137 3.3 16.7 1.0 O2 A:AKG304 4.1 31.1 1.0 O A:HOH487 4.2 24.7 1.0 CG A:HIS204 4.3 19.5 1.0 CG A:HIS137 4.3 21.6 1.0 ND1 A:HIS204 4.3 19.9 1.0 C3 A:AKG304 4.3 32.2 1.0 ND1 A:HIS137 4.4 17.3 1.0 CG2 A:THR199 4.5 19.5 1.0 NE2 A:HIS134 4.6 26.1 1.0 CE1 A:HIS134 4.6 26.3 1.0 CA A:LYS301 4.7 22.7 1.0 H32 A:AKG304 4.7 38.6 1.0 H41 A:AKG304 4.7 39.2 1.0 CG A:LYS301 4.8 23.6 1.0 H31 A:AKG304 4.8 38.6 1.0 CD2 A:LEU197 4.9 16.9 1.0

Iron binding site 2 out of 5 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:26.3 occ:1.00 O2 B:AKG304 2.1 32.7 1.0 NE2 B:HIS137 2.1 39.7 1.0 NE2 B:HIS204 2.3 29.9 1.0 O5 B:AKG304 2.3 33.6 1.0 CL B:CL303 2.4 27.2 1.0 C1 B:AKG304 2.9 34.0 1.0 C2 B:AKG304 2.9 34.5 1.0 CD2 B:HIS137 3.1 38.0 1.0 CE1 B:HIS137 3.1 39.4 1.0 CE1 B:HIS204 3.2 28.5 1.0 CD2 B:HIS204 3.2 29.8 1.0 O B:HOH491 4.0 32.5 1.0 O1 B:AKG304 4.1 34.7 1.0 ND1 B:HIS137 4.2 39.7 1.0 CG B:HIS137 4.2 38.5 1.0 ND1 B:HIS204 4.3 27.9 1.0 CG B:HIS204 4.3 28.8 1.0 C3 B:AKG304 4.4 34.7 1.0 CG2 B:THR199 4.5 23.1 1.0 CE1 B:HIS134 4.5 37.8 1.0 NE2 B:HIS134 4.6 37.9 1.0 H41 B:AKG304 4.7 42.9 1.0 CA B:LYS301 4.7 29.9 1.0 CD2 B:LEU197 4.8 25.8 1.0 CG B:LYS301 4.8 27.6 1.0 H32 B:AKG304 4.8 41.7 1.0 H31 B:AKG304 4.9 41.7 1.0 H42 B:AKG304 5.0 42.9 1.0 ND2 B:ASN219 5.0 30.5 1.0 C4 B:AKG304 5.0 35.7 1.0

Iron binding site 3 out of 5 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe305 b:19.2 occ:1.00 OE2 B:GLU225 1.7 50.5 1.0 O B:HOH464 2.2 33.4 1.0 O B:HOH412 2.2 34.0 1.0 O D:HOH410 2.3 38.6 1.0 CD B:GLU225 2.7 47.7 1.0 OE1 B:GLU225 3.1 48.5 1.0 OE2 D:GLU225 4.0 47.8 1.0 CG B:GLU225 4.0 43.9 1.0 O B:HOH517 4.1 45.5 1.0 OE1 D:GLU225 4.4 47.0 1.0 CD D:GLU225 4.6 45.9 1.0

Iron binding site 4 out of 5 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe302 b:32.7 occ:1.00 O2 C:AKG304 2.1 32.9 1.0 NE2 C:HIS137 2.2 34.3 1.0 NE2 C:HIS204 2.3 31.9 1.0 O5 C:AKG304 2.4 35.2 1.0 CL C:CL303 2.5 28.6 1.0 C1 C:AKG304 2.9 36.1 1.0 CD2 C:HIS137 3.0 34.5 1.0 C2 C:AKG304 3.0 36.1 1.0 CD2 C:HIS204 3.2 31.4 1.0 CE1 C:HIS204 3.3 31.3 1.0 CE1 C:HIS137 3.3 34.2 1.0 O1 C:AKG304 4.1 37.9 1.0 CG C:HIS137 4.2 38.3 1.0 O C:HOH480 4.2 34.4 1.0 ND1 C:HIS137 4.3 37.6 1.0 ND1 C:HIS204 4.3 30.4 1.0 CG C:HIS204 4.4 30.6 1.0 C3 C:AKG304 4.4 37.5 1.0 CE1 C:HIS134 4.5 38.6 1.0 CG C:LYS301 4.6 37.6 1.0 CG2 C:THR199 4.6 32.6 1.0 CA C:LYS301 4.6 35.5 1.0 NE2 C:HIS134 4.7 38.4 1.0 H41 C:AKG304 4.8 46.1 1.0 H32 C:AKG304 4.8 45.0 1.0 CD2 C:LEU197 4.8 31.0 1.0 H31 C:AKG304 4.9 45.0 1.0

Iron binding site 5 out of 5 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe302 b:25.6 occ:1.00 NE2 D:HIS204 2.1 33.4 1.0 NE2 D:HIS137 2.2 38.4 1.0 O1 D:AKG304 2.2 35.6 1.0 O5 D:AKG304 2.3 35.2 1.0 CL D:CL303 2.4 27.1 1.0 C1 D:AKG304 2.9 37.4 1.0 C2 D:AKG304 2.9 36.4 1.0 CD2 D:HIS204 3.0 30.0 1.0 CE1 D:HIS137 3.1 36.2 1.0 CE1 D:HIS204 3.1 29.7 1.0 CD2 D:HIS137 3.2 36.2 1.0 O2 D:AKG304 4.1 38.3 1.0 CG D:HIS204 4.2 28.7 1.0 ND1 D:HIS137 4.2 36.5 1.0 O D:HOH432 4.2 28.5 1.0 ND1 D:HIS204 4.2 28.3 1.0 CG D:HIS137 4.3 36.3 1.0 C3 D:AKG304 4.4 36.3 1.0 CE1 D:HIS134 4.4 38.8 1.0 NE2 D:HIS134 4.6 38.3 1.0 CA D:LYS301 4.7 30.7 1.0 H32 D:AKG304 4.7 43.6 1.0 CG2 D:THR199 4.7 27.4 1.0 H41 D:AKG304 4.7 42.9 1.0 CG D:LYS301 4.8 31.7 1.0 CD2 D:LEU197 4.8 25.7 1.0 H31 D:AKG304 4.9 43.6 1.0

M.E.Neugebauer, K.H.Sumida, J.G.Pelton, J.L.Mcmurry, J.A.Marchand, M.C.Y.Chang. A Family of Radical Halogenases For the Engineering of Amino-Acid-Based Products. Nat.Chem.Biol. V. 15 1009 2019.
ISSN: ESSN 1552-4469
PubMed: 31548692
DOI: 10.1038/S41589-019-0355-X