Chlorine 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:

Iron

(Fe)

5 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate, PDB code: 6nie:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl303 b:22.1 occ:1.00 FE A:FE2302 2.4 33.4 1.0 O A:HOH487 3.1 24.7 1.0 O1 A:AKG304 3.3 30.1 1.0 CA A:GLY139 3.4 21.5 1.0 NE2 A:HIS204 3.4 20.2 1.0 N A:GLY139 3.5 22.3 1.0 CD2 A:HIS137 3.5 20.9 1.0 CE1 A:HIS204 3.6 20.4 1.0 NE2 A:HIS137 3.6 16.4 1.0 C A:TRP138 3.7 22.7 1.0 O A:TRP138 3.7 22.8 1.0 CG2 A:THR199 3.8 19.5 1.0 CB A:THR199 3.8 20.3 1.0 CA A:LYS301 4.0 22.7 1.0 CG A:LYS301 4.0 23.6 1.0 N A:LYS301 4.1 21.6 1.0 C1 A:AKG304 4.5 30.5 1.0 O A:HOH476 4.5 20.6 1.0 O5 A:AKG304 4.5 30.7 1.0 O A:HOH453 4.6 25.3 1.0 CB A:LYS301 4.6 23.2 1.0 OG1 A:THR199 4.6 21.3 1.0 CA A:TRP138 4.7 21.4 1.0 CD2 A:HIS204 4.8 19.1 1.0 O A:THR199 4.8 21.0 1.0 CG A:HIS137 4.9 21.6 1.0 C A:GLY139 4.9 22.6 1.0 ND1 A:HIS204 4.9 19.9 1.0 CE1 A:HIS137 4.9 16.7 1.0 CA A:THR199 4.9 18.3 1.0

Chlorine binding site 2 out of 4 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl303 b:27.2 occ:1.00 FE B:FE2302 2.4 26.3 1.0 O B:HOH491 2.9 32.5 1.0 CA B:GLY139 3.3 27.7 1.0 O2 B:AKG304 3.3 32.7 1.0 NE2 B:HIS137 3.3 39.7 1.0 CD2 B:HIS137 3.4 38.0 1.0 N B:GLY139 3.4 27.2 1.0 NE2 B:HIS204 3.5 29.9 1.0 CE1 B:HIS204 3.6 28.5 1.0 C B:TRP138 3.6 28.4 1.0 CG2 B:THR199 3.6 23.1 1.0 O B:TRP138 3.7 30.7 1.0 CB B:THR199 3.9 23.4 1.0 CA B:LYS301 4.0 29.9 1.0 CG B:LYS301 4.0 27.6 1.0 N B:LYS301 4.2 30.1 1.0 C1 B:AKG304 4.5 34.0 1.0 O B:HOH458 4.6 28.0 1.0 CB B:LYS301 4.6 28.4 1.0 O B:HOH424 4.6 27.8 1.0 CA B:TRP138 4.6 27.4 1.0 CE1 B:HIS137 4.7 39.4 1.0 O5 B:AKG304 4.7 33.6 1.0 CG B:HIS137 4.7 38.5 1.0 OG1 B:THR199 4.7 24.6 1.0 C B:GLY139 4.8 28.7 1.0 O B:HOH416 4.8 25.1 1.0 CD2 B:HIS204 4.9 29.8 1.0 ND1 B:HIS204 4.9 27.9 1.0 O B:THR199 4.9 25.4 1.0 CA B:THR199 5.0 21.6 1.0

Chlorine binding site 3 out of 4 in the Besd with Fe(II), Chloride, and Alpha-Ketoglutarate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl303 b:28.6 occ:1.00 FE C:FE2302 2.5 32.7 1.0 O C:HOH480 3.1 34.4 1.0 CA C:GLY139 3.2 35.0 1.0 N C:GLY139 3.3 34.3 1.0 O2 C:AKG304 3.4 32.9 1.0 CD2 C:HIS137 3.5 34.5 1.0 C C:TRP138 3.5 34.5 1.0 NE2 C:HIS204 3.6 31.9 1.0 O C:TRP138 3.6 35.0 1.0 CE1 C:HIS204 3.7 31.3 1.0 NE2 C:HIS137 3.7 34.3 1.0 CG2 C:THR199 3.8 32.6 1.0 CB C:THR199 3.9 33.1 1.0 CG C:LYS301 3.9 37.6 1.0 CA C:LYS301 3.9 35.5 1.0 N C:LYS301 4.2 35.6 1.0 CB C:LYS301 4.5 36.6 1.0 O C:HOH482 4.5 27.9 1.0 O C:HOH454 4.5 44.0 1.0 CA C:TRP138 4.6 33.5 1.0 C1 C:AKG304 4.6 36.1 1.0 C C:GLY139 4.7 35.6 1.0 OG1 C:THR199 4.8 35.0 1.0 CG C:HIS137 4.8 38.3 1.0 O C:THR199 4.8 33.7 1.0 O C:HOH417 4.8 33.5 1.0 O5 C:AKG304 4.8 35.2 1.0 CD2 C:HIS204 4.9 31.4 1.0 CA C:THR199 4.9 32.1 1.0 ND1 C:HIS204 5.0 30.4 1.0 CE1 C:HIS137 5.0 34.2 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Besd with Fe(II), Chloride, and Alpha-Ketoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl303 b:27.1 occ:1.00 FE D:FE2302 2.4 25.6 1.0 O D:HOH432 3.3 28.5 1.0 NE2 D:HIS137 3.3 38.4 1.0 NE2 D:HIS204 3.3 33.4 1.0 CA D:GLY139 3.3 29.6 1.0 O1 D:AKG304 3.4 35.6 1.0 CD2 D:HIS137 3.4 36.2 1.0 N D:GLY139 3.5 27.5 1.0 CE1 D:HIS204 3.5 29.7 1.0 C D:TRP138 3.7 28.5 1.0 O D:TRP138 3.9 30.6 1.0 CG2 D:THR199 3.9 27.4 1.0 CB D:THR199 3.9 27.0 1.0 CG D:LYS301 3.9 31.7 1.0 CA D:LYS301 4.0 30.7 1.0 N D:LYS301 4.1 29.6 1.0 C1 D:AKG304 4.5 37.4 1.0 O D:HOH448 4.5 25.0 1.0 CB D:LYS301 4.6 31.6 1.0 O D:HOH477 4.6 28.2 1.0 CE1 D:HIS137 4.6 36.2 1.0 CD2 D:HIS204 4.7 30.0 1.0 O5 D:AKG304 4.7 35.2 1.0 CA D:TRP138 4.7 26.6 1.0 O D:THR199 4.8 25.4 1.0 OG1 D:THR199 4.8 27.4 1.0 CG D:HIS137 4.8 36.3 1.0 ND1 D:HIS204 4.8 28.3 1.0 C D:GLY139 4.8 30.8 1.0 CA D:THR199 4.9 26.1 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