Iron in PDB 6hto: Tryptophan Lyase 'Empty State'

The structure of Tryptophan Lyase 'Empty State', PDB code: 6hto was solved by P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.43 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.970, 92.610, 94.460, 90.00, 98.73, 90.00
R / Rfree (%)	16.8 / 19.2

The structure of Tryptophan Lyase 'Empty State' also contains other interesting chemical elements:

Chlorine

(Cl)

13 atoms

The binding sites of Iron atom in the Tryptophan Lyase 'Empty State' (pdb code 6hto). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Tryptophan Lyase 'Empty State', PDB code: 6hto:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:10.4 occ:1.00 FE1 A:SF4501 0.0 10.4 1.0 S2 A:SF4501 2.3 10.7 1.0 SG A:CYS95 2.3 11.1 1.0 S4 A:SF4501 2.3 10.6 1.0 S3 A:SF4501 2.3 11.1 1.0 FE3 A:SF4501 2.7 10.6 1.0 FE2 A:SF4501 2.7 10.8 1.0 FE4 A:SF4501 2.9 10.9 1.0 CB A:CYS95 3.3 10.0 1.0 S1 A:SF4501 3.9 10.8 1.0 N A:MET502 4.0 6.8 1.0 CB A:SER97 4.3 13.4 1.0 N A:GLU143 4.3 9.1 1.0 CA A:GLY142 4.5 10.1 1.0 CB A:MET104 4.6 10.1 1.0 N A:SER97 4.7 12.4 1.0 O A:MET104 4.7 11.4 1.0 CA A:CYS95 4.7 12.2 1.0 CA A:SER97 4.8 13.1 1.0 SG A:CYS102 4.8 10.2 1.0 C A:SER97 4.8 14.8 1.0 C A:MET104 4.8 12.6 1.0 O A:SER97 4.8 13.3 1.0 SG A:CYS99 4.8 11.1 1.0 OXT A:MET502 4.8 9.8 1.0 N A:ARG105 4.9 11.2 1.0 C A:GLY142 4.9 10.1 1.0

Iron binding site 2 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:10.8 occ:1.00 FE2 A:SF4501 0.0 10.8 1.0 S3 A:SF4501 2.2 11.1 1.0 S4 A:SF4501 2.3 10.6 1.0 SG A:CYS99 2.3 11.1 1.0 S1 A:SF4501 2.3 10.8 1.0 FE3 A:SF4501 2.6 10.6 1.0 FE1 A:SF4501 2.7 10.4 1.0 FE4 A:SF4501 2.9 10.9 1.0 CB A:CYS99 3.1 12.0 1.0 NZ A:LYS224 3.8 8.8 1.0 S2 A:SF4501 3.8 10.7 1.0 CD A:LYS224 3.9 9.8 1.0 OXT A:MET502 4.0 9.8 1.0 N A:CYS99 4.1 11.0 1.0 CA A:CYS99 4.2 10.9 1.0 CE A:LYS224 4.4 10.0 1.0 CB A:SER97 4.5 13.4 1.0 CB A:CYS102 4.6 9.8 1.0 SG A:CYS102 4.6 10.2 1.0 SG A:CYS95 4.7 11.1 1.0 O A:HOH694 4.7 13.5 1.0 N A:MET502 4.8 6.8 1.0

Iron binding site 3 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:10.6 occ:1.00 FE3 A:SF4501 0.0 10.6 1.0 S2 A:SF4501 2.2 10.7 1.0 S1 A:SF4501 2.3 10.8 1.0 S4 A:SF4501 2.3 10.6 1.0 SG A:CYS102 2.3 10.2 1.0 FE2 A:SF4501 2.6 10.8 1.0 FE1 A:SF4501 2.7 10.4 1.0 FE4 A:SF4501 2.9 10.9 1.0 CB A:CYS102 3.2 9.8 1.0 S3 A:SF4501 3.8 11.1 1.0 NE2 A:GLN363 3.8 13.8 1.0 CB A:MET104 4.1 10.1 1.0 SD A:MET502 4.3 9.8 1.0 CB A:CYS99 4.5 12.0 1.0 N A:ARG105 4.6 11.2 1.0 SG A:CYS99 4.6 11.1 1.0 CA A:CYS102 4.7 10.1 1.0 C A:MET104 4.7 12.6 1.0 CA A:MET104 4.7 12.8 1.0 N A:MET104 4.7 11.1 1.0 CD A:GLN363 4.8 12.1 1.0 CE A:MET502 4.8 11.3 1.0 N A:MET502 4.8 6.8 1.0 SG A:CYS95 4.8 11.1 1.0 OXT A:MET502 4.9 9.8 1.0 CG A:GLN363 4.9 14.8 1.0

Iron binding site 4 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:10.9 occ:1.00 FE4 A:SF4501 0.0 10.9 1.0 N A:MET502 2.2 6.8 1.0 OXT A:MET502 2.2 9.8 1.0 S2 A:SF4501 2.3 10.7 1.0 S1 A:SF4501 2.4 10.8 1.0 S3 A:SF4501 2.4 11.1 1.0 SD A:MET502 2.7 9.8 1.0 FE3 A:SF4501 2.9 10.6 1.0 FE2 A:SF4501 2.9 10.8 1.0 FE1 A:SF4501 2.9 10.4 1.0 C A:MET502 3.0 8.1 1.0 CA A:MET502 3.1 8.2 1.0 CG A:MET502 3.7 10.1 1.0 CE A:MET502 3.7 11.3 1.0 CB A:MET502 3.9 11.5 1.0 NZ A:LYS224 4.0 8.8 1.0 S4 A:SF4501 4.2 10.6 1.0 O A:MET502 4.2 11.2 1.0 NE2 A:GLN363 4.6 13.8 1.0 SG A:CYS95 4.8 11.1 1.0 CD A:LYS224 4.8 9.8 1.0 O A:THR141 4.8 9.5 1.0 N A:GLU143 4.9 9.1 1.0 CA A:GLY142 4.9 10.1 1.0 SG A:CYS102 4.9 10.2 1.0 SG A:CYS99 5.0 11.1 1.0

Iron binding site 5 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:13.1 occ:1.00 FE1 B:SF4501 0.0 13.1 1.0 S4 B:SF4501 2.3 13.6 1.0 SG B:CYS95 2.3 13.2 1.0 S3 B:SF4501 2.3 14.3 1.0 S2 B:SF4501 2.3 13.5 1.0 FE3 B:SF4501 2.7 13.8 1.0 FE2 B:SF4501 2.7 13.5 1.0 FE4 B:SF4501 2.9 13.5 1.0 CB B:CYS95 3.3 12.3 1.0 S1 B:SF4501 3.9 13.6 1.0 N B:MET502 4.0 10.3 1.0 N B:GLU143 4.3 11.5 1.0 CB B:SER97 4.3 20.6 1.0 CA B:GLY142 4.5 11.3 1.0 O B:MET104 4.7 13.7 1.0 CB B:MET104 4.7 15.1 1.0 N B:SER97 4.7 15.5 1.0 CA B:CYS95 4.7 13.9 1.0 C B:MET104 4.8 13.3 1.0 SG B:CYS102 4.8 13.7 1.0 CA B:SER97 4.8 15.1 1.0 C B:SER97 4.8 21.1 1.0 O B:MET502 4.8 11.7 1.0 SG B:CYS99 4.8 14.6 1.0 C B:GLY142 4.9 10.5 1.0 O B:SER97 4.9 19.6 1.0 N B:ARG105 4.9 14.7 1.0

Iron binding site 6 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:13.5 occ:1.00 FE2 B:SF4501 0.0 13.5 1.0 S3 B:SF4501 2.3 14.3 1.0 S1 B:SF4501 2.3 13.6 1.0 S4 B:SF4501 2.3 13.6 1.0 SG B:CYS99 2.3 14.6 1.0 FE3 B:SF4501 2.6 13.8 1.0 FE1 B:SF4501 2.7 13.1 1.0 FE4 B:SF4501 2.9 13.5 1.0 CB B:CYS99 3.1 14.8 1.0 NZ B:LYS224 3.7 12.6 1.0 S2 B:SF4501 3.8 13.5 1.0 CD B:LYS224 3.9 15.1 1.0 O B:MET502 4.0 11.7 1.0 N B:CYS99 4.1 15.3 1.0 CA B:CYS99 4.2 14.0 1.0 CE B:LYS224 4.4 12.4 1.0 CB B:SER97 4.5 20.6 1.0 SG B:CYS102 4.6 13.7 1.0 CB B:CYS102 4.7 15.5 1.0 SG B:CYS95 4.7 13.2 1.0 O B:HOH669 4.8 15.9 1.0 N B:MET502 4.8 10.3 1.0 CE B:MET101 5.0 17.2 1.0

Iron binding site 7 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:13.8 occ:1.00 FE3 B:SF4501 0.0 13.8 1.0 S2 B:SF4501 2.2 13.5 1.0 S1 B:SF4501 2.3 13.6 1.0 S4 B:SF4501 2.3 13.6 1.0 SG B:CYS102 2.3 13.7 1.0 FE2 B:SF4501 2.6 13.5 1.0 FE1 B:SF4501 2.7 13.1 1.0 FE4 B:SF4501 2.9 13.5 1.0 CB B:CYS102 3.2 15.5 1.0 S3 B:SF4501 3.8 14.3 1.0 NE2 B:GLN363 3.8 14.8 1.0 CB B:MET104 4.1 15.1 1.0 SD B:MET502 4.3 10.9 1.0 CB B:CYS99 4.5 14.8 1.0 N B:ARG105 4.6 14.7 1.0 SG B:CYS99 4.6 14.6 1.0 C B:MET104 4.6 13.3 1.0 CA B:CYS102 4.7 14.2 1.0 CA B:MET104 4.7 16.0 1.0 N B:MET104 4.7 14.9 1.0 CD B:GLN363 4.8 16.2 1.0 CG B:GLN363 4.8 14.7 1.0 N B:MET502 4.8 10.3 1.0 SG B:CYS95 4.8 13.2 1.0 CE B:MET502 4.9 12.7 1.0 O B:MET502 4.9 11.7 1.0

Iron binding site 8 out of 8 in the Tryptophan Lyase 'Empty State'


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Tryptophan Lyase 'Empty State' within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:13.5 occ:1.00 FE4 B:SF4501 0.0 13.5 1.0 O B:MET502 2.2 11.7 1.0 N B:MET502 2.2 10.3 1.0 S1 B:SF4501 2.3 13.6 1.0 S2 B:SF4501 2.4 13.5 1.0 S3 B:SF4501 2.4 14.3 1.0 SD B:MET502 2.6 10.9 1.0 FE3 B:SF4501 2.9 13.8 1.0 FE2 B:SF4501 2.9 13.5 1.0 FE1 B:SF4501 2.9 13.1 1.0 C B:MET502 3.0 11.0 1.0 CA B:MET502 3.1 9.1 1.0 CG B:MET502 3.6 11.2 1.0 CE B:MET502 3.8 12.7 1.0 CB B:MET502 3.9 13.4 1.0 NZ B:LYS224 4.0 12.6 1.0 S4 B:SF4501 4.2 13.6 1.0 OXT B:MET502 4.2 13.5 1.0 NE2 B:GLN363 4.5 14.8 1.0 CD B:LYS224 4.8 15.1 1.0 SG B:CYS95 4.8 13.2 1.0 O B:THR141 4.8 11.5 1.0 N B:GLU143 4.9 11.5 1.0 SG B:CYS102 5.0 13.7 1.0 CA B:GLY142 5.0 11.3 1.0 SG B:CYS99 5.0 14.6 1.0

P.Amara, J.M.Mouesca, M.Bella, L.Martin, C.Saragaglia, S.Gambarelli, Y.Nicolet. Radical S-Adenosyl-L-Methionine Tryptophan Lyase (Nosl): How the Protein Controls the Carboxyl Radical •CO2-Migration. J.Am.Chem.Soc. V. 140 16661 2018.
ISSN: ESSN 1520-5126
PubMed: 30418774
DOI: 10.1021/JACS.8B09142