Iron in PDB 6htm: X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin

The structure of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin, PDB code: 6htm was solved by P.Amara, J.M.Mouesca, M.Bella, 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)	47.05 / 1.70
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	94.530, 47.140, 113.900, 90.00, 108.90, 90.00
R / Rfree (%)	16.2 / 18.9

The structure of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Bromine	(Br)	6 atoms
Chlorine	(Cl)	7 atoms

The binding sites of Iron atom in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin (pdb code 6htm). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin, PDB code: 6htm:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2502 b:24.5 occ:1.00 FE1 A:SF42502 0.0 24.5 1.0 S2 A:SF42502 2.3 24.1 1.0 S3 A:SF42502 2.3 22.4 1.0 S4 A:SF42502 2.3 23.1 1.0 SG A:CYS102 2.4 27.1 1.0 FE3 A:SF42502 2.6 27.2 1.0 FE2 A:SF42502 2.7 23.4 1.0 FE4 A:SF42502 2.8 23.7 1.0 CB A:CYS102 3.2 28.3 1.0 S1 A:SF42502 3.8 23.2 1.0 NE2 A:GLN363 3.9 24.9 1.0 CB A:MET104 4.1 25.5 1.0 SD A:MET2503 4.3 29.5 1.0 CB A:CYS99 4.4 28.8 1.0 CA A:CYS102 4.6 27.8 1.0 SG A:CYS99 4.6 28.8 1.0 N A:ARG105 4.6 30.9 1.0 O A:MET2503 4.6 30.9 1.0 CD A:GLN363 4.7 24.2 1.0 C A:MET104 4.8 28.0 1.0 CA A:MET104 4.8 26.8 1.0 CE A:MET2503 4.8 32.1 1.0 N A:MET104 4.8 28.1 1.0 CG A:GLN363 4.8 26.3 1.0 N A:MET2503 4.9 23.6 1.0 SG A:CYS95 4.9 26.9 1.0

Iron binding site 2 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2502 b:23.4 occ:1.00 FE2 A:SF42502 0.0 23.4 1.0 S1 A:SF42502 2.2 23.2 1.0 S4 A:SF42502 2.3 23.1 1.0 S3 A:SF42502 2.3 22.4 1.0 SG A:CYS95 2.3 26.9 1.0 FE1 A:SF42502 2.7 24.5 1.0 FE3 A:SF42502 2.7 27.2 1.0 FE4 A:SF42502 2.9 23.7 1.0 CB A:CYS95 3.4 24.6 1.0 S2 A:SF42502 3.9 24.1 1.0 N A:MET2503 3.9 23.6 1.0 CB A:SER97 4.2 32.2 1.0 N A:GLU143 4.3 23.4 1.0 CA A:GLY142 4.5 21.8 1.0 O A:MET2503 4.6 30.9 1.0 N A:SER97 4.7 29.4 1.0 CB A:MET104 4.7 25.5 1.0 C A:SER97 4.8 33.0 1.0 CA A:SER97 4.8 31.2 1.0 O A:MET104 4.8 27.8 1.0 CA A:CYS95 4.8 25.1 1.0 SG A:CYS102 4.8 27.1 1.0 SG A:CYS99 4.9 28.8 1.0 O A:SER97 4.9 33.5 1.0 C A:MET104 4.9 28.0 1.0 C A:GLY142 4.9 23.8 1.0

Iron binding site 3 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2502 b:27.2 occ:1.00 FE3 A:SF42502 0.0 27.2 1.0 S4 A:SF42502 2.3 23.1 1.0 S1 A:SF42502 2.3 23.2 1.0 S2 A:SF42502 2.3 24.1 1.0 SG A:CYS99 2.4 28.8 1.0 FE1 A:SF42502 2.6 24.5 1.0 FE2 A:SF42502 2.7 23.4 1.0 FE4 A:SF42502 2.9 23.7 1.0 CB A:CYS99 3.1 28.8 1.0 NZ A:LYS224 3.7 25.8 1.0 O A:MET2503 3.8 30.9 1.0 S3 A:SF42502 3.8 22.4 1.0 CD A:LYS224 3.9 26.8 1.0 N A:CYS99 4.0 27.2 1.0 CA A:CYS99 4.2 28.6 1.0 CE A:LYS224 4.4 25.6 1.0 CB A:SER97 4.4 32.2 1.0 CB A:CYS102 4.6 28.3 1.0 SG A:CYS102 4.7 27.1 1.0 O A:HOH2685 4.7 27.0 1.0 SG A:CYS95 4.8 26.9 1.0 N A:MET2503 4.9 23.6 1.0 CE A:MET101 4.9 32.4 1.0 C A:MET2503 4.9 29.4 1.0 N A:GLU98 5.0 28.9 1.0

Iron binding site 4 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe2502 b:23.7 occ:1.00 FE4 A:SF42502 0.0 23.7 1.0 O A:MET2503 2.1 30.9 1.0 S3 A:SF42502 2.3 22.4 1.0 S2 A:SF42502 2.3 24.1 1.0 S1 A:SF42502 2.4 23.2 1.0 N A:MET2503 2.4 23.6 1.0 SD A:MET2503 2.7 29.5 1.0 FE1 A:SF42502 2.8 24.5 1.0 FE2 A:SF42502 2.9 23.4 1.0 FE3 A:SF42502 2.9 27.2 1.0 C A:MET2503 2.9 29.4 1.0 CA A:MET2503 3.1 24.4 1.0 CG A:MET2503 3.6 30.1 1.0 CE A:MET2503 3.7 32.1 1.0 CB A:MET2503 3.8 25.9 1.0 NZ A:LYS224 3.9 25.8 1.0 S4 A:SF42502 4.1 23.1 1.0 OXT A:MET2503 4.1 28.0 1.0 NE2 A:GLN363 4.6 24.9 1.0 CD A:LYS224 4.7 26.8 1.0 SG A:CYS95 4.8 26.9 1.0 O A:THR141 4.8 24.3 1.0 N A:GLU143 4.9 23.4 1.0 SG A:CYS102 5.0 27.1 1.0 CA A:GLY142 5.0 21.8 1.0

Iron binding site 5 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:19.7 occ:1.00 FE1 B:SF4501 0.0 19.7 1.0 S3 B:SF4501 2.3 19.6 1.0 S4 B:SF4501 2.3 20.9 1.0 S2 B:SF4501 2.3 18.3 1.0 SG B:CYS102 2.4 19.7 1.0 FE3 B:SF4501 2.6 20.8 1.0 FE2 B:SF4501 2.6 18.9 1.0 FE4 B:SF4501 2.8 17.7 1.0 CB B:CYS102 3.2 20.3 1.0 S1 B:SF4501 3.8 19.7 1.0 NE2 B:GLN363 3.9 20.5 1.0 CB B:MET104 4.1 21.6 1.0 SD B:MET503 4.3 19.0 1.0 CB B:CYS99 4.5 18.8 1.0 N B:ARG105 4.5 21.1 1.0 SG B:CYS99 4.6 20.8 1.0 CA B:CYS102 4.7 17.7 1.0 C B:MET104 4.7 21.3 1.0 CA B:MET104 4.7 20.1 1.0 N B:MET104 4.8 21.0 1.0 SG B:CYS95 4.8 18.4 1.0 CD B:GLN363 4.8 21.4 1.0 N B:MET503 4.8 17.9 1.0 O B:MET503 4.9 20.8 1.0 CE B:MET503 4.9 20.5 1.0 CG B:GLN363 5.0 21.7 1.0

Iron binding site 6 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:18.9 occ:1.00 FE2 B:SF4501 0.0 18.9 1.0 SG B:CYS95 2.2 18.4 1.0 S3 B:SF4501 2.3 19.6 1.0 S4 B:SF4501 2.3 20.9 1.0 S1 B:SF4501 2.3 19.7 1.0 FE1 B:SF4501 2.6 19.7 1.0 FE3 B:SF4501 2.7 20.8 1.0 FE4 B:SF4501 2.9 17.7 1.0 CB B:CYS95 3.4 16.6 1.0 S2 B:SF4501 3.9 18.3 1.0 N B:MET503 3.9 17.9 1.0 CB B:SER97 4.1 21.7 1.0 N B:GLU143 4.3 16.6 1.0 CA B:GLY142 4.5 14.7 1.0 CB B:MET104 4.6 21.6 1.0 N B:SER97 4.7 21.1 1.0 O B:MET104 4.7 21.8 1.0 C B:SER97 4.7 23.2 1.0 CA B:SER97 4.8 20.9 1.0 SG B:CYS102 4.8 19.7 1.0 O B:MET503 4.8 20.8 1.0 CA B:CYS95 4.8 19.5 1.0 C B:MET104 4.8 21.3 1.0 O B:SER97 4.8 22.3 1.0 SG B:CYS99 4.8 20.8 1.0 N B:ARG105 4.9 21.1 1.0 C B:GLY142 4.9 17.4 1.0

Iron binding site 7 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:20.8 occ:1.00 FE3 B:SF4501 0.0 20.8 1.0 S1 B:SF4501 2.3 19.7 1.0 S4 B:SF4501 2.3 20.9 1.0 S2 B:SF4501 2.3 18.3 1.0 SG B:CYS99 2.3 20.8 1.0 FE1 B:SF4501 2.6 19.7 1.0 FE2 B:SF4501 2.7 18.9 1.0 FE4 B:SF4501 2.9 17.7 1.0 CB B:CYS99 3.1 18.8 1.0 NZ B:LYS224 3.8 18.9 1.0 S3 B:SF4501 3.8 19.6 1.0 CD B:LYS224 3.9 18.1 1.0 O B:MET503 4.0 20.8 1.0 N B:CYS99 4.0 18.8 1.0 CA B:CYS99 4.2 19.7 1.0 CB B:SER97 4.3 21.7 1.0 CE B:LYS224 4.4 17.8 1.0 CB B:CYS102 4.6 20.3 1.0 SG B:CYS102 4.6 19.7 1.0 SG B:CYS95 4.6 18.4 1.0 O B:HOH737 4.7 20.1 1.0 N B:MET503 4.8 17.9 1.0 N B:GLU98 5.0 21.8 1.0 CE B:MET101 5.0 20.9 1.0

Iron binding site 8 out of 8 in the X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of X-Ray Structure of the Tryptophan Lyase Nosl in Complex with Bound Tryptamin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:17.7 occ:1.00 FE4 B:SF4501 0.0 17.7 1.0 O B:MET503 2.3 20.8 1.0 N B:MET503 2.3 17.9 1.0 S2 B:SF4501 2.3 18.3 1.0 S3 B:SF4501 2.3 19.6 1.0 S1 B:SF4501 2.4 19.7 1.0 SD B:MET503 2.7 19.0 1.0 FE1 B:SF4501 2.8 19.7 1.0 FE3 B:SF4501 2.9 20.8 1.0 FE2 B:SF4501 2.9 18.9 1.0 C B:MET503 3.0 19.2 1.0 CA B:MET503 3.1 16.9 1.0 CG B:MET503 3.7 17.7 1.0 CE B:MET503 3.8 20.5 1.0 CB B:MET503 3.9 16.1 1.0 NZ B:LYS224 4.0 18.9 1.0 S4 B:SF4501 4.1 20.9 1.0 OXT B:MET503 4.2 20.0 1.0 NE2 B:GLN363 4.6 20.5 1.0 CD B:LYS224 4.7 18.1 1.0 SG B:CYS95 4.7 18.4 1.0 O B:THR141 4.8 17.1 1.0 N B:GLU143 4.9 16.6 1.0 SG B:CYS102 5.0 19.7 1.0 SG B:CYS99 5.0 20.8 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