Iron in PDB 7pd2: Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans

The structure of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans, PDB code: 7pd2 was solved by P.Amara, C.Saragaglia, J.-M.Mouesca, L.Martin, Y.Nicolet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.46 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	175.09, 49.33, 85.21, 90, 96.91, 90
R / Rfree (%)	23 / 26.9

The binding sites of Iron atom in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans (pdb code 7pd2). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans, PDB code: 7pd2:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:36.4 occ:1.00 FE1 A:SF4401 0.0 36.4 1.0 N A:MET403 2.2 56.0 1.0 S3 A:SF4401 2.3 31.9 1.0 S4 A:SF4401 2.3 32.0 1.0 S2 A:SF4401 2.3 39.5 1.0 O A:MET403 2.7 59.0 1.0 FE2 A:SF4401 2.8 35.9 1.0 FE4 A:SF4401 2.8 35.5 1.0 FE3 A:SF4401 2.8 34.7 1.0 SD A:MET403 2.8 54.4 1.0 CA A:MET403 3.2 59.1 1.0 C A:MET403 3.3 60.5 1.0 CG A:MET403 3.8 58.8 1.0 CB A:MET403 3.9 58.9 1.0 CE A:MET403 4.0 55.3 1.0 S1 A:SF4401 4.0 39.9 1.0 NZ A:LYS199 4.2 37.1 1.0 NE2 A:GLN336 4.5 38.2 1.0 OXT A:MET403 4.5 63.3 1.0 SG A:CYS85 4.7 34.7 1.0 SG A:CYS92 4.8 32.6 1.0 SG A:CYS89 4.9 35.5 1.0

Iron binding site 2 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:35.9 occ:1.00 FE2 A:SF4401 0.0 35.9 1.0 SG A:CYS89 2.3 35.5 1.0 S4 A:SF4401 2.3 32.0 1.0 S3 A:SF4401 2.3 31.9 1.0 S1 A:SF4401 2.3 39.9 1.0 FE4 A:SF4401 2.7 35.5 1.0 FE3 A:SF4401 2.7 34.7 1.0 FE1 A:SF4401 2.8 36.4 1.0 CB A:CYS89 3.1 36.4 1.0 NZ A:LYS199 3.7 37.1 1.0 S2 A:SF4401 3.9 39.5 1.0 CD A:LYS199 4.0 38.4 1.0 CB A:ASN87 4.2 40.9 1.0 O A:MET403 4.3 59.0 1.0 CA A:CYS89 4.4 39.4 1.0 CB A:CYS92 4.4 33.7 1.0 N A:CYS89 4.4 41.4 1.0 CE A:LYS199 4.5 37.8 1.0 SG A:CYS92 4.5 32.6 1.0 SG A:CYS85 4.5 34.7 1.0 N A:MET403 4.7 56.0 1.0 OH A:TYR91 4.7 34.7 1.0 ND2 A:ASN87 4.8 38.3 1.0 CG A:ASN87 4.9 41.1 1.0

Iron binding site 3 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:34.7 occ:1.00 FE3 A:SF4401 0.0 34.7 1.0 SG A:CYS85 2.2 34.7 1.0 S1 A:SF4401 2.3 39.9 1.0 S2 A:SF4401 2.3 39.5 1.0 S4 A:SF4401 2.3 32.0 1.0 FE2 A:SF4401 2.7 35.9 1.0 FE4 A:SF4401 2.7 35.5 1.0 FE1 A:SF4401 2.8 36.4 1.0 CB A:CYS85 3.4 37.3 1.0 S3 A:SF4401 3.9 31.9 1.0 N A:MET403 3.9 56.0 1.0 CB A:ASN87 4.2 40.9 1.0 N A:GLU131 4.3 44.4 1.0 O A:PHE94 4.5 36.7 1.0 CA A:GLY130 4.6 40.7 1.0 ND2 A:ASN87 4.6 38.3 1.0 SG A:CYS89 4.7 35.5 1.0 CA A:CYS85 4.8 39.2 1.0 SG A:CYS92 4.8 32.6 1.0 CB A:PHE94 4.8 34.4 1.0 C A:PHE94 4.9 36.0 1.0 CB A:GLU131 4.9 48.7 1.0 CG A:ASN87 4.9 41.1 1.0 N A:ASN87 4.9 41.1 1.0 C A:GLY130 5.0 43.0 1.0 O A:ASN87 5.0 44.9 1.0

Iron binding site 4 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:35.5 occ:1.00 FE4 A:SF4401 0.0 35.5 1.0 SG A:CYS92 2.3 32.6 1.0 S2 A:SF4401 2.3 39.5 1.0 S1 A:SF4401 2.3 39.9 1.0 S3 A:SF4401 2.3 31.9 1.0 FE2 A:SF4401 2.7 35.9 1.0 FE3 A:SF4401 2.7 34.7 1.0 FE1 A:SF4401 2.8 36.4 1.0 CB A:CYS92 3.2 33.7 1.0 NE2 A:GLN336 3.7 38.2 1.0 S4 A:SF4401 3.9 32.0 1.0 CB A:PHE94 4.1 34.4 1.0 SD A:MET403 4.2 54.4 1.0 C A:PHE94 4.6 36.0 1.0 CD A:GLN336 4.6 37.4 1.0 CA A:CYS92 4.6 34.3 1.0 N A:PHE94 4.7 33.1 1.0 CA A:PHE94 4.7 34.5 1.0 CB A:CYS89 4.7 36.4 1.0 SG A:CYS89 4.7 35.5 1.0 N A:MET403 4.8 56.0 1.0 SG A:CYS85 4.8 34.7 1.0 O A:PHE94 4.8 36.7 1.0 N A:GLN95 4.8 38.4 1.0 CG A:GLN336 4.9 38.8 1.0 CE A:MET403 4.9 55.3 1.0 CG A:PHE94 5.0 36.3 1.0

Iron binding site 5 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:36.8 occ:1.00 FE1 B:SF4401 0.0 36.8 1.0 N B:MET403 2.1 62.5 1.0 S3 B:SF4401 2.3 38.8 1.0 S4 B:SF4401 2.3 33.9 1.0 S2 B:SF4401 2.3 32.3 1.0 FE4 B:SF4401 2.7 33.5 1.0 OXT B:MET403 2.7 50.3 1.0 FE3 B:SF4401 2.7 36.2 1.0 FE2 B:SF4401 2.8 35.6 1.0 SD B:MET403 2.9 51.8 1.0 CA B:MET403 3.1 51.6 1.0 C B:MET403 3.3 49.7 1.0 CG B:MET403 3.9 47.7 1.0 CE B:MET403 3.9 50.0 1.0 CB B:MET403 3.9 45.1 1.0 S1 B:SF4401 4.0 33.6 1.0 NZ B:LYS199 4.2 36.4 1.0 O B:MET403 4.5 48.2 1.0 SG B:CYS85 4.6 36.5 1.0 NE2 B:GLN336 4.7 39.6 1.0 SG B:CYS92 4.8 33.5 1.0 O B:THR129 4.9 35.9 1.0 CA B:GLY130 4.9 38.8 1.0 SG B:CYS89 4.9 40.9 1.0 N B:GLU131 5.0 40.5 1.0

Iron binding site 6 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:35.6 occ:1.00 FE2 B:SF4401 0.0 35.6 1.0 S4 B:SF4401 2.3 33.9 1.0 S3 B:SF4401 2.3 38.8 1.0 S1 B:SF4401 2.3 33.6 1.0 SG B:CYS89 2.3 40.9 1.0 FE4 B:SF4401 2.7 33.5 1.0 FE3 B:SF4401 2.7 36.2 1.0 FE1 B:SF4401 2.8 36.8 1.0 CB B:CYS89 3.2 39.6 1.0 NZ B:LYS199 3.7 36.4 1.0 S2 B:SF4401 3.9 32.3 1.0 CD B:LYS199 4.0 37.8 1.0 CB B:ASN87 4.0 43.7 1.0 OXT B:MET403 4.2 50.3 1.0 CE B:LYS199 4.4 37.2 1.0 CB B:CYS92 4.4 34.6 1.0 CA B:CYS89 4.5 40.0 1.0 SG B:CYS85 4.5 36.5 1.0 N B:MET403 4.5 62.5 1.0 SG B:CYS92 4.5 33.5 1.0 N B:CYS89 4.6 40.1 1.0 ND2 B:ASN87 4.6 46.3 1.0 CG B:ASN87 4.7 45.2 1.0 OH B:TYR91 4.9 39.4 1.0

Iron binding site 7 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:36.2 occ:1.00 FE3 B:SF4401 0.0 36.2 1.0 SG B:CYS85 2.2 36.5 1.0 S1 B:SF4401 2.3 33.6 1.0 S2 B:SF4401 2.3 32.3 1.0 S4 B:SF4401 2.3 33.9 1.0 FE4 B:SF4401 2.7 33.5 1.0 FE2 B:SF4401 2.7 35.6 1.0 FE1 B:SF4401 2.7 36.8 1.0 CB B:CYS85 3.3 38.8 1.0 N B:MET403 3.8 62.5 1.0 S3 B:SF4401 3.9 38.8 1.0 CB B:ASN87 4.1 43.7 1.0 N B:GLU131 4.3 40.5 1.0 CA B:GLY130 4.5 38.8 1.0 ND2 B:ASN87 4.5 46.3 1.0 O B:PHE94 4.7 39.9 1.0 SG B:CYS89 4.7 40.9 1.0 CB B:PHE94 4.7 40.1 1.0 SG B:CYS92 4.7 33.5 1.0 CA B:CYS85 4.7 41.2 1.0 O B:ASN87 4.7 44.2 1.0 N B:ASN87 4.9 44.0 1.0 C B:PHE94 4.9 40.2 1.0 CG B:ASN87 4.9 45.2 1.0 CA B:ASN87 4.9 43.9 1.0 C B:GLY130 5.0 39.3 1.0

Iron binding site 8 out of 8 in the Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of the Substrate-Free Radical Sam Tyrosine Lyase Thih (2-Iminoacetate Synthase) From Thermosinus Carboxydivorans within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:33.5 occ:1.00 FE4 B:SF4401 0.0 33.5 1.0 SG B:CYS92 2.3 33.5 1.0 S2 B:SF4401 2.3 32.3 1.0 S1 B:SF4401 2.3 33.6 1.0 S3 B:SF4401 2.3 38.8 1.0 FE3 B:SF4401 2.7 36.2 1.0 FE2 B:SF4401 2.7 35.6 1.0 FE1 B:SF4401 2.7 36.8 1.0 CB B:CYS92 3.2 34.6 1.0 S4 B:SF4401 3.8 33.9 1.0 NE2 B:GLN336 3.9 39.6 1.0 CB B:PHE94 4.1 40.1 1.0 SD B:MET403 4.3 51.8 1.0 N B:MET403 4.6 62.5 1.0 CA B:CYS92 4.6 35.5 1.0 N B:PHE94 4.7 37.9 1.0 SG B:CYS89 4.7 40.9 1.0 C B:PHE94 4.7 40.2 1.0 CA B:PHE94 4.7 39.8 1.0 CB B:CYS89 4.8 39.6 1.0 N B:GLN95 4.8 41.0 1.0 SG B:CYS85 4.8 36.5 1.0 CD B:GLN336 4.8 40.1 1.0 CG B:GLN336 4.9 41.2 1.0 CE B:MET403 4.9 50.0 1.0 CG B:PHE94 5.0 40.3 1.0 CD2 B:PHE94 5.0 39.9 1.0

P.Amara, C.Saragaglia, J.M.Mouesca, L.Martin, Y.Nicolet. L-Tyrosine-Bound Thih Structure Reveals C-C Bond Break Differences Within Radical Sam Aromatic Amino Acid Lyases. Nat Commun V. 13 2284 2022.
ISSN: ESSN 2041-1723
PubMed: 35477710
DOI: 10.1038/S41467-022-29980-4