Iron in PDB 7yra: Crystal Structure of [2FE-2S]-Ttpeta

All present enzymatic activity of Crystal Structure of [2FE-2S]-Ttpeta:
7.1.1.8;

The structure of Crystal Structure of [2FE-2S]-Ttpeta, PDB code: 7yra was solved by E.Tsutsumi, S.Niwa, K.Takeda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	32.409, 51.022, 98.805, 90, 93.45, 90
R / Rfree (%)	20.7 / 23.9

The structure of Crystal Structure of [2FE-2S]-Ttpeta also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iron atom in the Crystal Structure of [2FE-2S]-Ttpeta (pdb code 7yra). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of [2FE-2S]-Ttpeta, PDB code: 7yra:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of [2FE-2S]-Ttpeta


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 [2FE-2S]-Ttpeta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:16.1 occ:1.00 FE1 A:FES201 0.0 16.1 1.0 SG A:CYS152 2.2 15.9 1.0 S1 A:FES201 2.2 16.5 1.0 S2 A:FES201 2.3 15.7 1.0 SG A:CYS124 2.3 17.0 1.0 FE2 A:FES201 2.7 17.4 1.0 CB A:CYS152 3.1 14.6 1.0 CB A:CYS124 3.1 16.5 1.0 CB A:HIS126 4.0 17.7 1.0 CB A:CYS129 4.3 17.2 1.0 OG A:SER157 4.4 14.3 1.0 N A:HIS155 4.4 15.8 1.0 CB A:SER157 4.4 14.7 1.0 CB A:CYS154 4.4 15.6 1.0 ND1 A:HIS155 4.5 18.9 1.0 CA A:CYS124 4.5 16.9 1.0 ND1 A:HIS126 4.5 20.5 1.0 CA A:CYS152 4.5 14.5 1.0 N A:LEU127 4.8 19.0 1.0 CG A:HIS126 4.8 19.7 1.0 N A:CYS129 4.8 18.2 1.0 N A:SER157 4.9 15.4 1.0 N A:HIS126 5.0 16.7 1.0 C A:CYS152 5.0 15.1 1.0 C A:CYS124 5.0 17.4 1.0

Iron binding site 2 out of 4 in the Crystal Structure of [2FE-2S]-Ttpeta


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 [2FE-2S]-Ttpeta within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:17.4 occ:1.00 FE2 A:FES201 0.0 17.4 1.0 ND1 A:HIS155 2.0 18.9 1.0 ND1 A:HIS126 2.2 20.5 1.0 S2 A:FES201 2.2 15.7 1.0 S1 A:FES201 2.4 16.5 1.0 FE1 A:FES201 2.7 16.1 1.0 CG A:HIS155 3.0 16.9 1.0 CE1 A:HIS155 3.1 18.1 1.0 CG A:HIS126 3.1 19.7 1.0 CE1 A:HIS126 3.2 20.2 1.0 CB A:HIS155 3.3 16.0 1.0 CB A:HIS126 3.4 17.7 1.0 N A:HIS155 3.8 15.8 1.0 N A:LEU127 4.1 19.0 1.0 CA A:HIS155 4.1 16.4 1.0 NE2 A:HIS155 4.2 17.5 1.0 CD2 A:HIS155 4.2 18.6 1.0 CB A:CYS154 4.2 15.6 1.0 CD2 A:HIS126 4.3 20.6 1.0 NE2 A:HIS126 4.3 19.0 1.0 CB A:LEU127 4.4 21.0 1.0 SG A:CYS124 4.4 17.0 1.0 SG A:CYS152 4.5 15.9 1.0 CG A:LEU127 4.6 21.6 1.0 CD1 A:LEU127 4.6 22.2 1.0 CB A:PRO170 4.6 14.8 1.0 C A:CYS154 4.6 16.6 1.0 CA A:HIS126 4.7 18.6 1.0 C A:HIS126 4.8 18.4 1.0 OG A:SER157 4.8 14.3 1.0 C A:HIS155 4.8 17.8 1.0 CA A:LEU127 4.8 20.0 1.0

Iron binding site 3 out of 4 in the Crystal Structure of [2FE-2S]-Ttpeta


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 [2FE-2S]-Ttpeta within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:16.5 occ:1.00 FE1 B:FES201 0.0 16.5 1.0 S1 B:FES201 2.2 16.6 1.0 S2 B:FES201 2.3 16.0 1.0 SG B:CYS152 2.3 18.1 1.0 SG B:CYS124 2.3 15.1 1.0 FE2 B:FES201 2.7 17.1 1.0 CB B:CYS124 3.1 14.8 1.0 CB B:CYS152 3.2 12.1 1.0 CB B:HIS126 4.0 17.2 1.0 OG B:SER157 4.3 14.7 1.0 ND1 B:HIS126 4.3 20.3 1.0 N B:HIS155 4.4 17.0 1.0 CB B:CYS129 4.4 18.3 1.0 CB B:CYS154 4.4 15.3 1.0 CA B:CYS124 4.5 14.8 1.0 CB B:SER157 4.5 13.5 1.0 CA B:CYS152 4.6 13.6 1.0 N B:LEU127 4.7 17.8 1.0 ND1 B:HIS155 4.7 20.0 1.0 CG B:HIS126 4.7 19.4 1.0 N B:CYS129 4.8 18.0 1.0 N B:HIS126 4.9 15.9 1.0 N B:SER157 4.9 13.0 1.0 C B:CYS124 5.0 16.1 1.0

Iron binding site 4 out of 4 in the Crystal Structure of [2FE-2S]-Ttpeta


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 [2FE-2S]-Ttpeta within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:17.1 occ:1.00 FE2 B:FES201 0.0 17.1 1.0 ND1 B:HIS126 2.1 20.3 1.0 ND1 B:HIS155 2.2 20.0 1.0 S2 B:FES201 2.3 16.0 1.0 S1 B:FES201 2.4 16.6 1.0 FE1 B:FES201 2.7 16.5 1.0 CE1 B:HIS126 3.0 19.5 1.0 CG B:HIS126 3.1 19.4 1.0 CG B:HIS155 3.1 18.8 1.0 CE1 B:HIS155 3.3 18.9 1.0 CB B:HIS155 3.3 18.0 1.0 CB B:HIS126 3.4 17.2 1.0 N B:HIS155 3.6 17.0 1.0 N B:LEU127 4.1 17.8 1.0 CA B:HIS155 4.1 16.1 1.0 CB B:CYS154 4.1 15.3 1.0 NE2 B:HIS126 4.2 19.3 1.0 CD2 B:HIS126 4.2 20.3 1.0 CD2 B:HIS155 4.3 19.9 1.0 NE2 B:HIS155 4.3 19.1 1.0 SG B:CYS124 4.4 15.1 1.0 CB B:LEU127 4.5 19.0 1.0 SG B:CYS152 4.5 18.1 1.0 C B:CYS154 4.5 17.1 1.0 CA B:HIS126 4.7 18.3 1.0 CG B:LEU127 4.7 20.9 1.0 CB B:PRO170 4.7 15.4 1.0 CD1 B:LEU127 4.7 21.3 1.0 OG B:SER157 4.8 14.7 1.0 C B:HIS155 4.8 17.8 1.0 C B:HIS126 4.8 17.7 1.0 CA B:LEU127 4.8 18.6 1.0

E.Tsutsumi, S.Niwa, R.Takeda, N.Sakamoto, K.Okatsu, S.Fukai, H.Ago, S.Nagao, H.Sekiguchi, K.Takeda. Structure of A Putative Immature Form of A Rieske-Type Iron-Sulfur Protein in Complex with Zinc Chloride. Commun Chem V. 6 190 2023.
ISSN: ESSN 2399-3669
PubMed: 37689761
DOI: 10.1038/S42004-023-01000-6