Iron in PDB 1nyk: Crystal Structure of the Rieske Protein From Thermus Thermophilus

The structure of Crystal Structure of the Rieske Protein From Thermus Thermophilus, PDB code: 1nyk was solved by L.M.Hunsicker-Wang, A.Heine, Y.Chen, E.P.Luna, T.Todaro, Y.M.Zhang, P.A.Williams, D.E.Mcree, J.Hirst, C.D.Stout, J.A.Fee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.00 / 1.31
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	58.569, 78.267, 136.794, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 21.2

The structure of Crystal Structure of the Rieske Protein From Thermus Thermophilus also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Iron atom in the Crystal Structure of the Rieske Protein From Thermus Thermophilus (pdb code 1nyk). 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 the Rieske Protein From Thermus Thermophilus, PDB code: 1nyk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of the Rieske Protein From Thermus Thermophilus


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 Rieske Protein From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe211 b:14.3 occ:1.00 FE1 A:FES211 0.0 14.3 1.0 S1 A:FES211 2.2 14.8 1.0 S2 A:FES211 2.2 14.6 1.0 SG A:CYS151 2.3 14.6 1.0 SG A:CYS132 2.3 14.3 1.0 FE2 A:FES211 2.7 15.0 1.0 CB A:CYS151 3.1 14.3 1.0 CB A:CYS132 3.1 14.0 1.0 CB A:HIS134 4.2 14.1 1.0 ND1 A:HIS134 4.3 14.5 1.0 CB A:CYS153 4.3 15.0 1.0 CB A:CYS137 4.4 15.3 1.0 N A:HIS154 4.4 13.8 1.0 ND1 A:HIS154 4.5 13.7 1.0 CA A:CYS151 4.5 13.3 1.0 CA A:CYS132 4.6 13.8 1.0 N A:LEU135 4.7 14.6 1.0 CG A:HIS134 4.8 15.0 1.0 N A:CYS137 4.8 14.4 1.0 C A:CYS151 4.9 13.6 1.0 N A:GLY156 4.9 13.0 1.0 N A:CYS153 4.9 13.7 1.0 O A:CYS151 5.0 15.8 1.0 O A:CYS137 5.0 15.1 1.0

Iron binding site 2 out of 4 in the Crystal Structure of the Rieske Protein From Thermus Thermophilus


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 Rieske Protein From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe211 b:15.0 occ:1.00 FE2 A:FES211 0.0 15.0 1.0 ND1 A:HIS134 2.0 14.5 1.0 ND1 A:HIS154 2.1 13.7 1.0 S1 A:FES211 2.2 14.8 1.0 S2 A:FES211 2.3 14.6 1.0 FE1 A:FES211 2.7 14.3 1.0 CE1 A:HIS134 3.0 13.8 1.0 CE1 A:HIS154 3.1 14.6 1.0 CG A:HIS134 3.1 15.0 1.0 CG A:HIS154 3.1 14.7 1.0 CB A:HIS154 3.4 13.9 1.0 CB A:HIS134 3.4 14.1 1.0 N A:HIS154 3.7 13.8 1.0 CA A:HIS154 4.1 14.1 1.0 N A:LEU135 4.1 14.6 1.0 CB A:CYS153 4.1 15.0 1.0 NE2 A:HIS134 4.1 16.0 1.0 CD2 A:HIS134 4.2 15.5 1.0 CD2 A:HIS154 4.2 14.9 1.0 NE2 A:HIS154 4.2 15.2 1.0 CG A:PRO170 4.2 16.2 1.0 SG A:CYS132 4.3 14.3 1.0 CB A:LEU135 4.5 17.7 1.0 SG A:CYS151 4.5 14.6 1.0 C A:CYS153 4.5 14.6 1.0 CA A:HIS134 4.7 14.9 1.0 C A:HIS134 4.8 15.3 1.0 C A:HIS154 4.8 14.7 1.0 CA A:LEU135 4.8 15.2 1.0 CA A:CYS153 4.9 14.1 1.0 CG A:LEU135 4.9 16.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of the Rieske Protein From Thermus Thermophilus


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 Rieske Protein From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe211 b:13.1 occ:1.00 FE1 B:FES211 0.0 13.1 1.0 S1 B:FES211 2.2 13.4 1.0 S2 B:FES211 2.2 13.6 1.0 SG B:CYS151 2.3 13.3 1.0 SG B:CYS132 2.3 13.0 1.0 FE2 B:FES211 2.7 13.8 1.0 CB B:CYS151 3.1 13.8 1.0 CB B:CYS132 3.2 13.7 1.0 CB B:HIS134 4.1 14.6 1.0 CB B:CYS153 4.3 12.7 1.0 ND1 B:HIS134 4.3 12.8 1.0 CB B:CYS137 4.4 13.3 1.0 N B:HIS154 4.4 12.8 1.0 ND1 B:HIS154 4.5 14.0 1.0 CA B:CYS151 4.6 12.9 1.0 CA B:CYS132 4.6 12.6 1.0 N B:LEU135 4.7 14.2 1.0 CG B:HIS134 4.8 12.6 1.0 N B:CYS137 4.8 13.5 1.0 N B:GLY156 4.9 12.1 1.0 N B:CYS153 4.9 13.2 1.0 CG B:PRO171 4.9 13.2 1.0 C B:CYS151 4.9 11.9 1.0 O B:CYS137 5.0 15.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of the Rieske Protein From Thermus Thermophilus


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 Rieske Protein From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe211 b:13.8 occ:1.00 FE2 B:FES211 0.0 13.8 1.0 ND1 B:HIS134 2.1 12.8 1.0 ND1 B:HIS154 2.2 14.0 1.0 S1 B:FES211 2.2 13.4 1.0 S2 B:FES211 2.3 13.6 1.0 FE1 B:FES211 2.7 13.1 1.0 CE1 B:HIS134 3.0 15.6 1.0 CE1 B:HIS154 3.1 14.8 1.0 CG B:HIS134 3.1 12.6 1.0 CG B:HIS154 3.1 13.0 1.0 CB B:HIS154 3.4 13.0 1.0 CB B:HIS134 3.4 14.6 1.0 N B:HIS154 3.7 12.8 1.0 CA B:HIS154 4.1 13.0 1.0 N B:LEU135 4.1 14.2 1.0 CB B:CYS153 4.1 12.7 1.0 NE2 B:HIS134 4.2 14.7 1.0 NE2 B:HIS154 4.2 14.1 1.0 CD2 B:HIS154 4.3 13.8 1.0 CD2 B:HIS134 4.3 15.6 1.0 CG B:PRO170 4.3 13.4 1.0 SG B:CYS132 4.4 13.0 1.0 CB B:LEU135 4.5 16.5 1.0 SG B:CYS151 4.5 13.3 1.0 C B:CYS153 4.5 14.0 1.0 CA B:HIS134 4.7 13.2 1.0 C B:HIS154 4.8 13.6 1.0 C B:HIS134 4.8 14.3 1.0 CA B:LEU135 4.8 14.8 1.0 CA B:CYS153 4.9 13.2 1.0 CG B:LEU135 4.9 15.9 1.0

L.M.Hunsicker-Wang, A.Heine, Y.Chen, E.P.Luna, T.Todaro, Y.M.Zhang, P.A.Williams, D.E.Mcree, J.Hirst, C.D.Stout, J.A.Fee. High Resolution Structure of the Soluble, Respiratory-Type Rieske Protein From Thermus Thermophilus: Analysis and Comparison Biochemistry V. 42 7303 2003.
ISSN: ISSN 0006-2960
PubMed: 12809486
DOI: 10.1021/BI0342719