Iron in PDB 7vos: High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State

The structure of High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State, PDB code: 7vos was solved by Y.Hanazono, Y.Hirano, K.Takeda, K.Kusaka, T.Tamada, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 0.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.334, 58.855, 23.548, 90, 90, 90
R / Rfree (%)	15.4 / 16.8

The binding sites of Iron atom in the High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State (pdb code 7vos). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State, PDB code: 7vos:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.1 occ:1.00 FE1 A:SF4101 0.0 2.1 1.0 SG A:CYS43 2.2 2.4 1.0 S2 A:SF4101 2.2 2.4 1.0 S4 A:SF4101 2.3 2.3 1.0 S3 A:SF4101 2.3 2.3 1.0 FE3 A:SF4101 2.7 2.2 1.0 FE4 A:SF4101 2.7 2.2 1.0 FE2 A:SF4101 2.8 2.1 1.0 HA A:CYS43 3.0 2.8 1.0 CB A:CYS43 3.2 2.5 1.0 HB3 A:CYS43 3.2 3.0 1.0 HG12 A:ILE69 3.5 4.1 1.0 CA A:CYS43 3.6 2.3 1.0 S1 A:SF4101 3.8 2.4 1.0 HA A:TRP74 3.9 2.7 1.0 HE1 A:TYR19 4.1 3.8 1.0 HB2 A:CYS43 4.2 3.0 1.0 HD11 A:ILE69 4.2 5.5 1.0 HB3 A:CYS46 4.3 2.8 1.0 HD1 A:TYR19 4.3 3.7 1.0 H A:CYS43 4.3 2.1 1.0 HG22 A:ILE69 4.4 5.9 1.0 N A:CYS43 4.4 2.3 1.0 HB2 A:CYS61 4.4 3.5 1.0 CG1 A:ILE69 4.4 3.5 1.0 HB A:ILE69 4.5 3.6 1.0 HD12 A:ILE69 4.5 5.5 1.0 H A:CYS75 4.5 3.8 1.0 N A:CYS75 4.6 2.3 1.0 HB2 A:CYS46 4.6 2.8 1.0 CD1 A:ILE69 4.6 3.7 1.0 CA A:TRP74 4.7 2.3 1.0 HB3 A:CYS75 4.7 2.9 1.0 HD1 A:TRP78 4.7 3.0 1.0 C A:TRP74 4.7 2.2 1.0 SG A:CYS46 4.8 2.2 1.0 CB A:CYS46 4.8 2.4 1.0 SG A:CYS75 4.8 2.5 1.0 C A:CYS43 4.8 2.3 1.0 SG A:CYS61 4.8 2.7 1.0 N A:TRP74 4.8 2.4 1.0 HB2 A:MET49 4.8 4.2 0.6 CB A:ILE69 4.9 3.0 1.0 O A:CYS43 4.9 2.6 1.0 CE1 A:TYR19 4.9 3.2 1.0 HB2 A:MET49 5.0 3.2 0.4 C A:GLY73 5.0 2.3 1.0

Iron binding site 2 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.1 occ:1.00 FE2 A:SF4101 0.0 2.1 1.0 S1 A:SF4101 2.2 2.4 1.0 SG A:CYS46 2.2 2.2 1.0 S3 A:SF4101 2.3 2.3 1.0 S4 A:SF4101 2.3 2.3 1.0 FE3 A:SF4101 2.7 2.2 1.0 FE4 A:SF4101 2.7 2.2 1.0 FE1 A:SF4101 2.8 2.1 1.0 HB3 A:CYS46 3.1 2.8 1.0 CB A:CYS46 3.1 2.4 1.0 HB2 A:PHE48 3.2 3.3 1.0 HB2 A:CYS46 3.3 2.8 1.0 HA A:TRP78 3.3 2.8 1.0 HA A:CYS43 3.7 2.8 1.0 HD2 A:PHE48 3.7 4.7 1.0 S2 A:SF4101 3.9 2.4 1.0 H A:PHE48 4.0 4.1 0.9 D A:PHE48 4.0 4.1 0.1 HD1 A:TRP78 4.1 3.0 1.0 H A:THR79 4.2 3.4 1.0 CB A:PHE48 4.3 2.8 1.0 CA A:TRP78 4.3 2.3 1.0 CA A:CYS46 4.5 2.2 1.0 H A:MET49 4.6 3.6 0.6 D A:MET49 4.6 3.6 0.4 SG A:CYS61 4.6 2.7 1.0 N A:TRP78 4.6 2.5 1.0 CD2 A:PHE48 4.7 3.9 1.0 HB2 A:MET49 4.7 4.2 0.6 HB2 A:SER77 4.7 3.3 0.3 HB2 A:MET49 4.7 3.2 0.4 CA A:CYS43 4.7 2.3 1.0 CD1 A:TRP78 4.7 2.5 1.0 SG A:CYS75 4.7 2.5 1.0 SG A:CYS43 4.7 2.4 1.0 N A:PHE48 4.7 2.4 1.0 HB2 A:TRP78 4.8 2.9 1.0 HB3 A:PHE48 4.8 3.3 1.0 HB3 A:CYS43 4.8 3.0 1.0 N A:MET49 4.8 3.0 0.6 O A:SER77 4.9 2.9 1.0 N A:MET49 4.9 2.4 0.4 CA A:PHE48 4.9 2.5 1.0 C A:SER77 4.9 2.5 1.0 HA A:CYS46 5.0 2.7 1.0 O A:CYS43 5.0 2.6 1.0 C A:CYS46 5.0 2.2 1.0 CB A:CYS43 5.0 2.5 1.0 CG A:PHE48 5.0 3.0 1.0

Iron binding site 3 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.2 occ:1.00 FE3 A:SF4101 0.0 2.2 1.0 SG A:CYS61 2.2 2.7 1.0 S4 A:SF4101 2.3 2.3 1.0 S1 A:SF4101 2.3 2.4 1.0 S2 A:SF4101 2.3 2.4 1.0 FE1 A:SF4101 2.7 2.1 1.0 FE4 A:SF4101 2.7 2.2 1.0 FE2 A:SF4101 2.7 2.1 1.0 HB2 A:CYS61 3.0 3.5 1.0 CB A:CYS61 3.2 2.9 1.0 HB2 A:PHE48 3.5 3.3 1.0 HG12 A:ILE69 3.5 4.1 1.0 S3 A:SF4101 3.9 2.3 1.0 HD2 A:PHE64 3.9 4.0 1.0 HB3 A:CYS61 3.9 3.5 1.0 HE2 A:PHE64 4.0 4.7 1.0 HG22 A:ILE69 4.0 5.9 1.0 HG A:LEU63 4.1 3.9 1.0 HB3 A:PHE48 4.2 3.3 1.0 HA A:CYS61 4.2 3.3 1.0 HD13 A:LEU63 4.2 5.7 1.0 CB A:PHE48 4.3 2.8 1.0 CA A:CYS61 4.3 2.7 1.0 HB2 A:LEU63 4.5 3.6 1.0 H A:LEU63 4.5 3.3 1.0 SG A:CYS75 4.5 2.5 1.0 CG1 A:ILE69 4.6 3.5 1.0 CD2 A:PHE64 4.7 3.3 1.0 SG A:CYS46 4.7 2.2 1.0 SG A:CYS43 4.7 2.4 1.0 CE2 A:PHE64 4.7 3.9 1.0 HA A:MET49 4.8 3.4 0.6 HD2 A:PHE48 4.8 4.7 1.0 C A:PHE48 4.9 2.7 1.0 HA A:MET49 4.9 3.1 0.4 CD1 A:LEU63 4.9 3.8 1.0 HB2 A:SER77 4.9 3.3 0.3 CG A:LEU63 4.9 3.3 1.0 O A:PHE48 4.9 3.2 1.0 HG13 A:ILE69 5.0 4.1 1.0 HB3 A:CYS43 5.0 3.0 1.0 HD12 A:LEU63 5.0 5.7 1.0 CG2 A:ILE69 5.0 3.9 1.0

Iron binding site 4 out of 4 in the High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of High-Resolution Neutron and X-Ray Joint Refined Structure of High- Potential Iron-Sulfur Protein in the Oxidized State within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:2.2 occ:1.00 FE4 A:SF4101 0.0 2.2 1.0 SG A:CYS75 2.2 2.5 1.0 S1 A:SF4101 2.3 2.4 1.0 S3 A:SF4101 2.3 2.3 1.0 S2 A:SF4101 2.3 2.4 1.0 FE3 A:SF4101 2.7 2.2 1.0 FE2 A:SF4101 2.7 2.1 1.0 FE1 A:SF4101 2.7 2.1 1.0 HB3 A:CYS75 3.2 2.9 1.0 CB A:CYS75 3.3 2.4 1.0 HB2 A:SER77 3.4 3.3 0.3 H A:CYS75 3.6 3.8 1.0 N A:CYS75 3.6 2.3 1.0 S4 A:SF4101 3.8 2.3 1.0 CA A:CYS75 3.9 2.3 1.0 HB2 A:SER77 3.9 5.2 0.7 HE2 A:PHE64 4.0 4.7 1.0 H A:SER77 4.1 2.5 0.8 D A:SER77 4.1 2.5 0.2 HD1 A:TYR19 4.2 3.7 1.0 HD13 A:LEU63 4.2 5.7 1.0 O A:CYS75 4.2 2.5 1.0 HB2 A:CYS75 4.2 2.9 1.0 HA A:TRP78 4.2 2.8 1.0 C A:CYS75 4.2 2.3 1.0 D A:TRP78 4.3 4.1 0.0 H A:TRP78 4.3 4.1 1.0 C A:TRP74 4.4 2.2 1.0 N A:TRP78 4.4 2.5 1.0 CB A:SER77 4.5 2.7 0.3 HA A:TRP74 4.6 2.7 1.0 SG A:CYS61 4.6 2.7 1.0 HB2 A:TRP78 4.7 2.9 1.0 SG A:CYS43 4.7 2.4 1.0 C A:SER77 4.7 2.5 1.0 SG A:CYS46 4.7 2.2 1.0 CA A:TRP78 4.8 2.3 1.0 N A:SER77 4.9 2.9 1.0 HA A:CYS75 4.9 2.7 1.0 CB A:SER77 4.9 4.3 0.7 HB2 A:PHE48 4.9 3.3 1.0 HB3 A:SER77 4.9 3.3 0.3 CA A:SER77 4.9 2.5 0.3 HD11 A:LEU17 5.0 5.6 1.0 HD12 A:LEU63 5.0 5.7 1.0

Y.Hanazono, Y.Hirano, K.Takeda, K.Kusaka, T.Tamada, K.Miki. Revisiting the Concept of Peptide Bond Planarity in An Iron-Sulfur Protein By Neutron Structure Analysis. Sci Adv V. 8 N2276 2022.
ISSN: ESSN 2375-2548
PubMed: 35594350
DOI: 10.1126/SCIADV.ABN2276