Iron in PDB 5d8v: Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein

The structure of Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein, PDB code: 5d8v was solved by Y.Hirano, K.Takeda, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 0.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.478, 58.905, 23.436, 90.00, 90.00, 90.00
R / Rfree (%)	7.2 / 7.8

The binding sites of Iron atom in the Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein (pdb code 5d8v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein, PDB code: 5d8v:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:2.3 occ:1.00 FE1 A:SF484 0.0 2.3 1.0 S2 A:SF484 2.2 2.5 1.0 SG A:CYS43 2.3 2.5 1.0 S4 A:SF484 2.3 2.5 1.0 S3 A:SF484 2.3 2.4 1.0 FE4 A:SF484 2.7 2.3 1.0 FE3 A:SF484 2.7 2.4 1.0 FE2 A:SF484 2.7 2.3 1.0 HA A:CYS43 3.1 2.8 1.0 CB A:CYS43 3.2 2.5 1.0 HB3 A:CYS43 3.3 3.1 1.0 HG12 A:ILE69 3.6 4.1 1.0 CA A:CYS43 3.7 2.4 1.0 HA A:TRP74 3.8 2.7 1.0 S1 A:SF484 3.9 2.5 1.0 H A:CYS75 4.0 2.7 1.0 HE1 A:TYR19 4.0 3.8 1.0 HG22 A:ILE69 4.2 6.1 1.0 HB2 A:CYS43 4.2 3.1 1.0 HD12 A:ILE69 4.3 5.6 1.0 HD1 A:TYR19 4.3 3.7 1.0 H A:CYS43 4.3 2.9 1.0 HB3 A:CYS46 4.3 3.0 1.0 N A:CYS43 4.4 2.4 1.0 HB A:ILE69 4.4 3.7 1.0 HB2 A:CYS61 4.5 3.8 1.0 N A:CYS75 4.5 2.3 1.0 CG1 A:ILE69 4.5 3.4 1.0 HB2 A:CYS46 4.5 3.0 1.0 CA A:TRP74 4.6 2.3 1.0 HD1 A:TRP78 4.6 3.0 1.0 HB3 A:CYS75 4.6 2.9 1.0 C A:TRP74 4.7 2.2 1.0 CB A:CYS46 4.8 2.5 1.0 SG A:CYS46 4.8 2.4 1.0 N A:TRP74 4.8 2.4 1.0 HB2 A:MET49 4.8 3.8 0.7 CD1 A:ILE69 4.8 3.8 1.0 SG A:CYS75 4.8 2.4 1.0 SG A:CYS61 4.9 2.8 1.0 CE1 A:TYR19 4.9 3.2 1.0 C A:CYS43 4.9 2.4 1.0 CB A:ILE69 4.9 3.0 1.0 HD11 A:ILE69 4.9 5.6 1.0 HB2 A:MET49 5.0 4.7 0.3 C A:GLY73 5.0 2.3 1.0 CD1 A:TYR19 5.0 3.0 1.0

Iron binding site 2 out of 4 in the Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:2.3 occ:1.00 FE2 A:SF484 0.0 2.3 1.0 S1 A:SF484 2.2 2.5 1.0 SG A:CYS46 2.3 2.4 1.0 S3 A:SF484 2.3 2.4 1.0 S4 A:SF484 2.3 2.5 1.0 FE3 A:SF484 2.7 2.4 1.0 FE4 A:SF484 2.7 2.3 1.0 FE1 A:SF484 2.7 2.3 1.0 HB2 A:PHE48 3.1 3.5 1.0 HB3 A:CYS46 3.1 3.0 1.0 CB A:CYS46 3.1 2.5 1.0 HA A:TRP78 3.2 2.8 1.0 HB2 A:CYS46 3.3 3.0 1.0 HD2 A:PHE48 3.6 5.1 1.0 HA A:CYS43 3.7 2.8 1.0 S2 A:SF484 3.9 2.5 1.0 H A:PHE48 3.9 3.1 1.0 HD1 A:TRP78 4.1 3.0 1.0 CB A:PHE48 4.2 2.9 1.0 H A:THR79 4.2 3.0 1.0 CA A:TRP78 4.2 2.3 1.0 H A:MET49 4.5 3.6 0.7 N A:TRP78 4.6 2.5 1.0 CD2 A:PHE48 4.6 4.2 1.0 HB2 A:MET49 4.6 3.8 0.7 CA A:CYS46 4.6 2.4 1.0 SG A:CYS61 4.6 2.8 1.0 CD1 A:TRP78 4.7 2.5 1.0 HB3 A:PHE48 4.7 3.5 1.0 HB2 A:TRP78 4.7 2.9 1.0 N A:PHE48 4.7 2.6 1.0 H A:CYS75 4.7 2.7 1.0 CA A:CYS43 4.7 2.4 1.0 H A:MET49 4.7 2.8 0.3 HB2 A:MET49 4.8 4.7 0.3 SG A:CYS43 4.8 2.5 1.0 SG A:CYS75 4.8 2.4 1.0 HB3 A:CYS43 4.8 3.1 1.0 N A:MET49 4.8 3.0 0.7 CA A:PHE48 4.8 2.7 1.0 O A:SER77 4.8 3.1 1.0 HB3 A:SER77 4.8 3.5 0.3 C A:SER77 4.8 2.6 1.0 N A:MET49 4.9 2.4 0.3 CG A:PHE48 4.9 3.1 1.0 CB A:TRP78 4.9 2.5 1.0 C A:PHE48 5.0 2.8 1.0 HA A:CYS46 5.0 2.8 1.0 N A:THR79 5.0 2.5 1.0

Iron binding site 3 out of 4 in the Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:2.4 occ:1.00 FE3 A:SF484 0.0 2.4 1.0 S4 A:SF484 2.2 2.5 1.0 SG A:CYS61 2.3 2.8 1.0 S2 A:SF484 2.3 2.5 1.0 S1 A:SF484 2.3 2.5 1.0 FE2 A:SF484 2.7 2.3 1.0 FE1 A:SF484 2.7 2.3 1.0 FE4 A:SF484 2.7 2.3 1.0 HB2 A:CYS61 3.0 3.8 1.0 CB A:CYS61 3.3 3.1 1.0 HB2 A:PHE48 3.5 3.5 1.0 HG12 A:ILE69 3.6 4.1 1.0 HD2 A:PHE64 3.8 4.0 1.0 HG22 A:ILE69 3.9 6.1 1.0 S3 A:SF484 3.9 2.4 1.0 HE2 A:PHE64 3.9 4.8 1.0 HB3 A:CYS61 4.0 3.8 1.0 HG A:LEU63 4.0 3.9 1.0 HB3 A:PHE48 4.1 3.5 1.0 HD11 A:LEU63 4.2 6.0 1.0 HA A:CYS61 4.2 3.7 1.0 CB A:PHE48 4.3 2.9 1.0 CA A:CYS61 4.4 3.0 1.0 HB2 A:LEU63 4.4 3.6 1.0 H A:LEU63 4.5 3.2 1.0 SG A:CYS75 4.6 2.4 1.0 CD2 A:PHE64 4.6 3.4 1.0 CE2 A:PHE64 4.7 4.0 1.0 CG1 A:ILE69 4.7 3.4 1.0 SG A:CYS43 4.7 2.5 1.0 SG A:CYS46 4.7 2.4 1.0 HA A:MET49 4.8 3.7 0.7 HD2 A:PHE48 4.8 5.1 1.0 CG2 A:ILE69 4.8 4.1 1.0 HA A:MET49 4.8 3.2 0.3 CG A:LEU63 4.8 3.3 1.0 C A:PHE48 4.9 2.8 1.0 CD1 A:LEU63 4.9 4.0 1.0 HB3 A:CYS43 4.9 3.1 1.0 H A:GLN62 4.9 3.3 0.6 HD12 A:LEU63 5.0 6.0 1.0 O A:PHE48 5.0 3.5 1.0

Iron binding site 4 out of 4 in the Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Ultra-High Resolution Structure of High-Potential Iron-Sulfur Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:2.3 occ:1.00 FE4 A:SF484 0.0 2.3 1.0 S3 A:SF484 2.3 2.4 1.0 SG A:CYS75 2.3 2.4 1.0 S1 A:SF484 2.3 2.5 1.0 S2 A:SF484 2.3 2.5 1.0 FE1 A:SF484 2.7 2.3 1.0 FE2 A:SF484 2.7 2.3 1.0 FE3 A:SF484 2.7 2.4 1.0 H A:CYS75 3.2 2.7 1.0 HB3 A:CYS75 3.2 2.9 1.0 CB A:CYS75 3.3 2.4 1.0 N A:CYS75 3.6 2.3 1.0 HB3 A:SER77 3.8 3.5 0.3 HB2 A:SER77 3.8 4.0 0.7 CA A:CYS75 3.8 2.2 1.0 S4 A:SF484 3.9 2.5 1.0 HE2 A:PHE64 4.0 4.8 1.0 H A:SER77 4.0 3.1 1.0 HA A:TRP78 4.1 2.8 1.0 HD1 A:TYR19 4.1 3.7 1.0 HD11 A:LEU63 4.2 6.0 1.0 O A:CYS75 4.2 2.4 1.0 C A:CYS75 4.2 2.3 1.0 HB2 A:CYS75 4.2 2.9 1.0 H A:TRP78 4.3 3.0 1.0 N A:TRP78 4.3 2.5 1.0 C A:TRP74 4.4 2.2 1.0 HA A:TRP74 4.5 2.7 1.0 HB2 A:TRP78 4.6 2.9 1.0 C A:SER77 4.6 2.6 1.0 SG A:CYS61 4.7 2.8 1.0 CA A:TRP78 4.7 2.3 1.0 SG A:CYS43 4.8 2.5 1.0 CB A:SER77 4.8 3.3 0.7 CB A:SER77 4.8 2.9 0.3 N A:SER77 4.8 2.6 1.0 SG A:CYS46 4.8 2.4 1.0 HA A:CYS75 4.9 2.7 1.0 HD12 A:LEU17 4.9 6.3 1.0 HB2 A:PHE48 4.9 3.5 1.0 HD12 A:LEU63 4.9 6.0 1.0 CA A:SER77 4.9 2.7 1.0

Y.Hirano, K.Takeda, K.Miki. Charge-Density Analysis of An Iron-Sulfur Protein at An Ultra-High Resolution of 0.48 Angstrom Nature V. 534 281 2016.
ISSN: ESSN 1476-4687
PubMed: 27279229
DOI: 10.1038/NATURE18001