Iron in PDB 3a39: Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution

The structure of Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution, PDB code: 3a39 was solved by K.Takeda, K.Kusumoto, Y.Hirano, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 0.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.463, 58.960, 23.432, 90.00, 90.00, 90.00
R / Rfree (%)	6.8 / 7.6

The binding sites of Iron atom in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution (pdb code 3a39). 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 High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution, PDB code: 3a39:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution


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 High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:1.7 occ:1.00 FE1 A:SF484 0.0 1.7 1.0 S2 A:SF484 2.2 1.8 1.0 SG A:CYS61 2.3 2.2 1.0 S3 A:SF484 2.3 1.8 1.0 S4 A:SF484 2.3 1.9 1.0 FE3 A:SF484 2.7 1.6 1.0 FE4 A:SF484 2.7 1.6 1.0 FE2 A:SF484 2.7 1.7 1.0 HB2 A:CYS61 3.0 3.0 1.0 CB A:CYS61 3.3 2.5 1.0 HB2 A:PHE48 3.5 2.6 1.0 HG12 A:ILE69 3.7 3.1 1.0 HB3 A:CYS61 3.9 3.0 1.0 S1 A:SF484 3.9 1.8 1.0 HD2 A:PHE64 4.0 3.2 1.0 HG22 A:ILE69 4.0 5.2 1.0 HE2 A:PHE64 4.0 4.0 1.0 HB3 A:PHE48 4.1 2.6 1.0 HG A:LEU63 4.1 3.2 1.0 HA A:CYS61 4.2 2.9 1.0 HD11 A:LEU63 4.3 4.8 1.0 CB A:PHE48 4.3 2.2 1.0 CA A:CYS61 4.4 2.4 1.0 HB2 A:LEU63 4.5 2.8 1.0 SG A:CYS75 4.5 1.8 1.0 H A:LEU63 4.6 2.4 1.0 CD2 A:PHE64 4.7 2.7 1.0 HA A:MET49 4.7 1.8 0.3 CG1 A:ILE69 4.7 2.6 1.0 CE2 A:PHE64 4.7 3.4 1.0 SG A:CYS43 4.7 1.9 1.0 SG A:CYS46 4.7 1.7 1.0 CG A:LEU63 4.9 2.6 1.0 CG2 A:ILE69 4.9 3.5 1.0 CD1 A:LEU63 4.9 3.2 1.0 C A:PHE48 4.9 2.1 1.0 HD2 A:PHE48 4.9 4.3 1.0 HD12 A:LEU63 4.9 4.8 1.0 O A:PHE48 4.9 2.7 1.0 H A:GLN62 5.0 2.4 0.8 HG13 A:ILE69 5.0 3.1 1.0 HB3 A:CYS43 5.0 2.3 1.0 HA A:MET49 5.0 2.7 0.7

Iron binding site 2 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution


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 High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:1.7 occ:1.00 FE2 A:SF484 0.0 1.7 1.0 S1 A:SF484 2.3 1.8 1.0 SG A:CYS75 2.3 1.8 1.0 S4 A:SF484 2.3 1.9 1.0 S3 A:SF484 2.3 1.8 1.0 FE4 A:SF484 2.7 1.6 1.0 FE3 A:SF484 2.7 1.6 1.0 FE1 A:SF484 2.7 1.7 1.0 HB3 A:CYS75 3.2 2.2 1.0 H A:CYS75 3.3 2.0 1.0 CB A:CYS75 3.3 1.8 1.0 N A:CYS75 3.6 1.6 1.0 CA A:CYS75 3.8 1.6 1.0 S2 A:SF484 3.9 1.8 1.0 H A:SER77 4.0 1.5 0.2 HB2 A:CYS75 4.1 2.2 1.0 HE2 A:PHE64 4.1 4.0 1.0 O A:CYS75 4.2 1.9 1.0 HA A:TRP78 4.2 2.2 1.0 C A:CYS75 4.2 1.7 1.0 HD11 A:LEU63 4.2 4.8 1.0 H A:SER77 4.3 2.1 0.8 HD1 A:TYR19 4.3 2.9 1.0 N A:TRP78 4.3 1.9 1.0 H A:TRP78 4.3 2.2 1.0 C A:TRP74 4.4 1.6 1.0 C A:SER77 4.5 2.5 0.2 CB A:SER77 4.6 3.9 0.2 HA A:TRP74 4.6 2.1 1.0 N A:SER77 4.6 1.2 0.2 HB2 A:TRP78 4.7 2.2 1.0 C A:SER77 4.7 1.6 0.8 SG A:CYS61 4.7 2.2 1.0 CA A:TRP78 4.7 1.8 1.0 CA A:SER77 4.7 1.6 0.2 SG A:CYS43 4.7 1.9 1.0 HA A:CYS75 4.8 1.9 1.0 CB A:SER77 4.8 2.5 0.8 SG A:CYS46 4.8 1.7 1.0 N A:SER77 4.8 1.7 0.8 O A:SER77 4.9 1.5 0.2 HD12 A:LEU63 4.9 4.8 1.0 HD13 A:LEU17 5.0 5.2 1.0 CA A:SER77 5.0 1.7 0.8

Iron binding site 3 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution


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 High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:1.6 occ:1.00 FE3 A:SF484 0.0 1.6 1.0 S4 A:SF484 2.2 1.9 1.0 SG A:CYS46 2.3 1.7 1.0 S1 A:SF484 2.3 1.8 1.0 S2 A:SF484 2.3 1.8 1.0 FE1 A:SF484 2.7 1.7 1.0 FE2 A:SF484 2.7 1.7 1.0 FE4 A:SF484 2.7 1.6 1.0 HB3 A:CYS46 3.1 2.3 1.0 CB A:CYS46 3.1 1.9 1.0 HB2 A:PHE48 3.2 2.6 1.0 HB2 A:CYS46 3.3 2.3 1.0 HA A:TRP78 3.3 2.2 1.0 HD2 A:PHE48 3.8 4.3 1.0 HA A:CYS43 3.8 2.2 1.0 S3 A:SF484 3.9 1.8 1.0 H A:PHE48 4.0 2.3 1.0 HD1 A:TRP78 4.1 2.3 1.0 CB A:PHE48 4.2 2.2 1.0 CA A:TRP78 4.2 1.8 1.0 H A:THR79 4.3 2.1 1.0 H A:MET49 4.5 1.9 0.3 O A:SER77 4.5 1.5 0.2 N A:TRP78 4.6 1.9 1.0 CA A:CYS46 4.6 1.8 1.0 CD2 A:PHE48 4.6 3.5 1.0 HB3 A:PHE48 4.6 2.6 1.0 SG A:CYS61 4.6 2.2 1.0 HB2 A:MET49 4.7 2.7 0.7 CD1 A:TRP78 4.7 1.9 1.0 N A:PHE48 4.7 1.9 1.0 H A:MET49 4.7 2.5 0.7 HB2 A:TRP78 4.7 2.2 1.0 C A:SER77 4.7 2.5 0.2 CA A:CYS43 4.7 1.8 1.0 N A:MET49 4.7 1.6 0.3 SG A:CYS43 4.8 1.9 1.0 HB2 A:MET49 4.8 2.5 0.3 SG A:CYS75 4.8 1.8 1.0 HB3 A:CYS43 4.8 2.3 1.0 CA A:PHE48 4.8 2.1 1.0 H A:CYS75 4.8 2.0 1.0 C A:SER77 4.9 1.6 0.8 O A:SER77 4.9 1.9 0.8 N A:MET49 4.9 2.1 0.7 HA A:CYS46 4.9 2.2 1.0 CG A:PHE48 4.9 2.4 1.0 CB A:TRP78 4.9 1.9 1.0 C A:PHE48 5.0 2.1 1.0 N A:THR79 5.0 1.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution


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 High-Potential Iron-Sulfur Protein From Thermochromatium Tepidum at 0.72 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe84 b:1.6 occ:1.00 FE4 A:SF484 0.0 1.6 1.0 S3 A:SF484 2.2 1.8 1.0 SG A:CYS43 2.2 1.9 1.0 S2 A:SF484 2.3 1.8 1.0 S1 A:SF484 2.3 1.8 1.0 FE2 A:SF484 2.7 1.7 1.0 FE1 A:SF484 2.7 1.7 1.0 FE3 A:SF484 2.7 1.6 1.0 HA A:CYS43 3.1 2.2 1.0 CB A:CYS43 3.2 1.9 1.0 HB3 A:CYS43 3.2 2.3 1.0 CA A:CYS43 3.7 1.8 1.0 HG12 A:ILE69 3.7 3.1 1.0 S4 A:SF484 3.9 1.9 1.0 HA A:TRP74 3.9 2.1 1.0 H A:CYS75 4.1 2.0 1.0 HB2 A:CYS43 4.1 2.3 1.0 HE1 A:TYR19 4.1 3.0 1.0 HG22 A:ILE69 4.3 5.2 1.0 HD13 A:ILE69 4.3 4.5 1.0 HB3 A:CYS46 4.4 2.3 1.0 N A:CYS43 4.4 1.7 1.0 HD1 A:TYR19 4.4 2.9 1.0 H A:CYS43 4.5 2.1 1.0 HB A:ILE69 4.5 2.8 1.0 N A:CYS75 4.5 1.6 1.0 CG1 A:ILE69 4.5 2.6 1.0 HB2 A:CYS61 4.5 3.0 1.0 HB2 A:CYS46 4.5 2.3 1.0 CA A:TRP74 4.6 1.8 1.0 C A:TRP74 4.7 1.6 1.0 HB3 A:CYS75 4.7 2.2 1.0 HD1 A:TRP78 4.8 2.3 1.0 SG A:CYS46 4.8 1.7 1.0 CB A:CYS46 4.8 1.9 1.0 N A:TRP74 4.8 1.8 1.0 CD1 A:ILE69 4.8 3.0 1.0 SG A:CYS75 4.8 1.8 1.0 SG A:CYS61 4.8 2.2 1.0 HB2 A:MET49 4.9 2.5 0.3 CE1 A:TYR19 4.9 2.5 1.0 C A:CYS43 4.9 1.8 1.0 HD12 A:ILE69 4.9 4.5 1.0 CB A:ILE69 4.9 2.3 1.0 HB2 A:MET49 4.9 2.7 0.7 C A:GLY73 5.0 1.6 1.0

K.Takeda, K.Kusumoto, Y.Hirano, K.Miki. Detailed Assessment of X-Ray Induced Structural Perturbation in A Crystalline State Protein. J.Struct.Biol. V. 169 135 2010.
ISSN: ISSN 1047-8477
PubMed: 19782139
DOI: 10.1016/J.JSB.2009.09.012