Iron in PDB 3x15: Dimeric Aquifex Aeolicus Cytochrome C555

The structure of Dimeric Aquifex Aeolicus Cytochrome C555, PDB code: 3x15 was solved by M.Yamanaka, S.Nagao, H.Komori, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.12 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.591, 54.464, 65.403, 90.00, 114.47, 90.00
R / Rfree (%)	15 / 21.4

The binding sites of Iron atom in the Dimeric Aquifex Aeolicus Cytochrome C555 (pdb code 3x15). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dimeric Aquifex Aeolicus Cytochrome C555, PDB code: 3x15:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Dimeric Aquifex Aeolicus Cytochrome C555


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dimeric Aquifex Aeolicus Cytochrome C555 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:16.5 occ:1.00 FE A:HEC200 0.0 16.5 1.0 NC A:HEC200 2.0 15.2 1.0 NB A:HEC200 2.0 14.2 1.0 NE2 A:HIS16 2.0 14.9 1.0 NA A:HEC200 2.0 15.3 1.0 ND A:HEC200 2.0 16.7 1.0 SD G:MET61 2.3 16.7 1.0 CE1 A:HIS16 3.0 14.1 1.0 C1B A:HEC200 3.0 14.8 1.0 C4B A:HEC200 3.0 14.4 1.0 CD2 A:HIS16 3.0 14.5 1.0 C1C A:HEC200 3.0 13.8 1.0 C1A A:HEC200 3.0 15.9 1.0 C4C A:HEC200 3.0 15.2 1.0 C1D A:HEC200 3.1 18.0 1.0 C4A A:HEC200 3.1 14.9 1.0 C4D A:HEC200 3.1 16.8 1.0 CE G:MET61 3.3 15.8 1.0 CHC A:HEC200 3.4 14.4 1.0 CHA A:HEC200 3.4 19.3 1.0 CHD A:HEC200 3.4 14.8 1.0 CHB A:HEC200 3.4 15.8 1.0 CG G:MET61 3.5 17.9 1.0 ND1 A:HIS16 4.1 15.6 1.0 CG A:HIS16 4.2 14.1 1.0 C3B A:HEC200 4.3 14.9 1.0 C2B A:HEC200 4.3 14.2 1.0 C2A A:HEC200 4.3 16.1 1.0 C3C A:HEC200 4.3 15.6 1.0 C2C A:HEC200 4.3 15.2 1.0 C3A A:HEC200 4.3 16.7 1.0 CB G:MET61 4.3 20.7 1.0 C2D A:HEC200 4.3 20.1 1.0 C3D A:HEC200 4.3 19.9 1.0 CA G:MET61 4.9 19.2 1.0

Iron binding site 2 out of 4 in the Dimeric Aquifex Aeolicus Cytochrome C555


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dimeric Aquifex Aeolicus Cytochrome C555 within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:12.0 occ:1.00 FE D:HEC200 0.0 12.0 1.0 NE2 D:HIS16 2.0 10.7 1.0 NB D:HEC200 2.0 9.3 1.0 ND D:HEC200 2.0 10.8 1.0 NA D:HEC200 2.0 11.5 1.0 NC D:HEC200 2.1 12.6 1.0 SD J:MET61 2.3 12.6 1.0 CE1 D:HIS16 2.9 10.2 1.0 C4B D:HEC200 3.0 12.5 1.0 CD2 D:HIS16 3.0 11.4 1.0 C1D D:HEC200 3.0 10.4 1.0 C4D D:HEC200 3.1 11.3 1.0 C1B D:HEC200 3.1 10.4 1.0 C4A D:HEC200 3.1 9.9 1.0 C1C D:HEC200 3.1 12.1 1.0 C4C D:HEC200 3.1 11.1 1.0 C1A D:HEC200 3.1 10.5 1.0 CE J:MET61 3.3 12.8 1.0 CHC D:HEC200 3.4 10.9 1.0 CHD D:HEC200 3.4 12.5 1.0 CHA D:HEC200 3.4 10.9 1.0 CHB D:HEC200 3.5 12.0 1.0 CG J:MET61 3.5 12.8 1.0 ND1 D:HIS16 4.1 11.1 1.0 CG D:HIS16 4.2 11.7 1.0 CB J:MET61 4.2 12.4 1.0 C3B D:HEC200 4.2 13.0 1.0 C3D D:HEC200 4.3 11.5 1.0 C2D D:HEC200 4.3 10.9 1.0 C2B D:HEC200 4.3 12.8 1.0 C2C D:HEC200 4.3 12.6 1.0 C2A D:HEC200 4.3 10.1 1.0 C3A D:HEC200 4.3 10.0 1.0 C3C D:HEC200 4.3 11.3 1.0 CA J:MET61 4.8 12.4 1.0

Iron binding site 3 out of 4 in the Dimeric Aquifex Aeolicus Cytochrome C555


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dimeric Aquifex Aeolicus Cytochrome C555 within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe200 b:16.8 occ:1.00 FE G:HEC200 0.0 16.8 1.0 NA G:HEC200 2.0 15.8 1.0 NC G:HEC200 2.0 15.4 1.0 ND G:HEC200 2.1 17.0 1.0 NB G:HEC200 2.1 16.4 1.0 NE2 G:HIS16 2.1 15.7 1.0 SD A:MET61 2.3 18.5 1.0 CE1 G:HIS16 3.0 14.8 1.0 C4A G:HEC200 3.1 12.7 1.0 C1A G:HEC200 3.1 15.3 1.0 C4C G:HEC200 3.1 18.0 1.0 C1D G:HEC200 3.1 18.3 1.0 C1C G:HEC200 3.1 16.0 1.0 C4D G:HEC200 3.1 18.8 1.0 C1B G:HEC200 3.1 14.6 1.0 C4B G:HEC200 3.1 16.1 1.0 CD2 G:HIS16 3.1 15.7 1.0 CHD G:HEC200 3.4 18.7 1.0 CE A:MET61 3.4 18.5 1.0 CHB G:HEC200 3.4 15.6 1.0 CHC G:HEC200 3.4 15.9 1.0 CHA G:HEC200 3.4 16.9 1.0 CG A:MET61 3.5 17.3 1.0 ND1 G:HIS16 4.2 16.3 1.0 CB A:MET61 4.2 16.2 1.0 CG G:HIS16 4.2 17.6 1.0 C2A G:HEC200 4.3 14.9 1.0 C3A G:HEC200 4.3 13.8 1.0 C3C G:HEC200 4.3 16.1 1.0 C3D G:HEC200 4.3 19.8 1.0 C3B G:HEC200 4.3 14.7 1.0 C2C G:HEC200 4.3 15.5 1.0 C2D G:HEC200 4.3 20.2 1.0 C2B G:HEC200 4.3 16.0 1.0 CA A:MET61 4.8 18.9 1.0

Iron binding site 4 out of 4 in the Dimeric Aquifex Aeolicus Cytochrome C555


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dimeric Aquifex Aeolicus Cytochrome C555 within 5.0Å range: probe atom residue distance (Å) B Occ J:Fe200 b:19.8 occ:1.00 FE J:HEC200 0.0 19.8 1.0 NE2 J:HIS16 2.0 20.3 1.0 ND J:HEC200 2.0 16.1 1.0 NB J:HEC200 2.1 19.8 1.0 NA J:HEC200 2.1 21.8 1.0 NC J:HEC200 2.1 16.1 1.0 SD D:MET61 2.3 18.6 1.0 CE1 J:HIS16 2.9 18.8 1.0 CD2 J:HIS16 3.0 20.6 1.0 C1D J:HEC200 3.0 16.9 1.0 C1B J:HEC200 3.0 20.2 1.0 C4A J:HEC200 3.1 22.3 1.0 C4D J:HEC200 3.1 17.7 1.0 C4B J:HEC200 3.1 17.9 1.0 C4C J:HEC200 3.1 18.4 1.0 C1A J:HEC200 3.1 22.1 1.0 C1C J:HEC200 3.1 17.3 1.0 CE D:MET61 3.3 19.7 1.0 CHB J:HEC200 3.4 24.5 1.0 CHD J:HEC200 3.4 16.2 1.0 CHA J:HEC200 3.4 20.4 1.0 CHC J:HEC200 3.5 15.6 1.0 CG D:MET61 3.5 18.3 1.0 ND1 J:HIS16 4.0 22.0 1.0 CG J:HIS16 4.1 22.6 1.0 C2B J:HEC200 4.3 19.4 1.0 C3A J:HEC200 4.3 22.1 1.0 C3B J:HEC200 4.3 19.5 1.0 C2A J:HEC200 4.3 22.4 1.0 CB D:MET61 4.3 16.2 1.0 C3C J:HEC200 4.3 17.9 1.0 C2D J:HEC200 4.3 17.2 1.0 C3D J:HEC200 4.3 18.2 1.0 C2C J:HEC200 4.3 17.3 1.0 CA D:MET61 4.9 16.2 1.0

M.Yamanaka, S.Nagao, H.Komori, Y.Higuchi, S.Hirota. Change in Structure and Ligand Binding Properties of Hyperstable Cytochrome C555 From Aquifex Aeolicus By Domain Swapping Protein Sci. 2015.
ISSN: ESSN 1469-896X
PubMed: 25586341
DOI: 10.1002/PRO.2627