Iron in PDB 3zoo: Structure of the Y46F Mutant of Human Cytochrome C

The structure of Structure of the Y46F Mutant of Human Cytochrome C, PDB code: 3zoo was solved by B.S.Rajagopal, J.A.R.Worrall, M.A.Hough, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.59 / 1.35
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.367, 53.952, 58.950, 76.55, 88.73, 71.86
R / Rfree (%)	13.821 / 17.935

The binding sites of Iron atom in the Structure of the Y46F Mutant of Human Cytochrome C (pdb code 3zoo). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of the Y46F Mutant of Human Cytochrome C, PDB code: 3zoo:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of the Y46F Mutant of Human Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Y46F Mutant of Human Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:10.8 occ:1.00 FE A:HEM105 0.0 10.8 1.0 ND A:HEM105 1.9 10.0 1.0 NA A:HEM105 2.0 9.4 1.0 NE2 A:HIS18 2.0 11.4 1.0 NC A:HEM105 2.0 10.7 1.0 NB A:HEM105 2.1 9.6 1.0 SD A:MET80 2.3 11.5 1.0 CE1 A:HIS18 2.9 10.8 1.0 C1D A:HEM105 3.0 9.8 1.0 C1B A:HEM105 3.0 9.1 1.0 C4D A:HEM105 3.0 9.2 1.0 C4C A:HEM105 3.0 8.3 1.0 C4B A:HEM105 3.0 10.4 1.0 C4A A:HEM105 3.0 9.2 1.0 C1C A:HEM105 3.0 10.9 1.0 C1A A:HEM105 3.0 9.9 1.0 CD2 A:HIS18 3.0 10.4 1.0 CHB A:HEM105 3.4 9.9 1.0 CHD A:HEM105 3.4 9.7 1.0 CE A:MET80 3.4 11.7 1.0 CG A:MET80 3.4 10.7 1.0 CHA A:HEM105 3.4 9.9 1.0 CHC A:HEM105 3.4 10.6 1.0 ND1 A:HIS18 4.1 10.7 1.0 CG A:HIS18 4.1 10.4 1.0 C2A A:HEM105 4.2 10.0 1.0 C2C A:HEM105 4.2 11.3 1.0 C2B A:HEM105 4.2 10.3 1.0 C2D A:HEM105 4.2 10.2 1.0 C3B A:HEM105 4.2 11.7 1.0 CB A:MET80 4.3 10.4 1.0 C3A A:HEM105 4.3 9.0 1.0 C3D A:HEM105 4.3 9.2 1.0 C3C A:HEM105 4.3 9.2 1.0 OH A:TYR67 4.9 13.8 1.0

Iron binding site 2 out of 4 in the Structure of the Y46F Mutant of Human Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Y46F Mutant of Human Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe105 b:10.9 occ:1.00 FE B:HEM105 0.0 10.9 1.0 ND B:HEM105 1.9 9.4 1.0 NB B:HEM105 2.0 9.6 1.0 NA B:HEM105 2.0 10.6 1.0 NC B:HEM105 2.1 10.8 1.0 NE2 B:HIS18 2.1 10.1 1.0 SD B:MET80 2.3 11.3 1.0 C4D B:HEM105 3.0 9.5 1.0 C4B B:HEM105 3.0 9.6 1.0 C1A B:HEM105 3.0 10.5 1.0 CE1 B:HIS18 3.0 11.1 1.0 C1D B:HEM105 3.0 9.8 1.0 C1C B:HEM105 3.1 9.9 1.0 C4A B:HEM105 3.1 10.4 1.0 C1B B:HEM105 3.1 9.7 1.0 C4C B:HEM105 3.1 9.8 1.0 CD2 B:HIS18 3.1 9.9 1.0 CE B:MET80 3.4 11.1 1.0 CHD B:HEM105 3.4 10.4 1.0 CHC B:HEM105 3.4 9.5 1.0 CG B:MET80 3.4 12.0 1.0 CHB B:HEM105 3.4 10.2 1.0 CHA B:HEM105 3.4 9.1 1.0 ND1 B:HIS18 4.1 11.0 1.0 CG B:HIS18 4.2 11.0 1.0 CB B:MET80 4.2 10.3 1.0 C2A B:HEM105 4.2 10.2 1.0 C2B B:HEM105 4.2 9.4 1.0 C3A B:HEM105 4.2 9.5 1.0 C2D B:HEM105 4.3 10.0 1.0 C3C B:HEM105 4.3 10.8 1.0 C2C B:HEM105 4.3 11.8 1.0 C3D B:HEM105 4.3 10.0 1.0 C3B B:HEM105 4.3 9.8 1.0 OH B:TYR67 4.9 13.2 1.0

Iron binding site 3 out of 4 in the Structure of the Y46F Mutant of Human Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Y46F Mutant of Human Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe105 b:13.7 occ:1.00 FE C:HEM105 0.0 13.7 1.0 ND C:HEM105 1.9 14.3 1.0 NA C:HEM105 2.0 12.6 1.0 NE2 C:HIS18 2.0 31.0 1.0 NB C:HEM105 2.0 11.4 1.0 NC C:HEM105 2.1 11.7 1.0 SD C:MET80 2.2 12.0 1.0 C1D C:HEM105 2.9 12.2 1.0 C4D C:HEM105 2.9 13.3 1.0 CD2 C:HIS18 3.0 17.4 1.0 C1B C:HEM105 3.0 10.3 1.0 C4B C:HEM105 3.0 12.0 1.0 C4C C:HEM105 3.0 11.9 1.0 C1A C:HEM105 3.0 12.4 1.0 C4A C:HEM105 3.0 11.3 1.0 CE1 C:HIS18 3.1 22.5 1.0 C1C C:HEM105 3.1 10.9 1.0 CE C:MET80 3.4 11.1 1.0 CHA C:HEM105 3.4 13.0 1.0 CG C:MET80 3.4 10.6 1.0 CHB C:HEM105 3.4 11.1 1.0 CHC C:HEM105 3.4 10.7 1.0 CHD C:HEM105 3.4 13.1 1.0 ND1 C:HIS18 4.1 15.9 1.0 CG C:HIS18 4.1 17.4 1.0 CB C:MET80 4.2 10.5 1.0 C2D C:HEM105 4.2 13.6 1.0 C3D C:HEM105 4.2 14.0 1.0 C2B C:HEM105 4.2 10.7 1.0 C3A C:HEM105 4.2 11.8 1.0 C2A C:HEM105 4.2 12.3 1.0 C3C C:HEM105 4.2 11.4 1.0 C3B C:HEM105 4.3 11.6 1.0 C2C C:HEM105 4.3 11.7 1.0 OH C:TYR67 4.8 14.2 1.0

Iron binding site 4 out of 4 in the Structure of the Y46F Mutant of Human Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Y46F Mutant of Human Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe105 b:9.6 occ:1.00 FE D:HEM105 0.0 9.6 1.0 ND D:HEM105 1.9 11.1 1.0 NB D:HEM105 2.0 9.5 1.0 NA D:HEM105 2.0 7.8 1.0 NC D:HEM105 2.0 6.5 1.0 NE2 D:HIS18 2.0 11.5 1.0 SD D:MET80 2.3 10.5 1.0 C1D D:HEM105 2.9 8.9 1.0 C1B D:HEM105 3.0 7.0 1.0 C4D D:HEM105 3.0 9.6 1.0 C4B D:HEM105 3.0 7.3 1.0 CE1 D:HIS18 3.0 10.3 1.0 CD2 D:HIS18 3.0 10.2 1.0 C4A D:HEM105 3.0 7.9 1.0 C4C D:HEM105 3.0 7.6 1.0 C1A D:HEM105 3.1 8.8 1.0 C1C D:HEM105 3.1 7.6 1.0 CE D:MET80 3.3 10.8 1.0 CG D:MET80 3.4 8.9 1.0 CHA D:HEM105 3.4 9.3 1.0 CHB D:HEM105 3.4 7.4 1.0 CHD D:HEM105 3.4 8.3 1.0 CHC D:HEM105 3.4 7.4 1.0 ND1 D:HIS18 4.1 10.3 1.0 CB D:MET80 4.1 8.0 1.0 CG D:HIS18 4.2 9.3 1.0 C2D D:HEM105 4.2 8.7 1.0 C2B D:HEM105 4.2 8.1 1.0 C3D D:HEM105 4.2 7.6 1.0 C3B D:HEM105 4.2 7.3 1.0 C2A D:HEM105 4.3 9.4 1.0 C3A D:HEM105 4.3 8.6 1.0 C2C D:HEM105 4.3 8.2 1.0 C3C D:HEM105 4.3 8.2 1.0 OH D:TYR67 4.9 11.5 1.0

B.S.Rajagopal, A.N.Edzuma, M.A.Hough, K.L.I.M.Blundell, V.E.Kagan, A.A.Kapralov, L.A.Fraser, J.N.Butt, G.G.Silkstone, M.T.Wilson, D.A.Svistunenko, J.A.R.Worrall. The Hydrogen Peroxide Induced Radical Behaviour in Human Cytochrome C Phospholipid Complexes: Implications For the Enhanced Pro-Apoptotic Activity of the G41S Mutant Biochem.J. V. 456 441 2013.
ISSN: ISSN 0264-6021
PubMed: 24099549
DOI: 10.1042/BJ20130758