Iron in PDB 4q5p: Lysine-Ligated Yeast Iso-1 Cytochrome C

The structure of Lysine-Ligated Yeast Iso-1 Cytochrome C, PDB code: 4q5p was solved by J.F.Amacher, M.Q.Zhu, F.Zhong, E.V.Pletneva, D.R.Madden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.52 / 1.87
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	106.020, 106.020, 149.840, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 20.4

The binding sites of Iron atom in the Lysine-Ligated Yeast Iso-1 Cytochrome C (pdb code 4q5p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Lysine-Ligated Yeast Iso-1 Cytochrome C, PDB code: 4q5p:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Lysine-Ligated Yeast Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Lysine-Ligated Yeast Iso-1 Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:15.0 occ:1.00 FE A:HEM201 0.0 15.0 1.0 ND A:HEM201 2.0 14.0 1.0 NE2 A:HIS18 2.0 13.0 1.0 NA A:HEM201 2.0 13.6 1.0 NC A:HEM201 2.1 14.8 1.0 NZ A:LYS73 2.1 8.0 1.0 NB A:HEM201 2.1 16.2 1.0 CD2 A:HIS18 2.9 14.3 1.0 C4D A:HEM201 3.0 15.6 1.0 C1D A:HEM201 3.0 10.4 1.0 C4C A:HEM201 3.0 11.7 1.0 C1A A:HEM201 3.1 18.1 1.0 C4B A:HEM201 3.1 15.5 1.0 C1B A:HEM201 3.1 15.0 1.0 CE1 A:HIS18 3.1 17.9 1.0 C4A A:HEM201 3.1 18.4 1.0 C1C A:HEM201 3.1 15.4 1.0 CE A:LYS73 3.2 11.2 1.0 CHD A:HEM201 3.4 11.4 1.0 CHA A:HEM201 3.4 19.3 1.0 CHC A:HEM201 3.5 14.4 1.0 CHB A:HEM201 3.5 17.6 1.0 CG A:HIS18 4.1 11.5 1.0 ND1 A:HIS18 4.1 11.6 1.0 C3A A:HEM201 4.3 14.5 1.0 C2A A:HEM201 4.3 15.1 1.0 C3D A:HEM201 4.3 13.6 1.0 C2B A:HEM201 4.3 25.6 1.0 C3C A:HEM201 4.3 12.9 1.0 C2C A:HEM201 4.3 10.8 1.0 C2D A:HEM201 4.3 9.0 1.0 C3B A:HEM201 4.3 26.6 1.0 CD A:LYS73 4.4 14.2 1.0 OH A:TYR67 4.6 17.0 1.0

Iron binding site 2 out of 3 in the Lysine-Ligated Yeast Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Lysine-Ligated Yeast Iso-1 Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:23.3 occ:1.00 FE B:HEM201 0.0 23.3 1.0 ND B:HEM201 1.9 24.0 1.0 NA B:HEM201 2.0 24.0 1.0 NE2 B:HIS18 2.0 28.1 1.0 NC B:HEM201 2.1 24.9 1.0 NB B:HEM201 2.1 36.2 1.0 NZ B:LYS73 2.2 27.2 1.0 CE1 B:HIS18 3.0 23.9 1.0 C4D B:HEM201 3.0 23.6 1.0 C1D B:HEM201 3.0 24.6 1.0 C1A B:HEM201 3.0 19.0 1.0 CD2 B:HIS18 3.1 21.0 1.0 C4C B:HEM201 3.1 28.5 1.0 C4B B:HEM201 3.1 32.0 1.0 C4A B:HEM201 3.1 29.9 1.0 C1B B:HEM201 3.1 34.2 1.0 C1C B:HEM201 3.1 23.4 1.0 CE B:LYS73 3.1 22.8 1.0 CHA B:HEM201 3.4 20.9 1.0 CHD B:HEM201 3.4 27.0 1.0 CHC B:HEM201 3.5 29.3 1.0 CHB B:HEM201 3.5 30.5 1.0 ND1 B:HIS18 4.1 22.9 1.0 CG B:HIS18 4.2 20.6 1.0 C2A B:HEM201 4.2 26.9 1.0 C3D B:HEM201 4.3 18.9 1.0 C3A B:HEM201 4.3 24.9 1.0 C2D B:HEM201 4.3 18.8 1.0 C3C B:HEM201 4.3 30.6 1.0 C2C B:HEM201 4.3 27.6 1.0 C2B B:HEM201 4.3 40.5 1.0 C3B B:HEM201 4.3 36.9 1.0 CD B:LYS73 4.5 19.3 1.0 OH B:TYR67 4.8 31.7 1.0

Iron binding site 3 out of 3 in the Lysine-Ligated Yeast Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Lysine-Ligated Yeast Iso-1 Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:20.8 occ:1.00 FE C:HEM201 0.0 20.8 1.0 ND C:HEM201 2.0 25.2 1.0 NA C:HEM201 2.0 28.1 1.0 NE2 C:HIS18 2.0 17.1 1.0 NC C:HEM201 2.1 20.2 1.0 NB C:HEM201 2.1 23.1 1.0 NZ C:LYS73 2.4 20.6 1.0 CD2 C:HIS18 3.0 16.5 1.0 C1D C:HEM201 3.0 23.2 1.0 C4D C:HEM201 3.0 17.9 1.0 C1A C:HEM201 3.0 21.3 1.0 C4A C:HEM201 3.0 22.5 1.0 CE1 C:HIS18 3.0 16.4 1.0 C1B C:HEM201 3.1 25.6 1.0 C4B C:HEM201 3.1 27.1 1.0 C4C C:HEM201 3.1 23.5 1.0 C1C C:HEM201 3.1 21.2 1.0 CHA C:HEM201 3.4 17.4 1.0 CHD C:HEM201 3.4 19.8 1.0 CHB C:HEM201 3.4 25.7 1.0 CHC C:HEM201 3.5 26.7 1.0 CE C:LYS73 3.8 26.1 1.0 ND1 C:HIS18 4.1 15.8 1.0 CG C:HIS18 4.1 16.6 1.0 C2A C:HEM201 4.2 20.9 1.0 C3A C:HEM201 4.2 22.5 1.0 C3D C:HEM201 4.3 17.4 1.0 C2B C:HEM201 4.3 27.7 1.0 C2C C:HEM201 4.3 28.7 1.0 C3C C:HEM201 4.3 30.0 1.0 C2D C:HEM201 4.3 14.2 1.0 C3B C:HEM201 4.3 29.0 1.0 CD C:LYS73 4.5 34.3 1.0

J.F.Amacher, F.Zhong, M.Q.Zhu, G.P.Lisi, K.H.Hoke, D.R.Madden, E.V.Pletneva. Structural Details of Cytochrome C Transformation Into A Lysine-Ligated "Alkaline" Form: Sequence-Build-in Loop Refolding and Functional Implications of the Conformational Transition To Be Published.