Iron in PDB 5c0z: The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution

The structure of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution, PDB code: 5c0z was solved by B.F.P.Edwards, G.Mahapatra, A.A.Vaishnav, J.S.Brunzelle, M.Huttemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.22 / 1.12
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	34.401, 52.471, 61.647, 110.04, 92.77, 92.02
R / Rfree (%)	13.2 / 15.9

The binding sites of Iron atom in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution (pdb code 5c0z). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution, PDB code: 5c0z:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:7.5 occ:1.00 FE A:HEC201 0.0 7.5 1.0 ND A:HEC201 2.0 7.1 1.0 NA A:HEC201 2.0 7.3 1.0 NB A:HEC201 2.0 7.2 1.0 NC A:HEC201 2.0 8.1 1.0 NE2 A:HIS18 2.0 7.3 1.0 SD A:MET80 2.3 8.7 1.0 CE1 A:HIS18 3.0 7.5 1.0 C1D A:HEC201 3.0 8.0 1.0 C1B A:HEC201 3.0 7.3 1.0 C4D A:HEC201 3.0 7.5 1.0 C4A A:HEC201 3.0 7.3 1.0 C1A A:HEC201 3.0 7.4 1.0 C4C A:HEC201 3.0 8.0 1.0 C1C A:HEC201 3.0 7.8 1.0 C4B A:HEC201 3.0 7.1 1.0 CD2 A:HIS18 3.0 7.2 1.0 CE A:MET80 3.3 9.8 1.0 CHA A:HEC201 3.4 7.0 1.0 CHD A:HEC201 3.4 8.0 1.0 CHB A:HEC201 3.4 7.3 1.0 CHC A:HEC201 3.4 7.9 1.0 CG A:MET80 3.4 8.9 1.0 ND1 A:HIS18 4.1 7.8 1.0 CG A:HIS18 4.2 7.4 1.0 CB A:MET80 4.2 9.0 1.0 C2A A:HEC201 4.2 7.6 1.0 C3D A:HEC201 4.2 6.9 1.0 C2C A:HEC201 4.2 8.6 1.0 C2B A:HEC201 4.3 7.3 1.0 C2D A:HEC201 4.3 7.6 1.0 C3A A:HEC201 4.3 7.2 1.0 C3C A:HEC201 4.3 8.7 1.0 C3B A:HEC201 4.3 7.4 1.0 OH A:TYR67 4.8 14.7 1.0

Iron binding site 2 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:21.6 occ:0.28 FE2 A:FC6202 0.0 21.6 0.3 C21 A:FC6202 1.8 21.5 0.3 C24 A:FC6202 1.8 21.1 0.3 C22 A:FC6202 1.8 23.0 0.3 C11 A:FC6202 1.8 18.5 0.3 C23 A:FC6202 1.8 19.8 0.3 C26 A:FC6202 1.9 21.4 0.3 N25 A:FC6202 2.9 24.2 0.3 N24 A:FC6202 2.9 14.6 0.3 N22 A:FC6202 3.0 27.4 0.3 N23 A:FC6202 3.0 25.2 0.3 N11 A:FC6202 3.0 13.4 0.3 N21 A:FC6202 3.0 16.1 0.3 N24 A:FC6202 3.1 14.7 0.4 C24 A:FC6202 3.5 14.4 0.4 O A:HOH328 4.0 23.3 1.0 N25 A:FC6202 4.2 18.9 0.4 C21 A:FC6202 4.2 16.6 0.4 O D:HOH332 4.2 21.6 1.0 O A:HOH334 4.2 20.1 1.0 O D:HOH307 4.3 16.8 1.0 C26 A:FC6202 4.5 15.7 0.4 NZ D:LYS13 4.5 13.9 1.0 N21 A:FC6202 4.6 16.4 0.4 NZ A:LYS13 4.7 16.6 1.0 O A:HOH345 4.8 30.4 1.0 FE2 A:FC6202 4.8 15.0 0.4 O D:HOH301 4.9 23.8 1.0 O D:HOH302 5.0 20.0 1.0

Iron binding site 3 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:15.0 occ:0.37 FE2 A:FC6202 0.0 15.0 0.4 C26 A:FC6202 1.8 15.7 0.4 C21 A:FC6202 1.8 16.6 0.4 C23 A:FC6202 1.8 15.7 0.4 C11 A:FC6202 1.8 15.5 0.4 C22 A:FC6202 1.8 14.3 0.4 C24 A:FC6202 1.9 14.4 0.4 N23 A:FC6202 1.9 25.2 0.3 N21 A:FC6202 2.9 16.4 0.4 N23 A:FC6202 3.0 17.9 0.4 N11 A:FC6202 3.0 18.0 0.4 N25 A:FC6202 3.0 18.9 0.4 N22 A:FC6202 3.0 14.1 0.4 C23 A:FC6202 3.0 19.8 0.3 N24 A:FC6202 3.0 14.7 0.4 NZ D:LYS86 4.5 29.9 1.0 CD A:LYS86 4.5 30.0 1.0 NZ A:LYS87 4.6 22.6 1.0 CE D:LYS87 4.6 23.1 1.0 CE D:LYS86 4.6 24.7 1.0 NZ D:LYS87 4.7 28.6 1.0 FE2 A:FC6202 4.8 21.6 0.3 CE A:LYS87 4.8 19.4 1.0 CE A:LYS86 4.9 35.7 1.0 C26 A:FC6202 4.9 21.4 0.3 C24 A:FC6202 5.0 21.1 0.3

Iron binding site 4 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:7.7 occ:1.00 FE B:HEC201 0.0 7.7 1.0 ND B:HEC201 2.0 7.4 1.0 NB B:HEC201 2.0 7.9 1.0 NA B:HEC201 2.0 7.2 1.0 NC B:HEC201 2.0 7.9 1.0 NE2 B:HIS18 2.0 7.7 1.0 SD B:MET80 2.3 8.4 1.0 CE1 B:HIS18 2.9 7.7 1.0 C1D B:HEC201 3.0 7.8 1.0 C1B B:HEC201 3.0 8.2 1.0 C4D B:HEC201 3.0 7.2 1.0 C4A B:HEC201 3.0 8.0 1.0 C4C B:HEC201 3.0 7.8 1.0 C4B B:HEC201 3.0 8.0 1.0 C1A B:HEC201 3.0 7.4 1.0 CD2 B:HIS18 3.1 8.5 1.0 C1C B:HEC201 3.1 7.9 1.0 CE B:MET80 3.4 9.3 1.0 CHA B:HEC201 3.4 7.3 1.0 CHD B:HEC201 3.4 7.9 1.0 CG B:MET80 3.4 8.3 1.0 CHC B:HEC201 3.4 8.0 1.0 CHB B:HEC201 3.4 8.6 1.0 ND1 B:HIS18 4.1 8.1 1.0 CG B:HIS18 4.2 8.0 1.0 CB B:MET80 4.2 8.3 1.0 C3D B:HEC201 4.2 7.6 1.0 C2A B:HEC201 4.2 7.5 1.0 C3A B:HEC201 4.3 8.1 1.0 C2B B:HEC201 4.3 8.6 1.0 C2C B:HEC201 4.3 8.8 1.0 C3C B:HEC201 4.3 8.4 1.0 C2D B:HEC201 4.3 7.8 1.0 C3B B:HEC201 4.3 8.3 1.0 OH B:TYR67 4.8 14.7 1.0

Iron binding site 5 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:15.4 occ:0.93 FE2 B:FC6202 0.0 15.4 0.9 C26 B:FC6202 1.8 15.3 0.9 C24 B:FC6202 1.8 18.1 0.9 C11 B:FC6202 1.8 16.6 0.9 C23 B:FC6202 1.9 16.4 0.9 C22 B:FC6202 1.9 17.4 0.9 C21 B:FC6202 1.9 13.5 0.9 N21 B:FC6202 3.0 16.4 0.9 N23 B:FC6202 3.0 18.4 0.9 N25 B:FC6202 3.0 14.8 0.9 N22 B:FC6202 3.0 20.9 0.9 N11 B:FC6202 3.0 17.7 0.9 N24 B:FC6202 3.0 17.0 0.9 N B:GLY89 4.4 18.2 1.0 CA B:GLY89 4.8 17.6 1.0 CB B:LYS87 4.8 17.6 1.0 CG B:LYS87 4.9 17.4 1.0 O B:HOH308 5.0 31.2 1.0 CD B:LYS87 5.0 18.7 1.0

Iron binding site 6 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:20.5 occ:0.30 FE2 B:FC6203 0.0 20.5 0.3 C23 B:FC6203 1.8 20.9 0.3 C22 B:FC6203 1.8 18.7 0.3 C26 B:FC6203 1.8 17.4 0.3 C24 B:FC6203 1.8 21.3 0.3 C21 B:FC6203 1.8 22.2 0.3 C11 B:FC6203 1.8 21.2 0.3 N23 B:FC6203 2.9 25.2 0.3 N21 B:FC6203 3.0 12.6 0.3 N22 B:FC6203 3.0 15.2 0.3 N25 B:FC6203 3.0 24.9 0.3 N24 B:FC6203 3.0 21.9 0.3 N11 B:FC6203 3.0 18.2 0.3 N11 B:FC6203 3.1 15.7 0.3 C11 B:FC6203 3.6 15.1 0.3 N23 B:FC6203 4.0 18.8 0.3 O B:HOH326 4.0 22.7 1.0 C23 B:FC6203 4.1 16.0 0.3 O C:HOH357 4.2 26.4 1.0 O C:HOH336 4.2 17.8 1.0 O B:HOH336 4.3 22.8 1.0 C26 B:FC6203 4.5 15.0 0.3 NZ C:LYS13 4.6 14.5 1.0 N21 B:FC6203 4.6 15.1 0.3 NZ B:LYS13 4.7 18.0 1.0 FE2 B:FC6203 4.8 15.4 0.3 O C:HOH302 5.0 27.0 1.0 O C:HOH301 5.0 21.0 1.0

Iron binding site 7 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:15.4 occ:0.32 FE2 B:FC6203 0.0 15.4 0.3 C26 B:FC6203 1.8 15.0 0.3 C23 B:FC6203 1.8 16.0 0.3 C24 B:FC6203 1.8 15.7 0.3 C21 B:FC6203 1.8 17.6 0.3 C22 B:FC6203 1.8 15.3 0.3 C11 B:FC6203 1.8 15.1 0.3 N25 B:FC6203 2.1 24.9 0.3 N21 B:FC6203 2.9 15.1 0.3 N23 B:FC6203 3.0 18.8 0.3 N25 B:FC6203 3.0 19.1 0.3 N24 B:FC6203 3.0 18.1 0.3 N22 B:FC6203 3.0 14.7 0.3 N11 B:FC6203 3.0 15.7 0.3 C21 B:FC6203 3.1 22.2 0.3 NZ C:LYS86 4.4 30.2 1.0 CE C:LYS87 4.5 27.0 1.0 CD B:LYS86 4.6 29.9 1.0 NZ B:LYS87 4.6 27.2 1.0 C11 B:FC6203 4.7 21.2 0.3 FE2 B:FC6203 4.8 20.5 0.3 CE C:LYS86 4.8 26.8 1.0 CE B:LYS87 4.8 21.9 1.0 CE B:LYS86 4.9 33.6 1.0 NZ C:LYS87 4.9 33.5 1.0 C22 B:FC6203 5.0 18.7 0.3

Iron binding site 8 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:8.1 occ:1.00 FE C:HEC201 0.0 8.1 1.0 ND C:HEC201 2.0 8.3 1.0 NA C:HEC201 2.0 8.2 1.0 NC C:HEC201 2.0 8.5 1.0 NE2 C:HIS18 2.0 8.2 1.0 NB C:HEC201 2.0 8.0 1.0 SD C:MET80 2.3 8.7 1.0 CE1 C:HIS18 3.0 9.2 1.0 C1D C:HEC201 3.0 8.2 1.0 C1B C:HEC201 3.0 7.7 1.0 C4A C:HEC201 3.0 7.8 1.0 C4C C:HEC201 3.0 8.4 1.0 C4D C:HEC201 3.0 8.4 1.0 CD2 C:HIS18 3.0 8.5 1.0 C4B C:HEC201 3.0 7.9 1.0 C1C C:HEC201 3.0 8.5 1.0 C1A C:HEC201 3.1 8.4 1.0 CE C:MET80 3.3 9.1 1.0 CHB C:HEC201 3.4 8.5 1.0 CHD C:HEC201 3.4 8.7 1.0 CG C:MET80 3.4 8.8 1.0 CHC C:HEC201 3.4 8.0 1.0 CHA C:HEC201 3.4 8.0 1.0 ND1 C:HIS18 4.1 9.1 1.0 CG C:HIS18 4.2 9.2 1.0 CB C:MET80 4.2 8.6 1.0 C2B C:HEC201 4.2 8.6 1.0 C3D C:HEC201 4.2 8.6 1.0 C2C C:HEC201 4.2 9.1 1.0 C2A C:HEC201 4.3 8.5 1.0 C2D C:HEC201 4.3 9.2 1.0 C3C C:HEC201 4.3 9.0 1.0 C3A C:HEC201 4.3 8.7 1.0 C3B C:HEC201 4.3 8.6 1.0 OH C:TYR67 4.6 15.4 1.0

Iron binding site 9 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:12.2 occ:0.90 FE2 C:FC6202 0.0 12.2 0.9 C11 C:FC6202 1.8 13.3 0.9 C24 C:FC6202 1.8 13.6 0.9 C22 C:FC6202 1.8 12.8 0.9 C23 C:FC6202 1.9 13.0 0.9 C21 C:FC6202 1.9 12.8 0.9 C26 C:FC6202 1.9 13.2 0.9 N24 C:FC6202 3.0 14.2 0.9 N11 C:FC6202 3.0 12.8 0.9 N21 C:FC6202 3.0 15.2 0.9 N22 C:FC6202 3.0 13.4 0.9 N23 C:FC6202 3.0 12.6 0.9 N25 C:FC6202 3.0 13.2 0.9 N C:LYS88 4.6 12.1 1.0 O C:HOH393 4.7 35.3 1.0 O C:HOH396 4.8 35.0 1.0 O C:HOH397 4.8 35.1 1.0 CB C:LYS88 4.8 14.8 1.0

Iron binding site 10 out of 10 in the The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of The Structure of Oxidized Rat Cytochrome C at 1.13 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:9.9 occ:1.00 FE D:HEC201 0.0 9.9 1.0 ND D:HEC201 2.0 10.3 1.0 NA D:HEC201 2.0 9.9 1.0 NB D:HEC201 2.0 9.7 1.0 NE2 D:HIS18 2.0 10.8 1.0 NC D:HEC201 2.0 9.3 1.0 SD D:MET80 2.3 10.4 1.0 CE1 D:HIS18 3.0 10.5 1.0 C1B D:HEC201 3.0 9.3 1.0 C4D D:HEC201 3.0 10.0 1.0 C1D D:HEC201 3.0 9.9 1.0 C4B D:HEC201 3.0 9.2 1.0 C4A D:HEC201 3.0 9.8 1.0 C4C D:HEC201 3.0 9.9 1.0 CD2 D:HIS18 3.0 10.0 1.0 C1A D:HEC201 3.0 9.8 1.0 C1C D:HEC201 3.1 9.1 1.0 CHB D:HEC201 3.4 10.2 1.0 CG D:MET80 3.4 9.8 1.0 CE D:MET80 3.4 10.6 1.0 CHA D:HEC201 3.4 9.8 1.0 CHD D:HEC201 3.4 10.1 1.0 CHC D:HEC201 3.4 8.7 1.0 ND1 D:HIS18 4.1 10.7 1.0 CG D:HIS18 4.2 11.1 1.0 CB D:MET80 4.2 9.9 1.0 C2D D:HEC201 4.2 10.5 1.0 C2B D:HEC201 4.2 10.0 1.0 C2A D:HEC201 4.2 10.1 1.0 C3A D:HEC201 4.2 10.4 1.0 C3B D:HEC201 4.3 9.7 1.0 C3D D:HEC201 4.3 10.2 1.0 C3C D:HEC201 4.3 10.2 1.0 C2C D:HEC201 4.3 10.1 1.0 OH D:TYR67 4.8 16.2 1.0

H.A.Kalpage, A.Vaishnav, J.Liu, A.Varughese, J.Wan, A.A.Turner, Q.Ji, M.P.Zurek, A.A.Kapralov, V.E.Kagan, J.S.Brunzelle, M.A.Recanati, L.I.Grossman, T.H.Sanderson, I.Lee, A.R.Salomon, B.F.P.Edwards, M.Huttemann. Serine-47 Phosphorylation of Cytochromecin the Mammalian Brain Regulates Cytochromecoxidase and Caspase-3 Activity. Faseb J. 1120R 2019.
ISSN: ESSN 1530-6860
PubMed: 31570002
DOI: 10.1096/FJ.201901120R