Iron in PDB 3nbs: Crystal Structure of Dimeric Cytochrome C From Horse Heart

The structure of Crystal Structure of Dimeric Cytochrome C From Horse Heart, PDB code: 3nbs was solved by M.Taketa, H.Komori, S.Hirota, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.58 / 2.20
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	41.753, 56.305, 60.815, 66.28, 89.94, 73.66
R / Rfree (%)	21.5 / 27.3

The binding sites of Iron atom in the Crystal Structure of Dimeric Cytochrome C From Horse Heart (pdb code 3nbs). 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 Dimeric Cytochrome C From Horse Heart, PDB code: 3nbs:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Dimeric Cytochrome C From Horse Heart


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 Dimeric Cytochrome C From Horse Heart within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe105 b:10.7 occ:1.00 FE A:HEC105 0.0 10.7 1.0 NB A:HEC105 2.0 10.0 1.0 ND A:HEC105 2.0 12.3 1.0 NE2 A:HIS18 2.0 11.0 1.0 NC A:HEC105 2.0 10.7 1.0 NA A:HEC105 2.0 12.6 1.0 O A:HOH201 2.1 10.6 1.0 CD2 A:HIS18 2.9 10.9 1.0 CE1 A:HIS18 3.0 10.8 1.0 C1B A:HEC105 3.0 10.3 1.0 C1D A:HEC105 3.0 12.6 1.0 C1C A:HEC105 3.0 11.6 1.0 C4B A:HEC105 3.0 11.1 1.0 C4D A:HEC105 3.0 13.1 1.0 C4C A:HEC105 3.0 10.7 1.0 C4A A:HEC105 3.0 11.5 1.0 C1A A:HEC105 3.0 11.6 1.0 CHD A:HEC105 3.3 12.7 1.0 CHB A:HEC105 3.4 8.2 1.0 CHC A:HEC105 3.4 8.3 1.0 CHA A:HEC105 3.4 10.3 1.0 O A:HOH358 4.0 5.6 1.0 ND1 A:HIS18 4.1 11.5 1.0 CG A:HIS18 4.1 11.6 1.0 C2B A:HEC105 4.2 8.4 1.0 C3B A:HEC105 4.2 9.2 1.0 C2D A:HEC105 4.2 13.2 1.0 C3D A:HEC105 4.2 12.2 1.0 C2C A:HEC105 4.2 12.3 1.0 C3C A:HEC105 4.2 10.4 1.0 C3A A:HEC105 4.2 10.7 1.0 C2A A:HEC105 4.2 10.7 1.0 OH A:TYR67 4.4 12.0 1.0 CE2 B:PHE82 4.8 7.8 1.0 CD2 B:PHE82 4.9 9.8 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Dimeric Cytochrome C From Horse Heart


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 Dimeric Cytochrome C From Horse Heart within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe105 b:9.6 occ:1.00 FE B:HEC105 0.0 9.6 1.0 ND B:HEC105 2.0 12.8 1.0 NB B:HEC105 2.0 13.8 1.0 NA B:HEC105 2.0 14.2 1.0 NE2 B:HIS18 2.0 13.2 1.0 NC B:HEC105 2.0 13.9 1.0 O B:HOH202 2.1 13.7 1.0 CD2 B:HIS18 3.0 9.4 1.0 CE1 B:HIS18 3.0 13.5 1.0 C4D B:HEC105 3.0 11.9 1.0 C1D B:HEC105 3.0 14.1 1.0 C1B B:HEC105 3.0 13.9 1.0 C4B B:HEC105 3.0 13.9 1.0 C1C B:HEC105 3.0 14.6 1.0 C4A B:HEC105 3.0 13.7 1.0 C4C B:HEC105 3.0 14.3 1.0 C1A B:HEC105 3.0 13.3 1.0 CHB B:HEC105 3.3 13.8 1.0 CHA B:HEC105 3.4 12.5 1.0 CHC B:HEC105 3.4 14.1 1.0 CHD B:HEC105 3.4 13.8 1.0 ND1 B:HIS18 4.1 11.8 1.0 CG B:HIS18 4.1 11.3 1.0 C3D B:HEC105 4.2 12.7 1.0 C2D B:HEC105 4.2 13.8 1.0 C2B B:HEC105 4.2 13.9 1.0 C3B B:HEC105 4.2 13.4 1.0 C3C B:HEC105 4.2 15.8 1.0 C2C B:HEC105 4.2 15.2 1.0 C3A B:HEC105 4.2 13.0 1.0 C2A B:HEC105 4.2 13.2 1.0 O B:HOH284 4.4 11.2 1.0 OH B:TYR67 4.5 8.8 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Dimeric Cytochrome C From Horse Heart


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 Dimeric Cytochrome C From Horse Heart within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe105 b:8.9 occ:1.00 FE C:HEC105 0.0 8.9 1.0 NB C:HEC105 2.0 10.1 1.0 ND C:HEC105 2.0 11.4 1.0 NE2 C:HIS18 2.0 11.5 1.0 NA C:HEC105 2.0 12.6 1.0 NC C:HEC105 2.0 10.8 1.0 O C:HOH203 2.1 8.6 1.0 CD2 C:HIS18 2.9 10.5 1.0 C1D C:HEC105 3.0 10.5 1.0 C1B C:HEC105 3.0 10.1 1.0 C4B C:HEC105 3.0 10.7 1.0 C4D C:HEC105 3.0 10.9 1.0 CE1 C:HIS18 3.0 10.6 1.0 C4A C:HEC105 3.0 9.8 1.0 C4C C:HEC105 3.0 10.7 1.0 C1C C:HEC105 3.0 10.4 1.0 C1A C:HEC105 3.0 10.5 1.0 CHB C:HEC105 3.3 8.8 1.0 CHD C:HEC105 3.3 7.9 1.0 CHC C:HEC105 3.4 10.2 1.0 CHA C:HEC105 3.4 11.4 1.0 CG C:HIS18 4.1 10.1 1.0 ND1 C:HIS18 4.1 11.1 1.0 C3D C:HEC105 4.1 10.6 1.0 C2B C:HEC105 4.1 9.6 1.0 C2D C:HEC105 4.1 11.4 1.0 C3B C:HEC105 4.2 9.3 1.0 C3A C:HEC105 4.2 12.0 1.0 O C:HOH362 4.2 18.3 1.0 C2A C:HEC105 4.2 11.3 1.0 C3C C:HEC105 4.2 9.1 1.0 C2C C:HEC105 4.2 11.6 1.0 OH C:TYR67 4.4 9.5 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Dimeric Cytochrome C From Horse Heart


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 Dimeric Cytochrome C From Horse Heart within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe105 b:12.4 occ:1.00 FE D:HEC105 0.0 12.4 1.0 ND D:HEC105 1.9 10.2 1.0 NE2 D:HIS18 2.0 12.4 1.0 NB D:HEC105 2.0 10.9 1.0 NC D:HEC105 2.0 11.8 1.0 NA D:HEC105 2.0 10.9 1.0 O D:HOH204 2.1 14.5 1.0 CE1 D:HIS18 2.9 13.7 1.0 C4D D:HEC105 3.0 12.4 1.0 C1D D:HEC105 3.0 12.1 1.0 C1C D:HEC105 3.0 12.1 1.0 C1B D:HEC105 3.0 10.9 1.0 CD2 D:HIS18 3.0 13.2 1.0 C1A D:HEC105 3.0 10.4 1.0 C4B D:HEC105 3.0 11.1 1.0 C4A D:HEC105 3.0 10.0 1.0 C4C D:HEC105 3.0 12.4 1.0 CHD D:HEC105 3.3 10.8 1.0 CHA D:HEC105 3.4 10.1 1.0 CHC D:HEC105 3.4 10.0 1.0 CHB D:HEC105 3.4 8.4 1.0 ND1 D:HIS18 4.0 14.7 1.0 CG D:HIS18 4.1 14.9 1.0 C3D D:HEC105 4.1 12.6 1.0 C2D D:HEC105 4.1 12.3 1.0 C2C D:HEC105 4.2 12.9 1.0 C2A D:HEC105 4.2 10.6 1.0 C2B D:HEC105 4.2 10.3 1.0 C3B D:HEC105 4.2 10.2 1.0 O D:HOH312 4.2 12.5 1.0 C3A D:HEC105 4.2 10.4 1.0 C3C D:HEC105 4.2 12.8 1.0 OH D:TYR67 4.4 9.8 1.0 CE1 C:PHE82 4.8 14.5 1.0 CD1 C:PHE82 4.8 13.7 1.0

S.Hirota, Y.Hattori, S.Nagao, M.Taketa, H.Komori, H.Kamikubo, Z.Wang, I.Takahashi, S.Negi, Y.Sugiura, M.Kataoka, Y.Higuchi. Cytochrome C Polymerization By Successive Domain Swapping at the C-Terminal Helix Proc.Natl.Acad.Sci.Usa V. 107 12854 2010.
ISSN: ISSN 0027-8424
PubMed: 20615990
DOI: 10.1073/PNAS.1001839107