Iron in PDB 2cdv: Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution

The structure of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution, PDB code: 2cdv was solved by Y.Higuchi, M.Kusunoki, Y.Matsuura, N.Yasuoka, M.Kakudo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	N/A / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.900, 68.100, 34.900, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / n/a

The binding sites of Iron atom in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution (pdb code 2cdv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution, PDB code: 2cdv:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe108 b:6.0 occ:1.00 FE A:HEM108 0.0 6.0 1.0 NE2 A:HIS70 1.9 3.1 1.0 NE2 A:HIS106 1.9 9.0 1.0 NC A:HEM108 2.0 5.6 1.0 NB A:HEM108 2.0 6.5 1.0 ND A:HEM108 2.0 5.6 1.0 NA A:HEM108 2.0 6.5 1.0 CE1 A:HIS106 2.9 8.8 1.0 CE1 A:HIS70 2.9 3.4 1.0 CD2 A:HIS70 3.0 2.4 1.0 C4C A:HEM108 3.0 5.2 1.0 C1C A:HEM108 3.0 6.0 1.0 C4B A:HEM108 3.0 6.6 1.0 C1B A:HEM108 3.0 6.7 1.0 C1D A:HEM108 3.0 5.1 1.0 C4D A:HEM108 3.1 6.1 1.0 CD2 A:HIS106 3.1 8.9 1.0 C4A A:HEM108 3.1 6.7 1.0 C1A A:HEM108 3.1 6.8 1.0 CHC A:HEM108 3.4 7.0 1.0 CHD A:HEM108 3.4 5.0 1.0 CHA A:HEM108 3.4 6.2 1.0 CHB A:HEM108 3.4 6.7 1.0 ND1 A:HIS70 4.0 4.4 1.0 ND1 A:HIS106 4.1 9.1 1.0 CG A:HIS70 4.1 4.1 1.0 CG A:HIS106 4.2 8.7 1.0 C2C A:HEM108 4.2 5.7 1.0 C3B A:HEM108 4.2 6.6 1.0 C3C A:HEM108 4.2 6.0 1.0 C2B A:HEM108 4.2 6.3 1.0 C3D A:HEM108 4.3 5.6 1.0 C2D A:HEM108 4.3 5.0 1.0 C2A A:HEM108 4.3 7.2 1.0 C3A A:HEM108 4.3 7.2 1.0 CE2 A:TYR66 5.0 9.8 1.0

Iron binding site 2 out of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe109 b:6.7 occ:1.00 FE A:HEM109 0.0 6.7 1.0 ND A:HEM109 2.0 7.2 1.0 NB A:HEM109 2.0 5.7 1.0 NC A:HEM109 2.0 5.5 1.0 NA A:HEM109 2.0 5.6 1.0 NE2 A:HIS52 2.1 6.5 1.0 NE2 A:HIS35 2.1 3.9 1.0 CE1 A:HIS35 3.0 3.9 1.0 C1C A:HEM109 3.0 5.2 1.0 C4D A:HEM109 3.0 8.2 1.0 CE1 A:HIS52 3.0 7.0 1.0 C4B A:HEM109 3.0 5.0 1.0 C1D A:HEM109 3.0 7.5 1.0 C4C A:HEM109 3.0 5.3 1.0 C1B A:HEM109 3.0 5.7 1.0 C1A A:HEM109 3.1 5.9 1.0 CD2 A:HIS52 3.1 6.3 1.0 C4A A:HEM109 3.1 5.2 1.0 CD2 A:HIS35 3.1 4.2 1.0 CHC A:HEM109 3.3 5.0 1.0 CHD A:HEM109 3.4 6.4 1.0 CHA A:HEM109 3.4 6.9 1.0 CHB A:HEM109 3.4 4.9 1.0 ND1 A:HIS35 4.1 4.2 1.0 ND1 A:HIS52 4.1 6.0 1.0 CG A:HIS52 4.2 6.3 1.0 CG A:HIS35 4.2 4.0 1.0 C2D A:HEM109 4.2 7.9 1.0 C3D A:HEM109 4.2 8.4 1.0 C3B A:HEM109 4.2 4.9 1.0 C2B A:HEM109 4.2 5.2 1.0 C2C A:HEM109 4.2 5.0 1.0 C3C A:HEM109 4.3 5.2 1.0 C2A A:HEM109 4.3 5.8 1.0 C3A A:HEM109 4.3 4.5 1.0

Iron binding site 3 out of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe110 b:8.4 occ:1.00 FE A:HEM110 0.0 8.4 1.0 NE2 A:HIS34 1.9 6.1 1.0 ND A:HEM110 2.0 7.5 1.0 NC A:HEM110 2.0 7.4 1.0 NA A:HEM110 2.0 9.6 1.0 NB A:HEM110 2.0 9.4 1.0 NE2 A:HIS22 2.0 7.0 1.0 CE1 A:HIS34 2.9 6.6 1.0 CE1 A:HIS22 2.9 8.0 1.0 CD2 A:HIS34 2.9 5.8 1.0 C1D A:HEM110 3.0 7.3 1.0 C4D A:HEM110 3.0 8.1 1.0 C1C A:HEM110 3.0 6.9 1.0 C1A A:HEM110 3.0 10.9 1.0 C4B A:HEM110 3.0 9.4 1.0 C4A A:HEM110 3.0 11.5 1.0 C4C A:HEM110 3.1 6.8 1.0 C1B A:HEM110 3.1 9.8 1.0 CD2 A:HIS22 3.1 6.8 1.0 CHC A:HEM110 3.4 8.0 1.0 CHD A:HEM110 3.4 6.6 1.0 CHA A:HEM110 3.4 10.0 1.0 CHB A:HEM110 3.4 10.5 1.0 ND1 A:HIS34 4.0 5.2 1.0 CG A:HIS34 4.1 6.1 1.0 ND1 A:HIS22 4.1 7.3 1.0 CG A:HIS22 4.2 7.3 1.0 C2D A:HEM110 4.2 8.2 1.0 C3D A:HEM110 4.2 8.3 1.0 C2C A:HEM110 4.2 6.7 1.0 C3C A:HEM110 4.2 5.9 1.0 C2A A:HEM110 4.3 12.2 1.0 C3B A:HEM110 4.3 9.6 1.0 C2B A:HEM110 4.3 9.5 1.0 C3A A:HEM110 4.3 11.6 1.0 CD A:PRO5 4.6 30.4 1.0 CE2 A:PHE20 4.7 3.9 1.0

Iron binding site 4 out of 4 in the Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Refined Structure of Cytochrome C3 at 1.8 Angstroms Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe111 b:7.2 occ:1.00 FE A:HEM111 0.0 7.2 1.0 NE2 A:HIS83 1.9 7.4 1.0 NC A:HEM111 2.0 6.6 1.0 NA A:HEM111 2.0 7.4 1.0 NB A:HEM111 2.0 7.5 1.0 ND A:HEM111 2.0 7.5 1.0 NE2 A:HIS25 2.1 9.8 1.0 CE1 A:HIS83 2.8 7.8 1.0 CD2 A:HIS25 2.9 9.2 1.0 C1B A:HEM111 3.0 7.2 1.0 C1D A:HEM111 3.0 7.1 1.0 C4D A:HEM111 3.0 7.7 1.0 C4C A:HEM111 3.0 7.3 1.0 C1A A:HEM111 3.0 7.0 1.0 C4A A:HEM111 3.0 6.7 1.0 C4B A:HEM111 3.0 7.3 1.0 C1C A:HEM111 3.0 7.5 1.0 CD2 A:HIS83 3.1 6.7 1.0 CE1 A:HIS25 3.3 9.8 1.0 CHB A:HEM111 3.4 7.3 1.0 CHA A:HEM111 3.4 7.2 1.0 CHC A:HEM111 3.4 7.1 1.0 CHD A:HEM111 3.4 6.6 1.0 ND1 A:HIS83 4.0 6.1 1.0 CG A:HIS83 4.1 6.8 1.0 CG A:HIS25 4.1 9.4 1.0 C3D A:HEM111 4.3 8.3 1.0 C3C A:HEM111 4.3 7.2 1.0 C2A A:HEM111 4.3 7.3 1.0 C3A A:HEM111 4.3 7.4 1.0 C2D A:HEM111 4.3 7.5 1.0 C2B A:HEM111 4.3 6.5 1.0 ND1 A:HIS25 4.3 9.5 1.0 C2C A:HEM111 4.3 7.5 1.0 C3B A:HEM111 4.3 7.5 1.0 CE1 A:PHE20 5.0 4.8 1.0

Y.Higuchi, M.Kusunoki, Y.Matsuura, N.Yasuoka, M.Kakudo. Refined Structure of Cytochrome C3 at 1.8 A Resolution J.Mol.Biol. V. 172 109 1984.
ISSN: ISSN 0022-2836
PubMed: 6319712
DOI: 10.1016/0022-2836(84)90417-0