Iron in PDB 6k7c: Dimeric Shewanella Violacea Cytochrome C5

The structure of Dimeric Shewanella Violacea Cytochrome C5, PDB code: 6k7c was solved by H.Yang, M.Yamanaka, S.Nagao, K.Yasuhara, N.Shibata, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.91 / 1.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	34.772, 52.542, 80.070, 90.00, 90.00, 90.00
R / Rfree (%)	13.8 / 15.7

The binding sites of Iron atom in the Dimeric Shewanella Violacea Cytochrome C5 (pdb code 6k7c). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Dimeric Shewanella Violacea Cytochrome C5, PDB code: 6k7c:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Dimeric Shewanella Violacea Cytochrome C5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dimeric Shewanella Violacea Cytochrome C5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:9.0 occ:1.00 FE A:HEC101 0.0 9.0 1.0 NC A:HEC101 2.0 8.6 1.0 NA A:HEC101 2.0 8.7 1.0 NE2 A:HIS15 2.0 8.2 1.0 ND A:HEC101 2.1 8.4 1.0 NB A:HEC101 2.1 8.5 1.0 SD C:MET53 2.4 8.0 1.0 CE1 A:HIS15 3.0 7.8 1.0 C1C A:HEC101 3.0 9.3 1.0 C4A A:HEC101 3.0 8.4 1.0 C4C A:HEC101 3.0 8.4 1.0 C1A A:HEC101 3.0 8.6 1.0 C1D A:HEC101 3.1 8.3 1.0 C1B A:HEC101 3.1 8.0 1.0 C4D A:HEC101 3.1 8.4 1.0 C4B A:HEC101 3.1 8.5 1.0 CD2 A:HIS15 3.1 8.3 1.0 CHA A:HEC101 3.4 8.8 1.0 CHC A:HEC101 3.4 8.9 1.0 CHD A:HEC101 3.5 8.2 1.0 CHB A:HEC101 3.5 7.9 1.0 CE C:MET53 3.5 8.3 1.0 CG C:MET53 3.5 8.4 1.0 CB C:MET53 4.0 7.8 1.0 ND1 A:HIS15 4.1 8.0 1.0 CG A:HIS15 4.2 8.2 1.0 C2C A:HEC101 4.3 8.9 1.0 C3C A:HEC101 4.3 8.7 1.0 C2A A:HEC101 4.3 8.5 1.0 C3A A:HEC101 4.3 8.5 1.0 C3D A:HEC101 4.3 8.9 1.0 C3B A:HEC101 4.3 8.6 1.0 C2D A:HEC101 4.3 8.5 1.0 C2B A:HEC101 4.4 8.0 1.0

Iron binding site 2 out of 2 in the Dimeric Shewanella Violacea Cytochrome C5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dimeric Shewanella Violacea Cytochrome C5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe101 b:10.2 occ:1.00 FE C:HEC101 0.0 10.2 1.0 NC C:HEC101 2.0 9.3 1.0 NA C:HEC101 2.0 9.5 1.0 NE2 C:HIS15 2.0 8.7 1.0 NB C:HEC101 2.0 9.0 1.0 ND C:HEC101 2.1 9.3 1.0 SD A:MET53 2.3 9.5 1.0 CE1 C:HIS15 3.0 8.6 1.0 C1C C:HEC101 3.0 8.9 1.0 C1A C:HEC101 3.0 10.1 1.0 C4A C:HEC101 3.0 10.0 1.0 C4C C:HEC101 3.0 9.3 1.0 C1B C:HEC101 3.0 9.3 1.0 C4B C:HEC101 3.1 8.5 1.0 C4D C:HEC101 3.1 9.3 1.0 C1D C:HEC101 3.1 9.2 1.0 CD2 C:HIS15 3.1 9.0 1.0 CHC C:HEC101 3.4 8.8 1.0 CHB C:HEC101 3.4 9.7 1.0 CHA C:HEC101 3.4 9.9 1.0 CHD C:HEC101 3.4 9.1 1.0 CE A:MET53 3.5 9.9 1.0 CG A:MET53 3.5 9.6 1.0 CB A:MET53 4.0 10.1 1.0 ND1 C:HIS15 4.1 8.4 1.0 CG C:HIS15 4.2 8.4 1.0 C2C C:HEC101 4.3 9.2 1.0 C3C C:HEC101 4.3 9.1 1.0 C2A C:HEC101 4.3 10.7 1.0 C3A C:HEC101 4.3 10.6 1.0 C3B C:HEC101 4.3 8.6 1.0 C3D C:HEC101 4.3 10.1 1.0 C2B C:HEC101 4.3 8.8 1.0 C2D C:HEC101 4.3 9.9 1.0

H.Yang, M.Yamanaka, S.Nagao, K.Yasuhara, N.Shibata, Y.Higuchi, S.Hirota. Protein Surface Charge Effect on 3D Domain Swapping in Cells For C-Type Cytochromes. Biochim Biophys Acta V.1867 40265 2019PROTEINS Proteom.
ISSN: ISSN 1878-1454
PubMed: 31437585
DOI: 10.1016/J.BBAPAP.2019.140265