Iron in PDB 5b6q: Crystal Structure of Monomeric Cytochrome C5 From Shewanella Violacea

The structure of Crystal Structure of Monomeric Cytochrome C5 From Shewanella Violacea, PDB code: 5b6q was solved by M.Masanari, S.Fujii, K.Kawahara, H.Oki, H.Tsujino, T.Maruno, Y.Kobayashi, T.Ohkubo, M.Nishiyama, Y.Harada, S.Wakai, Y.Sambongi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.95 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	26.588, 50.075, 97.609, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 23.8

The binding sites of Iron atom in the Crystal Structure of Monomeric Cytochrome C5 From Shewanella Violacea (pdb code 5b6q). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Monomeric Cytochrome C5 From Shewanella Violacea, PDB code: 5b6q:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Monomeric Cytochrome C5 From Shewanella Violacea


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 Monomeric Cytochrome C5 From Shewanella Violacea within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:19.0 occ:1.00 FE A:HEC101 0.0 19.0 1.0 ND A:HEC101 1.9 20.4 1.0 NA A:HEC101 2.0 19.0 1.0 NC A:HEC101 2.1 20.1 1.0 NB A:HEC101 2.1 19.0 1.0 NE2 A:HIS15 2.2 19.1 1.0 SD A:MET53 2.3 25.5 1.0 C1D A:HEC101 2.9 21.2 1.0 C4D A:HEC101 2.9 22.1 1.0 C1A A:HEC101 3.0 19.9 1.0 C4C A:HEC101 3.0 21.1 1.0 C4B A:HEC101 3.1 17.0 1.0 CE1 A:HIS15 3.1 21.9 1.0 C4A A:HEC101 3.1 20.4 1.0 C1C A:HEC101 3.1 19.5 1.0 C1B A:HEC101 3.1 17.0 1.0 CD2 A:HIS15 3.2 17.9 1.0 CHD A:HEC101 3.3 22.5 1.0 CHA A:HEC101 3.4 22.4 1.0 CG A:MET53 3.4 28.7 1.0 CHC A:HEC101 3.5 18.8 1.0 CHB A:HEC101 3.5 19.9 1.0 CE A:MET53 3.7 25.1 1.0 CB A:MET53 4.1 29.5 1.0 C2D A:HEC101 4.1 23.8 1.0 C3D A:HEC101 4.2 22.8 1.0 C2A A:HEC101 4.2 22.6 1.0 ND1 A:HIS15 4.2 21.7 1.0 C3C A:HEC101 4.2 19.5 1.0 C3A A:HEC101 4.3 22.5 1.0 C2C A:HEC101 4.3 19.3 1.0 CG A:HIS15 4.3 18.3 1.0 C2B A:HEC101 4.3 17.2 1.0 C3B A:HEC101 4.4 15.3 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Monomeric Cytochrome C5 From Shewanella Violacea


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 Monomeric Cytochrome C5 From Shewanella Violacea within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:21.8 occ:1.00 FE B:HEC101 0.0 21.8 1.0 ND B:HEC101 1.9 22.5 1.0 NA B:HEC101 2.0 19.2 1.0 NC B:HEC101 2.1 22.2 1.0 NB B:HEC101 2.1 22.6 1.0 NE2 B:HIS15 2.2 23.0 1.0 N1 B:IMD102 2.2 23.4 1.0 C1D B:HEC101 2.9 22.3 1.0 C4D B:HEC101 2.9 24.5 1.0 C1A B:HEC101 3.0 22.5 1.0 C4C B:HEC101 3.0 22.8 1.0 C4B B:HEC101 3.1 21.6 1.0 C4A B:HEC101 3.1 22.0 1.0 C1C B:HEC101 3.1 23.7 1.0 C1B B:HEC101 3.1 23.5 1.0 C2 B:IMD102 3.1 27.7 1.0 CE1 B:HIS15 3.1 20.9 1.0 CD2 B:HIS15 3.2 19.8 1.0 C5 B:IMD102 3.2 27.1 1.0 CHD B:HEC101 3.3 24.0 1.0 CHA B:HEC101 3.4 21.9 1.0 CHC B:HEC101 3.5 21.8 1.0 CHB B:HEC101 3.5 22.2 1.0 C2D B:HEC101 4.1 25.1 1.0 C3D B:HEC101 4.1 25.2 1.0 C2A B:HEC101 4.2 23.3 1.0 C3C B:HEC101 4.2 22.7 1.0 C3A B:HEC101 4.3 24.2 1.0 ND1 B:HIS15 4.3 21.9 1.0 C2C B:HEC101 4.3 23.8 1.0 N3 B:IMD102 4.3 31.0 1.0 CG B:HIS15 4.3 21.7 1.0 C4 B:IMD102 4.3 31.1 1.0 C2B B:HEC101 4.3 24.3 1.0 C3B B:HEC101 4.4 21.0 1.0

M.Masanari, S.Fujii, K.Kawahara, H.Oki, H.Tsujino, T.Maruno, Y.Kobayashi, T.Ohkubo, S.Wakai, Y.Sambongi. Comparative Study on Stabilization Mechanism of Monomeric Cytochrome C5 From Deep-Sea Piezophilic Shewanella Violacea Biosci.Biotechnol.Biochem. 2016.
ISSN: ISSN 0916-8451
PubMed: 27648635
DOI: 10.1080/09168451.2016.1232155