Iron in PDB 3ner: Structure of Human Type B Cytochrome B5

The structure of Structure of Human Type B Cytochrome B5, PDB code: 3ner was solved by S.Terzyan, C.Zhang, M.Rivera, D.B.Benson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.24 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.316, 40.034, 58.744, 90.00, 98.61, 90.00
R / Rfree (%)	17.7 / 21.5

The structure of Structure of Human Type B Cytochrome B5 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Iron atom in the Structure of Human Type B Cytochrome B5 (pdb code 3ner). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Human Type B Cytochrome B5, PDB code: 3ner:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Human Type B Cytochrome B5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:13.0 occ:0.50 FE A:HEM201 0.0 13.0 0.5 FE A:HEM201 0.6 12.1 0.5 NC A:HEM201 1.5 13.6 0.5 NE2 A:HIS63 1.9 14.5 1.0 NB A:HEM201 1.9 12.2 0.5 NC A:HEM201 2.0 13.2 0.5 ND A:HEM201 2.0 12.9 0.5 NA A:HEM201 2.0 13.4 0.5 NB A:HEM201 2.0 13.0 0.5 ND A:HEM201 2.0 13.7 0.5 NE2 A:HIS39 2.2 15.2 1.0 NA A:HEM201 2.5 14.5 0.5 C4C A:HEM201 2.6 15.1 0.5 C1C A:HEM201 2.6 13.6 0.5 CD2 A:HIS63 2.9 15.8 1.0 CE1 A:HIS63 2.9 14.5 1.0 C1D A:HEM201 2.9 14.8 0.5 C4B A:HEM201 2.9 13.5 0.5 C1B A:HEM201 3.0 14.6 0.5 C1C A:HEM201 3.0 13.5 0.5 C4B A:HEM201 3.0 14.9 0.5 C4A A:HEM201 3.0 14.3 0.5 C1D A:HEM201 3.0 16.0 0.5 C4C A:HEM201 3.0 14.1 0.5 C1A A:HEM201 3.1 16.6 0.5 C4D A:HEM201 3.1 16.5 0.5 CHD A:HEM201 3.1 15.4 0.5 CD2 A:HIS39 3.1 15.8 1.0 CHC A:HEM201 3.1 13.4 0.5 CE1 A:HIS39 3.2 17.2 1.0 C1B A:HEM201 3.2 13.1 0.5 C4D A:HEM201 3.3 16.6 0.5 CHB A:HEM201 3.4 14.4 0.5 CHC A:HEM201 3.4 14.2 0.5 CHD A:HEM201 3.4 12.4 0.5 CHA A:HEM201 3.5 15.5 0.5 C4A A:HEM201 3.5 14.1 0.5 C1A A:HEM201 3.5 15.5 0.5 CHB A:HEM201 3.8 14.7 0.5 CHA A:HEM201 3.8 15.4 0.5 C2C A:HEM201 3.8 14.5 0.5 C3C A:HEM201 3.8 16.2 0.5 ND1 A:HIS63 4.0 15.7 1.0 CG A:HIS63 4.0 14.9 1.0 C2B A:HEM201 4.2 16.7 0.5 C2C A:HEM201 4.2 12.9 0.5 C2D A:HEM201 4.2 15.1 0.5 C3A A:HEM201 4.2 15.6 0.5 C2A A:HEM201 4.2 16.3 0.5 C3B A:HEM201 4.3 14.0 0.5 C3C A:HEM201 4.3 14.4 0.5 CG A:HIS39 4.3 15.8 1.0 C3B A:HEM201 4.3 15.1 0.5 C2D A:HEM201 4.3 16.1 0.5 ND1 A:HIS39 4.3 17.4 1.0 C2B A:HEM201 4.3 12.9 0.5 C3D A:HEM201 4.3 16.8 0.5 C3D A:HEM201 4.4 17.5 0.5 C3A A:HEM201 4.7 16.8 0.5 C2A A:HEM201 4.7 16.5 0.5 CE1 A:PHE58 4.8 15.3 1.0 CD1 A:PHE58 5.0 13.9 1.0

Iron binding site 2 out of 4 in the Structure of Human Type B Cytochrome B5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:12.1 occ:0.50 FE A:HEM201 0.0 12.1 0.5 FE A:HEM201 0.6 13.0 0.5 ND A:HEM201 1.5 12.9 0.5 NE2 A:HIS39 1.9 15.2 1.0 NA A:HEM201 1.9 14.5 0.5 NB A:HEM201 2.0 13.0 0.5 ND A:HEM201 2.0 13.7 0.5 NC A:HEM201 2.0 13.6 0.5 NA A:HEM201 2.1 13.4 0.5 NC A:HEM201 2.1 13.2 0.5 NE2 A:HIS63 2.2 14.5 1.0 NB A:HEM201 2.5 12.2 0.5 C1D A:HEM201 2.6 16.0 0.5 C4D A:HEM201 2.6 16.5 0.5 CE1 A:HIS39 2.8 17.2 1.0 C4C A:HEM201 2.9 14.1 0.5 C1A A:HEM201 2.9 16.6 0.5 CD2 A:HIS39 3.0 15.8 1.0 C1B A:HEM201 3.0 13.1 0.5 C4A A:HEM201 3.0 14.1 0.5 C1A A:HEM201 3.0 15.5 0.5 C4D A:HEM201 3.0 16.6 0.5 C1D A:HEM201 3.1 14.8 0.5 C4B A:HEM201 3.1 13.5 0.5 CHD A:HEM201 3.1 12.4 0.5 C4C A:HEM201 3.1 15.1 0.5 C1C A:HEM201 3.1 13.6 0.5 CHA A:HEM201 3.1 15.5 0.5 CE1 A:HIS63 3.1 14.5 1.0 CD2 A:HIS63 3.2 15.8 1.0 C4A A:HEM201 3.2 14.3 0.5 C1C A:HEM201 3.3 13.5 0.5 CHB A:HEM201 3.4 14.7 0.5 CHA A:HEM201 3.4 15.4 0.5 CHD A:HEM201 3.4 15.4 0.5 CHC A:HEM201 3.5 13.4 0.5 C1B A:HEM201 3.5 14.6 0.5 C4B A:HEM201 3.5 14.9 0.5 CHB A:HEM201 3.8 14.4 0.5 C2D A:HEM201 3.8 16.1 0.5 CHC A:HEM201 3.8 14.2 0.5 C3D A:HEM201 3.8 16.8 0.5 ND1 A:HIS39 4.0 17.4 1.0 CG A:HIS39 4.1 15.8 1.0 C2A A:HEM201 4.2 16.3 0.5 C3A A:HEM201 4.2 16.8 0.5 C2A A:HEM201 4.2 16.5 0.5 C2B A:HEM201 4.2 12.9 0.5 C3C A:HEM201 4.2 14.4 0.5 ND1 A:HIS63 4.3 15.7 1.0 C3D A:HEM201 4.3 17.5 0.5 C2D A:HEM201 4.3 15.1 0.5 C3B A:HEM201 4.3 14.0 0.5 C2C A:HEM201 4.3 14.5 0.5 C3A A:HEM201 4.3 15.6 0.5 CG A:HIS63 4.3 14.9 1.0 C3C A:HEM201 4.3 16.2 0.5 C2C A:HEM201 4.4 12.9 0.5 N A:GLY41 4.6 19.5 1.0 C2B A:HEM201 4.7 16.7 0.5 C3B A:HEM201 4.8 15.1 0.5 CA A:GLY41 4.9 19.8 1.0 CG1 A:VAL61 4.9 22.1 1.0

Iron binding site 3 out of 4 in the Structure of Human Type B Cytochrome B5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.9 occ:0.50 FE B:HEM201 0.0 9.9 0.5 FE B:HEM201 0.4 13.3 0.5 NC B:HEM201 1.9 12.8 0.5 NE2 B:HIS63 1.9 11.8 1.0 NB B:HEM201 1.9 15.3 0.5 NA B:HEM201 1.9 11.7 0.5 NB B:HEM201 2.0 10.6 0.5 ND B:HEM201 2.0 13.9 0.5 NC B:HEM201 2.0 12.9 0.5 ND B:HEM201 2.1 14.8 0.5 NA B:HEM201 2.2 14.7 0.5 NE2 B:HIS39 2.2 12.6 1.0 CE1 B:HIS63 2.8 13.7 1.0 C1C B:HEM201 2.9 13.1 0.5 C4B B:HEM201 2.9 16.3 0.5 CD2 B:HIS63 2.9 15.0 1.0 C4C B:HEM201 2.9 14.9 0.5 C1B B:HEM201 3.0 15.3 0.5 C4A B:HEM201 3.0 11.2 0.5 C1B B:HEM201 3.0 12.2 0.5 C1A B:HEM201 3.0 13.1 0.5 C1D B:HEM201 3.0 14.8 0.5 C1D B:HEM201 3.1 15.8 0.5 C4B B:HEM201 3.1 12.4 0.5 C4C B:HEM201 3.1 14.2 0.5 C4D B:HEM201 3.1 15.8 0.5 C1C B:HEM201 3.1 13.5 0.5 CE1 B:HIS39 3.1 13.6 1.0 C4A B:HEM201 3.1 14.8 0.5 CD2 B:HIS39 3.2 12.3 1.0 C4D B:HEM201 3.2 16.9 0.5 CHC B:HEM201 3.3 14.8 0.5 C1A B:HEM201 3.3 16.2 0.5 CHB B:HEM201 3.4 12.7 0.5 CHD B:HEM201 3.4 15.6 0.5 CHB B:HEM201 3.4 15.5 0.5 CHD B:HEM201 3.4 14.6 0.5 CHA B:HEM201 3.5 14.3 0.5 CHC B:HEM201 3.5 14.9 0.5 CHA B:HEM201 3.7 16.9 0.5 ND1 B:HIS63 4.0 15.4 1.0 CG B:HIS63 4.0 15.3 1.0 C2C B:HEM201 4.1 13.2 0.5 C2B B:HEM201 4.1 15.0 0.5 C3C B:HEM201 4.2 15.2 0.5 C3B B:HEM201 4.2 15.8 0.5 C3A B:HEM201 4.2 11.4 0.5 C2A B:HEM201 4.2 11.4 0.5 C2B B:HEM201 4.2 12.6 0.5 ND1 B:HIS39 4.3 11.2 1.0 C3B B:HEM201 4.3 14.6 0.5 C2D B:HEM201 4.3 18.4 0.5 C2C B:HEM201 4.3 14.7 0.5 C3C B:HEM201 4.3 14.3 0.5 C3D B:HEM201 4.3 17.8 0.5 CG B:HIS39 4.3 12.1 1.0 C2D B:HEM201 4.4 15.2 0.5 C3A B:HEM201 4.4 17.8 0.5 C3D B:HEM201 4.4 17.9 0.5 C2A B:HEM201 4.5 18.0 0.5 CE1 B:PHE58 4.8 16.9 1.0 CD1 B:PHE58 5.0 16.8 1.0 CG1 B:VAL61 5.0 22.4 1.0

Iron binding site 4 out of 4 in the Structure of Human Type B Cytochrome B5


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:13.3 occ:0.50 FE B:HEM201 0.0 13.3 0.5 FE B:HEM201 0.4 9.9 0.5 ND B:HEM201 1.8 13.9 0.5 NE2 B:HIS39 1.8 12.6 1.0 NA B:HEM201 1.9 11.7 0.5 NA B:HEM201 2.0 14.7 0.5 ND B:HEM201 2.0 14.8 0.5 NB B:HEM201 2.0 15.3 0.5 NC B:HEM201 2.0 12.8 0.5 NC B:HEM201 2.2 12.9 0.5 NB B:HEM201 2.2 10.6 0.5 NE2 B:HIS63 2.2 11.8 1.0 CE1 B:HIS39 2.8 13.6 1.0 C4D B:HEM201 2.9 15.8 0.5 C1A B:HEM201 2.9 13.1 0.5 CD2 B:HIS39 2.9 12.3 1.0 C1D B:HEM201 2.9 14.8 0.5 C4A B:HEM201 3.0 11.2 0.5 C4A B:HEM201 3.0 14.8 0.5 C1B B:HEM201 3.0 15.3 0.5 C1D B:HEM201 3.0 15.8 0.5 C4D B:HEM201 3.1 16.9 0.5 C1A B:HEM201 3.1 16.2 0.5 C4C B:HEM201 3.1 14.9 0.5 C4B B:HEM201 3.1 16.3 0.5 C1C B:HEM201 3.1 13.1 0.5 C4C B:HEM201 3.1 14.2 0.5 C1B B:HEM201 3.1 12.2 0.5 CE1 B:HIS63 3.2 13.7 1.0 CD2 B:HIS63 3.2 15.0 1.0 CHA B:HEM201 3.3 14.3 0.5 C4B B:HEM201 3.3 12.4 0.5 C1C B:HEM201 3.3 13.5 0.5 CHB B:HEM201 3.3 15.5 0.5 CHD B:HEM201 3.4 14.6 0.5 CHD B:HEM201 3.4 15.6 0.5 CHB B:HEM201 3.4 12.7 0.5 CHC B:HEM201 3.5 14.8 0.5 CHA B:HEM201 3.5 16.9 0.5 CHC B:HEM201 3.7 14.9 0.5 ND1 B:HIS39 3.9 11.2 1.0 CG B:HIS39 4.0 12.1 1.0 C2A B:HEM201 4.1 11.4 0.5 C3D B:HEM201 4.1 17.8 0.5 C2D B:HEM201 4.1 18.4 0.5 C3A B:HEM201 4.1 11.4 0.5 C3A B:HEM201 4.2 17.8 0.5 C2B B:HEM201 4.2 15.0 0.5 C2A B:HEM201 4.2 18.0 0.5 C2D B:HEM201 4.3 15.2 0.5 C2C B:HEM201 4.3 13.2 0.5 C3C B:HEM201 4.3 15.2 0.5 C3D B:HEM201 4.3 17.9 0.5 C3B B:HEM201 4.3 15.8 0.5 ND1 B:HIS63 4.3 15.4 1.0 CG B:HIS63 4.4 15.3 1.0 C2B B:HEM201 4.4 12.6 0.5 C3C B:HEM201 4.4 14.3 0.5 C2C B:HEM201 4.5 14.7 0.5 C3B B:HEM201 4.5 14.6 0.5 N B:GLY41 4.8 18.6 1.0

S.Parthasarathy, A.Altuve, S.Terzyan, X.Zhang, K.Kuczera, M.Rivera, D.R.Benson. Accommodating A Non-Conservative Internal Mutation By Water-Mediated Hydrogen-Bonding Between Beta-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome B5 Biochemistry V. 50 5544 2011.
ISSN: ISSN 0006-2960
PubMed: 21574570
DOI: 10.1021/BI2004729