Iron in PDB 4hil: 1.25A Resolution Structure of Rat Type B Cytochrome B5

The structure of 1.25A Resolution Structure of Rat Type B Cytochrome B5, PDB code: 4hil was solved by S.Lovell, K.P.Battaile, S.Parthasarathy, N.Sun, S.Terzyan, X.Zhang, M.Rivera, K.Kuczera, D.R.Benson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.17 / 1.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.609, 67.847, 70.342, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 15.2

The structure of 1.25A Resolution Structure of Rat Type B Cytochrome B5 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Iron atom in the 1.25A Resolution Structure of Rat Type B Cytochrome B5 (pdb code 4hil). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the 1.25A Resolution Structure of Rat Type B Cytochrome B5, PDB code: 4hil:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the 1.25A Resolution Structure of Rat 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 1.25A Resolution Structure of Rat Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:9.4 occ:0.50 FE A:HEM101 0.0 9.4 0.5 FE A:HEM101 0.1 9.1 0.5 NA A:HEM101 1.9 9.4 0.5 ND A:HEM101 2.0 9.4 0.5 NC A:HEM101 2.0 10.0 0.5 NA A:HEM101 2.0 9.8 0.5 NE2 A:HIS39 2.0 9.5 1.0 NB A:HEM101 2.0 9.4 0.5 NE2 A:HIS63 2.0 10.2 1.0 ND A:HEM101 2.1 8.8 0.5 NC A:HEM101 2.1 9.5 0.5 NB A:HEM101 2.1 9.1 0.5 C1A A:HEM101 2.9 8.9 0.5 C4A A:HEM101 3.0 9.7 0.5 C4D A:HEM101 3.0 9.1 0.5 CE1 A:HIS39 3.0 9.5 1.0 C1D A:HEM101 3.0 9.0 0.5 C1C A:HEM101 3.0 10.5 0.5 CD2 A:HIS39 3.0 8.8 1.0 CE1 A:HIS63 3.0 10.2 1.0 C4C A:HEM101 3.0 10.1 0.5 C4A A:HEM101 3.0 9.8 0.5 C1A A:HEM101 3.0 9.2 0.5 C4B A:HEM101 3.0 10.1 0.5 CD2 A:HIS63 3.0 9.9 1.0 C4C A:HEM101 3.0 10.2 0.5 C1D A:HEM101 3.1 9.0 0.5 C1B A:HEM101 3.1 9.7 0.5 C4D A:HEM101 3.1 8.6 0.5 C1B A:HEM101 3.1 9.4 0.5 C1C A:HEM101 3.1 10.3 0.5 C4B A:HEM101 3.2 9.9 0.5 CHA A:HEM101 3.3 8.8 0.5 CHD A:HEM101 3.4 9.5 0.5 CHB A:HEM101 3.4 9.5 0.5 CHC A:HEM101 3.4 10.1 0.5 CHD A:HEM101 3.4 9.8 0.5 CHA A:HEM101 3.4 8.3 0.5 CHB A:HEM101 3.4 8.9 0.5 CHC A:HEM101 3.5 9.8 0.5 ND1 A:HIS39 4.1 9.5 1.0 ND1 A:HIS63 4.1 9.7 1.0 C2A A:HEM101 4.1 9.1 0.5 C3A A:HEM101 4.1 9.7 0.5 CG A:HIS39 4.2 9.7 1.0 CG A:HIS63 4.2 10.5 1.0 C3D A:HEM101 4.2 9.6 0.5 C2C A:HEM101 4.2 11.1 0.5 C2D A:HEM101 4.2 8.5 0.5 C3A A:HEM101 4.2 10.6 0.5 C3C A:HEM101 4.2 11.6 0.5 C2A A:HEM101 4.2 10.9 0.5 C3B A:HEM101 4.3 10.2 0.5 C3C A:HEM101 4.3 11.3 0.5 C2B A:HEM101 4.3 9.9 0.5 C2D A:HEM101 4.3 9.4 0.5 C3D A:HEM101 4.3 9.8 0.5 C2B A:HEM101 4.3 11.1 0.5 C2C A:HEM101 4.3 10.8 0.5 C3B A:HEM101 4.4 11.3 0.5 N A:GLY41 4.8 10.2 1.0

Iron binding site 2 out of 4 in the 1.25A Resolution Structure of Rat 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 1.25A Resolution Structure of Rat Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe101 b:9.1 occ:0.50 FE A:HEM101 0.0 9.1 0.5 FE A:HEM101 0.1 9.4 0.5 NC A:HEM101 1.9 10.0 0.5 NB A:HEM101 2.0 9.4 0.5 NC A:HEM101 2.0 9.5 0.5 NE2 A:HIS63 2.0 10.2 1.0 NA A:HEM101 2.0 9.4 0.5 NB A:HEM101 2.0 9.1 0.5 NE2 A:HIS39 2.0 9.5 1.0 ND A:HEM101 2.0 9.4 0.5 NA A:HEM101 2.1 9.8 0.5 ND A:HEM101 2.1 8.8 0.5 C1C A:HEM101 2.9 10.5 0.5 C4B A:HEM101 2.9 10.1 0.5 CE1 A:HIS63 3.0 10.2 1.0 C4C A:HEM101 3.0 10.2 0.5 C4C A:HEM101 3.0 10.1 0.5 C4A A:HEM101 3.0 9.7 0.5 CE1 A:HIS39 3.0 9.5 1.0 C1B A:HEM101 3.0 9.4 0.5 C1D A:HEM101 3.0 9.0 0.5 CD2 A:HIS63 3.0 9.9 1.0 C1B A:HEM101 3.0 9.7 0.5 CD2 A:HIS39 3.0 8.8 1.0 C1C A:HEM101 3.0 10.3 0.5 C1A A:HEM101 3.0 8.9 0.5 C4A A:HEM101 3.1 9.8 0.5 C4B A:HEM101 3.1 9.9 0.5 C4D A:HEM101 3.1 9.1 0.5 C1D A:HEM101 3.1 9.0 0.5 C1A A:HEM101 3.1 9.2 0.5 C4D A:HEM101 3.2 8.6 0.5 CHC A:HEM101 3.3 10.1 0.5 CHD A:HEM101 3.4 9.5 0.5 CHB A:HEM101 3.4 9.5 0.5 CHB A:HEM101 3.4 8.9 0.5 CHD A:HEM101 3.4 9.8 0.5 CHC A:HEM101 3.4 9.8 0.5 CHA A:HEM101 3.4 8.8 0.5 CHA A:HEM101 3.5 8.3 0.5 ND1 A:HIS63 4.1 9.7 1.0 ND1 A:HIS39 4.1 9.5 1.0 C2C A:HEM101 4.1 11.1 0.5 CG A:HIS63 4.2 10.5 1.0 CG A:HIS39 4.2 9.7 1.0 C3B A:HEM101 4.2 10.2 0.5 C3C A:HEM101 4.2 11.6 0.5 C3A A:HEM101 4.2 9.7 0.5 C3C A:HEM101 4.2 11.3 0.5 C2B A:HEM101 4.2 9.9 0.5 C2A A:HEM101 4.2 9.1 0.5 C2C A:HEM101 4.2 10.8 0.5 C2B A:HEM101 4.3 11.1 0.5 C2D A:HEM101 4.3 8.5 0.5 C3B A:HEM101 4.3 11.3 0.5 C3A A:HEM101 4.3 10.6 0.5 C3D A:HEM101 4.3 9.6 0.5 C2A A:HEM101 4.3 10.9 0.5 C2D A:HEM101 4.4 9.4 0.5 C3D A:HEM101 4.4 9.8 0.5 N A:GLY41 4.9 10.2 1.0

Iron binding site 3 out of 4 in the 1.25A Resolution Structure of Rat 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 1.25A Resolution Structure of Rat Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:8.3 occ:0.50 FE B:HEM101 0.0 8.3 0.5 FE B:HEM101 0.2 7.5 0.5 ND B:HEM101 1.8 7.0 0.5 NE2 B:HIS39 2.0 8.3 1.0 NC B:HEM101 2.0 8.3 0.5 ND B:HEM101 2.0 8.5 0.5 NC B:HEM101 2.0 8.0 0.5 NA B:HEM101 2.0 8.7 0.5 NA B:HEM101 2.0 6.9 0.5 NB B:HEM101 2.1 8.1 0.5 NE2 B:HIS63 2.1 7.9 1.0 NB B:HEM101 2.2 8.3 0.5 C1D B:HEM101 2.8 7.3 0.5 C4D B:HEM101 2.9 6.5 0.5 CE1 B:HIS39 2.9 8.1 1.0 C4C B:HEM101 2.9 8.5 0.5 CD2 B:HIS39 3.0 7.7 1.0 C1A B:HEM101 3.0 6.7 0.5 C1D B:HEM101 3.0 8.8 0.5 C1A B:HEM101 3.0 8.3 0.5 C4D B:HEM101 3.0 8.5 0.5 C4C B:HEM101 3.0 9.0 0.5 C1C B:HEM101 3.0 8.2 0.5 C1C B:HEM101 3.0 8.5 0.5 CE1 B:HIS63 3.1 8.8 1.0 C4B B:HEM101 3.1 8.1 0.5 C4A B:HEM101 3.1 8.0 0.5 C1B B:HEM101 3.1 7.8 0.5 CD2 B:HIS63 3.1 8.0 1.0 C4A B:HEM101 3.2 7.1 0.5 C4B B:HEM101 3.2 8.3 0.5 CHD B:HEM101 3.2 7.9 0.5 C1B B:HEM101 3.2 8.2 0.5 CHA B:HEM101 3.3 6.6 0.5 CHA B:HEM101 3.4 8.3 0.5 CHD B:HEM101 3.4 9.2 0.5 CHC B:HEM101 3.4 8.5 0.5 CHB B:HEM101 3.5 7.7 0.5 CHC B:HEM101 3.5 8.6 0.5 CHB B:HEM101 3.6 7.4 0.5 ND1 B:HIS39 4.0 8.2 1.0 C2D B:HEM101 4.1 6.9 0.5 C3D B:HEM101 4.1 7.1 0.5 CG B:HIS39 4.1 7.7 1.0 C3C B:HEM101 4.2 9.3 0.5 ND1 B:HIS63 4.2 8.6 1.0 C2C B:HEM101 4.2 9.2 0.5 C2C B:HEM101 4.2 9.2 0.5 C2D B:HEM101 4.2 8.8 0.5 C3D B:HEM101 4.2 9.2 0.5 C2A B:HEM101 4.2 9.1 0.5 C3C B:HEM101 4.3 10.0 0.5 C2A B:HEM101 4.3 7.2 0.5 CG B:HIS63 4.3 8.8 1.0 C3A B:HEM101 4.3 8.8 0.5 C3B B:HEM101 4.3 8.5 0.5 C3A B:HEM101 4.3 7.6 0.5 C2B B:HEM101 4.4 8.2 0.5 C3B B:HEM101 4.4 8.7 0.5 C2B B:HEM101 4.5 8.3 0.5 N B:GLY41 4.9 8.7 1.0 CG1 B:VAL61 5.0 11.9 1.0

Iron binding site 4 out of 4 in the 1.25A Resolution Structure of Rat 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 1.25A Resolution Structure of Rat Type B Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe101 b:7.5 occ:0.50 FE B:HEM101 0.0 7.5 0.5 FE B:HEM101 0.2 8.3 0.5 NC B:HEM101 1.8 8.0 0.5 NC B:HEM101 2.0 8.3 0.5 NE2 B:HIS63 2.0 7.9 1.0 ND B:HEM101 2.0 8.5 0.5 ND B:HEM101 2.0 7.0 0.5 NB B:HEM101 2.0 8.3 0.5 NA B:HEM101 2.0 6.9 0.5 NE2 B:HIS39 2.1 8.3 1.0 NB B:HEM101 2.1 8.1 0.5 NA B:HEM101 2.2 8.7 0.5 C4C B:HEM101 2.9 9.0 0.5 C1C B:HEM101 2.9 8.2 0.5 C1D B:HEM101 2.9 8.8 0.5 CE1 B:HIS63 3.0 8.8 1.0 C1C B:HEM101 3.0 8.5 0.5 C4C B:HEM101 3.0 8.5 0.5 CD2 B:HIS63 3.0 8.0 1.0 C1D B:HEM101 3.0 7.3 0.5 C4B B:HEM101 3.0 8.3 0.5 C4D B:HEM101 3.0 6.5 0.5 C4B B:HEM101 3.0 8.1 0.5 C1A B:HEM101 3.0 6.7 0.5 C4D B:HEM101 3.1 8.5 0.5 CD2 B:HIS39 3.1 7.7 1.0 CE1 B:HIS39 3.1 8.1 1.0 C4A B:HEM101 3.1 7.1 0.5 C1B B:HEM101 3.1 8.2 0.5 C1A B:HEM101 3.2 8.3 0.5 C1B B:HEM101 3.2 7.8 0.5 CHD B:HEM101 3.2 9.2 0.5 C4A B:HEM101 3.3 8.0 0.5 CHC B:HEM101 3.3 8.5 0.5 CHD B:HEM101 3.4 7.9 0.5 CHC B:HEM101 3.4 8.6 0.5 CHA B:HEM101 3.4 6.6 0.5 CHB B:HEM101 3.5 7.4 0.5 CHA B:HEM101 3.5 8.3 0.5 CHB B:HEM101 3.6 7.7 0.5 C2C B:HEM101 4.1 9.2 0.5 ND1 B:HIS63 4.1 8.6 1.0 C3C B:HEM101 4.1 10.0 0.5 CG B:HIS63 4.1 8.8 1.0 C3C B:HEM101 4.2 9.3 0.5 C2C B:HEM101 4.2 9.2 0.5 ND1 B:HIS39 4.2 8.2 1.0 C2D B:HEM101 4.2 8.8 0.5 CG B:HIS39 4.2 7.7 1.0 C3B B:HEM101 4.3 8.7 0.5 C2D B:HEM101 4.3 6.9 0.5 C3D B:HEM101 4.3 9.2 0.5 C2A B:HEM101 4.3 7.2 0.5 C3D B:HEM101 4.3 7.1 0.5 C3A B:HEM101 4.3 7.6 0.5 C2B B:HEM101 4.3 8.3 0.5 C3B B:HEM101 4.3 8.5 0.5 C2B B:HEM101 4.4 8.2 0.5 C2A B:HEM101 4.4 9.1 0.5 C3A B:HEM101 4.5 8.8 0.5 CG1 B:VAL61 5.0 11.9 1.0

S.Parthasarathy, N.Sun, S.Lovell, K.P.Battaile, S.Terzyan, X.Zhang, M.Rivera, K.Kuczera, D.R.Benson. 1.25A Resolution Structure of Rat Type B Cytochrome B5 To Be Published.