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

Protein crystallography data

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

Other elements in 4hil:

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

Sodium (Na) 1 atom

Iron Binding Sites:

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 4hil

Go back to Iron Binding Sites List in 4hil
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 4hil

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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 4hil

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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 4hil

Go back to Iron Binding Sites List in 4hil
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

Reference:

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.
Page generated: Sun Dec 13 15:36:31 2020

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