Iron in PDB 7bwh: Soluble Cytochrome B5 From Ramazzottius Varieornatus

Protein crystallography data

The structure of Soluble Cytochrome B5 From Ramazzottius Varieornatus, PDB code: 7bwh was solved by J.Kim, T.Inoue, Y.Fukuda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.80 / 1.40
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 34.004, 37.495, 77.546, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.1

Other elements in 7bwh:

The structure of Soluble Cytochrome B5 From Ramazzottius Varieornatus also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Soluble Cytochrome B5 From Ramazzottius Varieornatus (pdb code 7bwh). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Soluble Cytochrome B5 From Ramazzottius Varieornatus, PDB code: 7bwh:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in 7bwh

Go back to Iron Binding Sites List in 7bwh
Iron binding site 1 out of 3 in the Soluble Cytochrome B5 From Ramazzottius Varieornatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Soluble Cytochrome B5 From Ramazzottius Varieornatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:12.9
occ:0.25
FE A:HEM201 0.0 12.9 0.2
FE A:HEM201 0.0 21.8 0.3
FE A:HEM201 0.0 29.1 0.5
ND A:HEM201 1.9 29.2 0.5
ND A:HEM201 1.9 12.7 0.2
ND A:HEM201 1.9 21.4 0.3
NA A:HEM201 2.0 22.9 0.3
NA A:HEM201 2.0 14.2 0.2
NC A:HEM201 2.0 28.0 0.5
NA A:HEM201 2.1 27.9 0.5
NC A:HEM201 2.1 12.5 0.2
NB A:HEM201 2.1 20.4 0.3
NB A:HEM201 2.1 13.7 0.2
NC A:HEM201 2.1 20.8 0.3
NB A:HEM201 2.1 26.6 0.5
NE2 A:HIS56 2.1 21.2 1.0
NE2 A:HIS80 2.2 17.8 1.0
C1D A:HEM201 2.9 31.2 0.5
C4D A:HEM201 2.9 31.6 0.5
C4D A:HEM201 2.9 13.8 0.2
C4D A:HEM201 2.9 23.3 0.3
C1D A:HEM201 3.0 12.9 0.2
C1D A:HEM201 3.0 22.5 0.3
C1A A:HEM201 3.0 24.4 0.3
C4C A:HEM201 3.0 28.9 0.5
C1A A:HEM201 3.0 15.2 0.2
C4A A:HEM201 3.0 23.9 0.3
C1A A:HEM201 3.0 29.5 0.5
C4C A:HEM201 3.0 12.2 0.2
C1B A:HEM201 3.1 21.1 0.3
C4A A:HEM201 3.1 14.8 0.2
C4B A:HEM201 3.1 27.2 0.5
C4B A:HEM201 3.1 20.9 0.3
C4C A:HEM201 3.1 20.9 0.3
C4B A:HEM201 3.1 14.4 0.2
C1B A:HEM201 3.1 14.3 0.2
C1C A:HEM201 3.1 29.1 0.5
C1B A:HEM201 3.1 26.2 0.5
C1C A:HEM201 3.1 12.9 0.2
CD2 A:HIS56 3.1 21.6 1.0
C1C A:HEM201 3.1 21.0 0.3
C4A A:HEM201 3.1 27.9 0.5
CD2 A:HIS80 3.1 18.1 1.0
CE1 A:HIS56 3.1 24.0 1.0
CE1 A:HIS80 3.2 20.4 1.0
CHD A:HEM201 3.3 30.7 0.5
CHA A:HEM201 3.4 23.9 0.3
CHA A:HEM201 3.4 14.7 0.2
CHA A:HEM201 3.4 30.1 0.5
CHD A:HEM201 3.4 12.5 0.2
CHD A:HEM201 3.4 21.7 0.3
CHB A:HEM201 3.4 23.1 0.3
CHB A:HEM201 3.5 15.2 0.2
CHC A:HEM201 3.5 27.9 0.5
CHC A:HEM201 3.5 13.5 0.2
CHC A:HEM201 3.5 20.9 0.3
CHB A:HEM201 3.5 27.0 0.5
C2D A:HEM201 4.2 32.5 0.5
C3D A:HEM201 4.2 33.2 0.5
C2A A:HEM201 4.2 26.0 0.3
C3A A:HEM201 4.2 25.4 0.3
C2A A:HEM201 4.2 16.7 0.2
C3C A:HEM201 4.2 29.3 0.5
C3D A:HEM201 4.2 13.8 0.2
C2D A:HEM201 4.2 13.3 0.2
C3D A:HEM201 4.2 23.9 0.3
C3A A:HEM201 4.2 16.1 0.2
C2D A:HEM201 4.2 23.2 0.3
C2C A:HEM201 4.2 29.9 0.5
ND1 A:HIS56 4.2 23.7 1.0
C2A A:HEM201 4.3 29.4 0.5
C3C A:HEM201 4.3 12.8 0.2
ND1 A:HIS80 4.3 20.0 1.0
CG A:HIS56 4.3 23.8 1.0
C2C A:HEM201 4.3 12.9 0.2
CG A:HIS80 4.3 19.0 1.0
C3C A:HEM201 4.3 21.6 0.3
C2B A:HEM201 4.3 21.1 0.3
C3A A:HEM201 4.3 28.2 0.5
C2C A:HEM201 4.3 21.3 0.3
C2B A:HEM201 4.3 15.5 0.2
C3B A:HEM201 4.3 20.8 0.3
C3B A:HEM201 4.3 15.7 0.2
C2B A:HEM201 4.3 27.1 0.5
C3B A:HEM201 4.3 27.6 0.5
N A:GLY58 4.9 27.8 1.0
CE1 A:PHE75 4.9 17.6 1.0

Iron binding site 2 out of 3 in 7bwh

Go back to Iron Binding Sites List in 7bwh
Iron binding site 2 out of 3 in the Soluble Cytochrome B5 From Ramazzottius Varieornatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Soluble Cytochrome B5 From Ramazzottius Varieornatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:21.8
occ:0.30
FE A:HEM201 0.0 21.8 0.3
FE A:HEM201 0.0 29.1 0.5
FE A:HEM201 0.0 12.9 0.2
ND A:HEM201 1.9 12.7 0.2
ND A:HEM201 1.9 21.4 0.3
ND A:HEM201 1.9 29.2 0.5
NA A:HEM201 2.0 22.9 0.3
NA A:HEM201 2.0 14.2 0.2
NA A:HEM201 2.0 27.9 0.5
NC A:HEM201 2.1 12.5 0.2
NC A:HEM201 2.1 28.0 0.5
NC A:HEM201 2.1 20.8 0.3
NB A:HEM201 2.1 26.6 0.5
NB A:HEM201 2.1 20.4 0.3
NB A:HEM201 2.1 13.7 0.2
NE2 A:HIS80 2.1 17.8 1.0
NE2 A:HIS56 2.2 21.2 1.0
C1D A:HEM201 2.9 31.2 0.5
C4D A:HEM201 2.9 31.6 0.5
C1D A:HEM201 2.9 12.9 0.2
C4D A:HEM201 2.9 13.8 0.2
C4D A:HEM201 2.9 23.3 0.3
C1D A:HEM201 2.9 22.5 0.3
C1A A:HEM201 3.0 24.4 0.3
C1A A:HEM201 3.0 15.2 0.2
C4C A:HEM201 3.0 28.9 0.5
C4C A:HEM201 3.0 12.2 0.2
C1A A:HEM201 3.0 29.5 0.5
C4C A:HEM201 3.0 20.9 0.3
C4B A:HEM201 3.0 27.2 0.5
C4A A:HEM201 3.1 23.9 0.3
C1B A:HEM201 3.1 21.1 0.3
C4B A:HEM201 3.1 20.9 0.3
C4A A:HEM201 3.1 14.8 0.2
C4B A:HEM201 3.1 14.4 0.2
C1C A:HEM201 3.1 29.1 0.5
C1B A:HEM201 3.1 26.2 0.5
C1B A:HEM201 3.1 14.3 0.2
C1C A:HEM201 3.1 12.9 0.2
C4A A:HEM201 3.1 27.9 0.5
CD2 A:HIS80 3.1 18.1 1.0
C1C A:HEM201 3.1 21.0 0.3
CD2 A:HIS56 3.1 21.6 1.0
CE1 A:HIS80 3.1 20.4 1.0
CE1 A:HIS56 3.2 24.0 1.0
CHD A:HEM201 3.4 30.7 0.5
CHA A:HEM201 3.4 23.9 0.3
CHD A:HEM201 3.4 12.5 0.2
CHA A:HEM201 3.4 14.7 0.2
CHA A:HEM201 3.4 30.1 0.5
CHD A:HEM201 3.4 21.7 0.3
CHB A:HEM201 3.5 23.1 0.3
CHC A:HEM201 3.5 27.9 0.5
CHB A:HEM201 3.5 15.2 0.2
CHC A:HEM201 3.5 13.5 0.2
CHC A:HEM201 3.5 20.9 0.3
CHB A:HEM201 3.5 27.0 0.5
C2D A:HEM201 4.2 32.5 0.5
C3D A:HEM201 4.2 33.2 0.5
C2D A:HEM201 4.2 13.3 0.2
C3D A:HEM201 4.2 13.8 0.2
C2A A:HEM201 4.2 26.0 0.3
C2D A:HEM201 4.2 23.2 0.3
C3D A:HEM201 4.2 23.9 0.3
C2A A:HEM201 4.2 16.7 0.2
C3C A:HEM201 4.2 29.3 0.5
C3A A:HEM201 4.2 25.4 0.3
C2C A:HEM201 4.2 29.9 0.5
C3C A:HEM201 4.2 12.8 0.2
ND1 A:HIS80 4.2 20.0 1.0
C2A A:HEM201 4.2 29.4 0.5
C3A A:HEM201 4.2 16.1 0.2
CG A:HIS80 4.3 19.0 1.0
C2C A:HEM201 4.3 12.9 0.2
C3C A:HEM201 4.3 21.6 0.3
ND1 A:HIS56 4.3 23.7 1.0
C3A A:HEM201 4.3 28.2 0.5
C2C A:HEM201 4.3 21.3 0.3
CG A:HIS56 4.3 23.8 1.0
C2B A:HEM201 4.3 27.1 0.5
C2B A:HEM201 4.3 21.1 0.3
C3B A:HEM201 4.3 27.6 0.5
C2B A:HEM201 4.3 15.5 0.2
C3B A:HEM201 4.3 20.8 0.3
C3B A:HEM201 4.3 15.7 0.2
CE1 A:PHE75 4.9 17.6 1.0
N A:GLY58 4.9 27.8 1.0

Iron binding site 3 out of 3 in 7bwh

Go back to Iron Binding Sites List in 7bwh
Iron binding site 3 out of 3 in the Soluble Cytochrome B5 From Ramazzottius Varieornatus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Soluble Cytochrome B5 From Ramazzottius Varieornatus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe201

b:29.1
occ:0.45
FE A:HEM201 0.0 29.1 0.5
FE A:HEM201 0.0 21.8 0.3
FE A:HEM201 0.0 12.9 0.2
ND A:HEM201 1.9 12.7 0.2
ND A:HEM201 1.9 21.4 0.3
ND A:HEM201 1.9 29.2 0.5
NA A:HEM201 2.0 22.9 0.3
NA A:HEM201 2.0 27.9 0.5
NA A:HEM201 2.0 14.2 0.2
NC A:HEM201 2.1 12.5 0.2
NC A:HEM201 2.1 28.0 0.5
NC A:HEM201 2.1 20.8 0.3
NB A:HEM201 2.1 26.6 0.5
NB A:HEM201 2.1 20.4 0.3
NB A:HEM201 2.1 13.7 0.2
NE2 A:HIS80 2.2 17.8 1.0
NE2 A:HIS56 2.2 21.2 1.0
C4D A:HEM201 2.9 31.6 0.5
C4D A:HEM201 2.9 13.8 0.2
C4D A:HEM201 2.9 23.3 0.3
C1D A:HEM201 2.9 12.9 0.2
C1D A:HEM201 2.9 31.2 0.5
C1D A:HEM201 2.9 22.5 0.3
C1A A:HEM201 3.0 24.4 0.3
C1A A:HEM201 3.0 15.2 0.2
C1A A:HEM201 3.0 29.5 0.5
C4C A:HEM201 3.0 12.2 0.2
C4C A:HEM201 3.0 28.9 0.5
C4C A:HEM201 3.0 20.9 0.3
C4A A:HEM201 3.1 23.9 0.3
C4B A:HEM201 3.1 27.2 0.5
C4A A:HEM201 3.1 14.8 0.2
C4A A:HEM201 3.1 27.9 0.5
C1B A:HEM201 3.1 26.2 0.5
C1B A:HEM201 3.1 21.1 0.3
C4B A:HEM201 3.1 20.9 0.3
C4B A:HEM201 3.1 14.4 0.2
C1C A:HEM201 3.1 29.1 0.5
CD2 A:HIS56 3.1 21.6 1.0
C1B A:HEM201 3.1 14.3 0.2
C1C A:HEM201 3.1 12.9 0.2
CD2 A:HIS80 3.1 18.1 1.0
C1C A:HEM201 3.1 21.0 0.3
CE1 A:HIS56 3.2 24.0 1.0
CE1 A:HIS80 3.2 20.4 1.0
CHA A:HEM201 3.4 23.9 0.3
CHA A:HEM201 3.4 14.7 0.2
CHA A:HEM201 3.4 30.1 0.5
CHD A:HEM201 3.4 12.5 0.2
CHD A:HEM201 3.4 30.7 0.5
CHD A:HEM201 3.4 21.7 0.3
CHB A:HEM201 3.5 23.1 0.3
CHB A:HEM201 3.5 15.2 0.2
CHB A:HEM201 3.5 27.0 0.5
CHC A:HEM201 3.5 27.9 0.5
CHC A:HEM201 3.5 13.5 0.2
CHC A:HEM201 3.5 20.9 0.3
C3D A:HEM201 4.2 33.2 0.5
C2D A:HEM201 4.2 32.5 0.5
C2D A:HEM201 4.2 13.3 0.2
C3D A:HEM201 4.2 13.8 0.2
C3D A:HEM201 4.2 23.9 0.3
C2D A:HEM201 4.2 23.2 0.3
C2A A:HEM201 4.2 26.0 0.3
C2A A:HEM201 4.2 16.7 0.2
C3A A:HEM201 4.2 25.4 0.3
C2A A:HEM201 4.2 29.4 0.5
C3A A:HEM201 4.2 16.1 0.2
C3C A:HEM201 4.2 29.3 0.5
C3C A:HEM201 4.2 12.8 0.2
C3A A:HEM201 4.3 28.2 0.5
ND1 A:HIS56 4.3 23.7 1.0
C2C A:HEM201 4.3 29.9 0.5
ND1 A:HIS80 4.3 20.0 1.0
CG A:HIS80 4.3 19.0 1.0
CG A:HIS56 4.3 23.8 1.0
C3C A:HEM201 4.3 21.6 0.3
C2C A:HEM201 4.3 12.9 0.2
C2C A:HEM201 4.3 21.3 0.3
C2B A:HEM201 4.3 27.1 0.5
C3B A:HEM201 4.3 27.6 0.5
C2B A:HEM201 4.3 21.1 0.3
C2B A:HEM201 4.3 15.5 0.2
C3B A:HEM201 4.3 20.8 0.3
C3B A:HEM201 4.4 15.7 0.2
N A:GLY58 4.9 27.8 1.0
CE1 A:PHE75 4.9 17.6 1.0

Reference:

Y.Fukuda, J.Kim, T.Inoue. Structure of Cytochrome B 5 Unique to Tardigrades Protein Sci. 2020.
ISSN: ESSN 1469-896X
DOI: 10.1002/PRO.3896
Page generated: Sun Dec 13 18:36:19 2020

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