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Iron in PDB 4o79: Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes

Enzymatic activity of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes

All present enzymatic activity of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes:
1.16.5.1;

Protein crystallography data

The structure of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes, PDB code: 4o79 was solved by P.Lu, D.Ma, C.Yan, X.Gong, M.Du, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.59 / 2.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.193, 108.648, 111.389, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 21.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes (pdb code 4o79). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes, PDB code: 4o79:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4o79

Go back to Iron Binding Sites List in 4o79
Iron binding site 1 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes


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 Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:32.4
occ:1.00
 FE A:HEM301 0.0 32.4 1.0
NC A:HEM301 2.0 31.4 1.0
NB A:HEM301 2.0 31.7 1.0
ND A:HEM301 2.1 30.8 1.0
NA A:HEM301 2.1 33.6 1.0
NE2 A:HIS51 2.2 36.2 1.0
NE2 A:HIS118 2.2 30.4 1.0
C4C A:HEM301 3.0 25.5 1.0
C1C A:HEM301 3.1 25.4 1.0
C4B A:HEM301 3.1 27.6 1.0
C1B A:HEM301 3.1 26.6 1.0
C4A A:HEM301 3.1 28.0 1.0
C1D A:HEM301 3.1 34.3 1.0
C4D A:HEM301 3.1 32.5 1.0
CE1 A:HIS118 3.1 27.7 1.0
C1A A:HEM301 3.1 32.9 1.0
CE1 A:HIS51 3.1 32.5 1.0
CD2 A:HIS51 3.2 35.5 1.0
CD2 A:HIS118 3.2 27.9 1.0
CHD A:HEM301 3.4 29.0 1.0
CHC A:HEM301 3.4 26.4 1.0
CHB A:HEM301 3.4 25.7 1.0
CHA A:HEM301 3.5 32.0 1.0
C3C A:HEM301 4.2 28.1 1.0
C2C A:HEM301 4.3 32.6 1.0
ND1 A:HIS118 4.3 24.1 1.0
ND1 A:HIS51 4.3 34.0 1.0
C3B A:HEM301 4.3 30.8 1.0
C2B A:HEM301 4.3 29.2 1.0
C3A A:HEM301 4.3 32.3 1.0
CG A:HIS51 4.3 33.3 1.0
C2D A:HEM301 4.3 29.5 1.0
C3D A:HEM301 4.3 31.0 1.0
CG A:HIS118 4.3 27.3 1.0
C2A A:HEM301 4.3 34.5 1.0
CA A:GLY175 4.9 34.7 1.0

Iron binding site 2 out of 4 in 4o79

Go back to Iron Binding Sites List in 4o79
Iron binding site 2 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes


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 Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:33.0
occ:1.00
 FE A:HEM302 0.0 33.0 1.0
NB A:HEM302 2.0 28.8 1.0
NA A:HEM302 2.1 37.0 1.0
ND A:HEM302 2.1 34.0 1.0
NC A:HEM302 2.1 31.9 1.0
NE2 A:HIS157 2.3 35.3 1.0
NE2 A:HIS84 2.3 32.2 1.0
C4B A:HEM302 3.1 34.1 1.0
C1D A:HEM302 3.1 30.0 1.0
C4D A:HEM302 3.1 32.3 1.0
C1A A:HEM302 3.1 34.1 1.0
C1B A:HEM302 3.1 31.1 1.0
C1C A:HEM302 3.1 31.2 1.0
C4C A:HEM302 3.1 32.3 1.0
C4A A:HEM302 3.1 34.6 1.0
CD2 A:HIS157 3.1 31.7 1.0
CD2 A:HIS84 3.1 31.2 1.0
CE1 A:HIS157 3.4 38.2 1.0
CE1 A:HIS84 3.4 35.2 1.0
CHA A:HEM302 3.4 29.7 1.0
CHD A:HEM302 3.4 30.6 1.0
CHC A:HEM302 3.4 26.8 1.0
CHB A:HEM302 3.5 32.0 1.0
C3B A:HEM302 4.3 31.9 1.0
C2B A:HEM302 4.3 28.7 1.0
C2A A:HEM302 4.3 38.0 1.0
C3D A:HEM302 4.3 40.2 1.0
C3A A:HEM302 4.3 38.4 1.0
CG A:HIS157 4.3 38.4 1.0
C2D A:HEM302 4.3 35.1 1.0
C3C A:HEM302 4.3 34.8 1.0
C2C A:HEM302 4.3 34.7 1.0
CG A:HIS84 4.3 35.3 1.0
ND1 A:HIS157 4.4 34.1 1.0
ND1 A:HIS84 4.4 34.8 1.0
OH A:TYR70 4.8 41.9 1.0
NE2 A:GLN132 4.8 29.8 1.0
CE1 A:TYR70 4.8 42.0 1.0

Iron binding site 3 out of 4 in 4o79

Go back to Iron Binding Sites List in 4o79
Iron binding site 3 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:30.1
occ:1.00
 FE B:HEM301 0.0 30.1 1.0
NC B:HEM301 2.0 26.6 1.0
NA B:HEM301 2.1 30.4 1.0
NB B:HEM301 2.1 24.8 1.0
ND B:HEM301 2.1 27.0 1.0
NE2 B:HIS118 2.2 31.2 1.0
NE2 B:HIS51 2.3 30.0 1.0
C4C B:HEM301 3.0 31.5 1.0
C1C B:HEM301 3.0 31.9 1.0
C4B B:HEM301 3.1 24.1 1.0
C1D B:HEM301 3.1 29.1 1.0
C4A B:HEM301 3.1 31.0 1.0
C4D B:HEM301 3.1 30.8 1.0
C1A B:HEM301 3.1 31.7 1.0
C1B B:HEM301 3.1 26.3 1.0
CE1 B:HIS118 3.1 26.6 1.0
CD2 B:HIS51 3.1 32.5 1.0
CD2 B:HIS118 3.2 27.6 1.0
CE1 B:HIS51 3.3 34.0 1.0
CHD B:HEM301 3.4 24.9 1.0
CHC B:HEM301 3.4 27.3 1.0
CHA B:HEM301 3.5 31.7 1.0
CHB B:HEM301 3.5 24.8 1.0
C3C B:HEM301 4.2 29.9 1.0
C2C B:HEM301 4.2 31.1 1.0
ND1 B:HIS118 4.3 25.0 1.0
C3A B:HEM301 4.3 35.9 1.0
C3B B:HEM301 4.3 28.4 1.0
C2A B:HEM301 4.3 36.2 1.0
C2D B:HEM301 4.3 31.5 1.0
C2B B:HEM301 4.3 30.2 1.0
C3D B:HEM301 4.3 31.6 1.0
CG B:HIS51 4.3 32.0 1.0
CG B:HIS118 4.3 25.6 1.0
ND1 B:HIS51 4.4 27.9 1.0
CG B:MET55 5.0 32.0 1.0

Iron binding site 4 out of 4 in 4o79

Go back to Iron Binding Sites List in 4o79
Iron binding site 4 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 10 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:34.8
occ:1.00
 FE B:HEM302 0.0 34.8 1.0
ND B:HEM302 2.1 40.1 1.0
NC B:HEM302 2.1 34.8 1.0
NA B:HEM302 2.1 31.0 1.0
NB B:HEM302 2.1 29.2 1.0
NE2 B:HIS84 2.2 32.2 1.0
NE2 B:HIS157 2.4 37.6 1.0
CD2 B:HIS157 3.0 35.8 1.0
CD2 B:HIS84 3.0 34.5 1.0
C1D B:HEM302 3.1 35.4 1.0
C4C B:HEM302 3.1 35.5 1.0
C4D B:HEM302 3.1 36.3 1.0
C1A B:HEM302 3.1 37.9 1.0
C1B B:HEM302 3.1 33.3 1.0
C4A B:HEM302 3.1 30.4 1.0
C4B B:HEM302 3.1 34.3 1.0
C1C B:HEM302 3.1 39.1 1.0
CE1 B:HIS84 3.3 35.2 1.0
CHD B:HEM302 3.4 37.0 1.0
CHA B:HEM302 3.4 32.6 1.0
CHB B:HEM302 3.5 30.7 1.0
CHC B:HEM302 3.5 33.9 1.0
CE1 B:HIS157 3.5 41.9 1.0
CG B:HIS84 4.2 40.5 1.0
CG B:HIS157 4.3 41.2 1.0
C3C B:HEM302 4.3 38.6 1.0
C3D B:HEM302 4.3 35.8 1.0
C2D B:HEM302 4.3 38.0 1.0
C2A B:HEM302 4.3 31.1 1.0
C2B B:HEM302 4.3 31.1 1.0
C3A B:HEM302 4.3 30.3 1.0
C2C B:HEM302 4.3 38.2 1.0
C3B B:HEM302 4.4 31.9 1.0
ND1 B:HIS84 4.4 36.9 1.0
ND1 B:HIS157 4.5 41.1 1.0
CE1 B:TYR70 4.8 39.1 1.0
NE2 B:GLN132 4.9 33.7 1.0
OH B:TYR70 4.9 40.6 1.0

Reference:

P.Lu, D.Ma, C.Yan, X.Gong, M.Du, Y.Shi. Structure and Mechanism of A Eukaryotic Transmembrane Ascorbate-Dependent Oxidoreductase Proc.Natl.Acad.Sci.Usa V. 111 1813 2014.
ISSN: ISSN 0027-8424
PubMed: 24449903
DOI: 10.1073/PNAS.1323931111
Page generated: Mon Aug 5 08:08:25 2024

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