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Iron in PDB 4o7g: Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 Minutes

Enzymatic activity of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 Minutes

All present enzymatic activity of Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 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 40 Minutes, PDB code: 4o7g 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) 28.08 / 2.21
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.186, 108.705, 111.762, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.9

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 40 Minutes (pdb code 4o7g). 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 40 Minutes, PDB code: 4o7g:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4o7g

Go back to Iron Binding Sites List in 4o7g
Iron binding site 1 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 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 40 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:42.4
occ:1.00
 FE A:HEM301 0.0 42.4 1.0
NA A:HEM301 2.0 38.4 1.0
NC A:HEM301 2.1 48.2 1.0
ND A:HEM301 2.1 38.4 1.0
NB A:HEM301 2.1 45.6 1.0
NE2 A:HIS51 2.1 44.3 1.0
NE2 A:HIS118 2.1 39.5 1.0
CD2 A:HIS51 3.0 34.7 1.0
C4A A:HEM301 3.0 44.4 1.0
C1A A:HEM301 3.0 43.8 1.0
CD2 A:HIS118 3.0 36.8 1.0
C4C A:HEM301 3.1 40.8 1.0
C1D A:HEM301 3.1 42.1 1.0
C1B A:HEM301 3.1 37.0 1.0
C1C A:HEM301 3.1 43.5 1.0
C4D A:HEM301 3.1 45.4 1.0
C4B A:HEM301 3.1 43.0 1.0
CE1 A:HIS51 3.1 37.5 1.0
CE1 A:HIS118 3.2 38.3 1.0
CHB A:HEM301 3.4 43.1 1.0
CHD A:HEM301 3.4 39.2 1.0
CHA A:HEM301 3.4 44.7 1.0
CHC A:HEM301 3.5 41.1 1.0
CG A:HIS51 4.2 41.5 1.0
ND1 A:HIS51 4.2 41.9 1.0
CG A:HIS118 4.2 40.0 1.0
ND1 A:HIS118 4.2 38.6 1.0
C3A A:HEM301 4.2 42.4 1.0
C2A A:HEM301 4.3 42.5 1.0
C3C A:HEM301 4.3 36.6 1.0
C2C A:HEM301 4.3 42.4 1.0
C3B A:HEM301 4.3 48.4 1.0
C2B A:HEM301 4.3 43.3 1.0
C2D A:HEM301 4.3 35.9 1.0
C3D A:HEM301 4.3 38.7 1.0
CA A:GLY175 5.0 41.6 1.0

Iron binding site 2 out of 4 in 4o7g

Go back to Iron Binding Sites List in 4o7g
Iron binding site 2 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 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 40 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:42.8
occ:1.00
 FE A:HEM302 0.0 42.8 1.0
NB A:HEM302 2.0 31.4 1.0
NC A:HEM302 2.0 49.5 1.0
NA A:HEM302 2.0 43.4 1.0
ND A:HEM302 2.1 45.0 1.0
NE2 A:HIS157 2.2 47.9 1.0
NE2 A:HIS84 2.2 38.6 1.0
CD2 A:HIS84 3.0 37.5 1.0
C4B A:HEM302 3.0 45.4 1.0
C1C A:HEM302 3.0 48.7 1.0
C1A A:HEM302 3.0 49.0 1.0
C1B A:HEM302 3.0 37.5 1.0
C4A A:HEM302 3.1 46.6 1.0
CD2 A:HIS157 3.1 44.3 1.0
C4C A:HEM302 3.1 50.1 1.0
C4D A:HEM302 3.1 44.6 1.0
C1D A:HEM302 3.1 44.4 1.0
CE1 A:HIS157 3.2 43.7 1.0
CE1 A:HIS84 3.3 38.0 1.0
CHC A:HEM302 3.4 41.9 1.0
CHA A:HEM302 3.4 46.2 1.0
CHB A:HEM302 3.4 40.9 1.0
CHD A:HEM302 3.5 44.3 1.0
CG A:HIS84 4.2 42.5 1.0
CG A:HIS157 4.3 42.7 1.0
C3B A:HEM302 4.3 41.4 1.0
C2B A:HEM302 4.3 36.4 1.0
C2A A:HEM302 4.3 50.3 1.0
C2C A:HEM302 4.3 46.7 1.0
C3C A:HEM302 4.3 50.1 1.0
ND1 A:HIS157 4.3 43.1 1.0
C3A A:HEM302 4.3 49.9 1.0
ND1 A:HIS84 4.3 40.3 1.0
C3D A:HEM302 4.3 49.3 1.0
C2D A:HEM302 4.4 43.7 1.0
NE2 A:GLN132 4.9 34.7 1.0
CE2 A:TYR70 4.9 52.4 1.0

Iron binding site 3 out of 4 in 4o7g

Go back to Iron Binding Sites List in 4o7g
Iron binding site 3 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 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 40 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:39.1
occ:1.00
 FE B:HEM301 0.0 39.1 1.0
NB B:HEM301 2.0 37.6 1.0
NC B:HEM301 2.0 44.8 1.0
ND B:HEM301 2.1 44.7 1.0
NE2 B:HIS118 2.1 38.4 1.0
NA B:HEM301 2.1 33.3 1.0
NE2 B:HIS51 2.1 34.6 1.0
CD2 B:HIS51 3.0 38.0 1.0
C4B B:HEM301 3.0 36.8 1.0
C1C B:HEM301 3.0 45.5 1.0
CE1 B:HIS118 3.1 39.9 1.0
C1B B:HEM301 3.1 32.5 1.0
C4D B:HEM301 3.1 41.8 1.0
C4C B:HEM301 3.1 44.8 1.0
C1A B:HEM301 3.1 38.6 1.0
CD2 B:HIS118 3.1 33.3 1.0
C1D B:HEM301 3.1 42.8 1.0
C4A B:HEM301 3.1 39.4 1.0
CE1 B:HIS51 3.2 38.7 1.0
CHC B:HEM301 3.4 44.9 1.0
CHA B:HEM301 3.4 40.1 1.0
CHB B:HEM301 3.5 33.8 1.0
CHD B:HEM301 3.5 38.2 1.0
ND1 B:HIS118 4.2 38.3 1.0
CG B:HIS51 4.2 41.9 1.0
C3B B:HEM301 4.2 38.6 1.0
CG B:HIS118 4.2 34.6 1.0
C2B B:HEM301 4.2 42.3 1.0
ND1 B:HIS51 4.3 43.0 1.0
C2C B:HEM301 4.3 44.3 1.0
C3C B:HEM301 4.3 36.5 1.0
C3D B:HEM301 4.3 40.7 1.0
C2A B:HEM301 4.3 42.5 1.0
C3A B:HEM301 4.3 46.5 1.0
C2D B:HEM301 4.4 40.4 1.0
CA B:GLY175 4.9 33.4 1.0

Iron binding site 4 out of 4 in 4o7g

Go back to Iron Binding Sites List in 4o7g
Iron binding site 4 out of 4 in the Crystal Structure of Ascorbate-Bound Cytochrome B561, Crystal Soaked in 1 M L-Ascorbate For 40 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 40 Minutes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:43.4
occ:1.00
 FE B:HEM302 0.0 43.4 1.0
NE2 B:HIS157 2.0 52.3 1.0
NC B:HEM302 2.0 49.2 1.0
NA B:HEM302 2.0 40.8 1.0
ND B:HEM302 2.1 43.1 1.0
NB B:HEM302 2.1 44.9 1.0
NE2 B:HIS84 2.2 42.6 1.0
CE1 B:HIS157 2.9 46.7 1.0
C1A B:HEM302 3.0 48.5 1.0
CD2 B:HIS84 3.0 44.9 1.0
C4C B:HEM302 3.1 50.6 1.0
C1C B:HEM302 3.1 44.6 1.0
C4D B:HEM302 3.1 46.4 1.0
CD2 B:HIS157 3.1 36.4 1.0
C4B B:HEM302 3.1 42.1 1.0
C4A B:HEM302 3.1 44.3 1.0
C1D B:HEM302 3.1 48.3 1.0
C1B B:HEM302 3.1 46.0 1.0
CE1 B:HIS84 3.3 38.9 1.0
CHA B:HEM302 3.4 44.9 1.0
CHC B:HEM302 3.4 44.4 1.0
CHD B:HEM302 3.5 51.2 1.0
CHB B:HEM302 3.5 42.5 1.0
ND1 B:HIS157 4.1 46.2 1.0
CG B:HIS157 4.2 45.6 1.0
CG B:HIS84 4.2 50.6 1.0
C2A B:HEM302 4.2 44.2 1.0
C3C B:HEM302 4.3 40.2 1.0
C2C B:HEM302 4.3 47.4 1.0
C3A B:HEM302 4.3 40.1 1.0
ND1 B:HIS84 4.3 44.9 1.0
C3D B:HEM302 4.3 48.3 1.0
C3B B:HEM302 4.3 45.5 1.0
C2D B:HEM302 4.3 50.9 1.0
C2B B:HEM302 4.3 42.0 1.0
CE1 B:TYR70 4.7 41.9 1.0
NE2 B:GLN132 4.9 37.2 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 08:08:32 2024

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