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Iron in PDB 4i7z: Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain

Enzymatic activity of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain

All present enzymatic activity of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain:
1.10.9.1;

Protein crystallography data

The structure of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain, PDB code: 4i7z was solved by S.S.Hasan, J.T.Stofleth, E.Yamashita, W.A.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.52 / 2.80
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 159.451, 159.451, 362.746, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 27.2

Other elements in 4i7z:

The structure of Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Cadmium (Cd) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain (pdb code 4i7z). 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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain, PDB code: 4i7z:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 4i7z

Go back to Iron Binding Sites List in 4i7z
Iron binding site 1 out of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:57.0
occ:1.00
FE A:HEM301 0.0 57.0 1.0
NC A:HEM301 2.0 54.0 1.0
NB A:HEM301 2.0 51.5 1.0
ND A:HEM301 2.1 51.8 1.0
NA A:HEM301 2.1 49.3 1.0
NE2 A:HIS86 2.1 51.7 1.0
NE2 A:HIS187 2.2 54.1 1.0
CE1 A:HIS187 3.0 55.2 1.0
CE1 A:HIS86 3.0 51.8 1.0
C1D A:HEM301 3.0 53.0 1.0
C4C A:HEM301 3.0 57.5 1.0
C4B A:HEM301 3.1 50.6 1.0
C4D A:HEM301 3.1 51.3 1.0
C1C A:HEM301 3.1 52.5 1.0
C1B A:HEM301 3.1 49.4 1.0
HE1 A:HIS187 3.1 66.2 1.0
C1A A:HEM301 3.1 46.6 1.0
C4A A:HEM301 3.1 49.5 1.0
CD2 A:HIS86 3.1 53.9 1.0
HE1 A:HIS86 3.1 62.2 1.0
CD2 A:HIS187 3.3 55.4 1.0
HD2 A:HIS86 3.4 64.7 1.0
CHD A:HEM301 3.4 57.8 1.0
CHC A:HEM301 3.4 50.5 1.0
CHA A:HEM301 3.5 46.2 1.0
CHB A:HEM301 3.5 50.0 1.0
HD2 A:HIS187 3.5 66.4 1.0
HE21 A:GLN47 3.9 72.7 1.0
ND1 A:HIS86 4.1 53.0 1.0
HE22 A:GLN47 4.1 72.7 1.0
ND1 A:HIS187 4.2 57.1 1.0
CG A:HIS86 4.2 54.2 1.0
C3C A:HEM301 4.3 58.1 1.0
C2D A:HEM301 4.3 49.1 1.0
C3B A:HEM301 4.3 46.4 1.0
C2C A:HEM301 4.3 54.6 1.0
C2B A:HEM301 4.3 45.5 1.0
C3D A:HEM301 4.3 52.7 1.0
CG A:HIS187 4.3 57.3 1.0
C2A A:HEM301 4.3 46.9 1.0
C3A A:HEM301 4.3 47.5 1.0
NE2 A:GLN47 4.4 60.6 1.0
HA2 A:GLY51 4.4 69.2 1.0
HA3 A:GLY135 4.5 77.8 1.0
HA3 A:GLY51 4.7 69.2 1.0
HD2 A:PHE131 4.7 68.7 1.0
HD12 A:LEU138 4.7 71.2 1.0
HE3 A:MET54 4.8 89.2 1.0
HA2 A:GLY135 4.8 77.8 1.0
HD1 A:HIS86 4.9 63.6 1.0
HD1 A:HIS187 4.9 68.6 1.0
HE1 A:MET54 5.0 89.2 1.0

Iron binding site 2 out of 4 in 4i7z

Go back to Iron Binding Sites List in 4i7z
Iron binding site 2 out of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe302

b:61.5
occ:1.00
FE A:HEM302 0.0 61.5 1.0
NA A:HEM302 2.0 63.3 1.0
NB A:HEM302 2.1 60.8 1.0
NC A:HEM302 2.1 69.5 1.0
NE2 A:HIS100 2.1 60.8 1.0
ND A:HEM302 2.1 72.2 1.0
NE2 A:HIS202 2.2 52.8 1.0
CE1 A:HIS100 2.9 62.3 1.0
HE1 A:HIS100 3.0 74.8 1.0
C4C A:HEM302 3.0 70.9 1.0
CE1 A:HIS202 3.0 54.7 1.0
C1A A:HEM302 3.0 64.5 1.0
C4A A:HEM302 3.0 61.4 1.0
C1D A:HEM302 3.1 73.3 1.0
C1B A:HEM302 3.1 60.4 1.0
C1C A:HEM302 3.1 67.7 1.0
C4D A:HEM302 3.1 71.7 1.0
C4B A:HEM302 3.1 61.2 1.0
HE1 A:HIS202 3.1 65.7 1.0
CD2 A:HIS100 3.1 63.0 1.0
CD2 A:HIS202 3.2 57.0 1.0
CHD A:HEM302 3.4 73.8 1.0
HD2 A:HIS100 3.4 75.6 1.0
CHA A:HEM302 3.4 69.0 1.0
CHB A:HEM302 3.4 60.2 1.0
CHC A:HEM302 3.5 63.6 1.0
HD2 A:HIS202 3.5 68.3 1.0
ND1 A:HIS100 4.1 64.4 1.0
HD11 A:ILE206 4.1 82.2 1.0
ND1 A:HIS202 4.2 56.4 1.0
CG A:HIS100 4.2 63.4 1.0
C3C A:HEM302 4.2 71.2 1.0
C2C A:HEM302 4.2 67.5 1.0
C2A A:HEM302 4.2 60.4 1.0
C3A A:HEM302 4.3 60.4 1.0
C2B A:HEM302 4.3 57.2 1.0
C2D A:HEM302 4.3 73.1 1.0
C3D A:HEM302 4.3 72.2 1.0
HG21 A:VAL104 4.3 68.9 1.0
C3B A:HEM302 4.3 59.5 1.0
CG A:HIS202 4.3 57.0 1.0
HG22 A:THR117 4.6 82.8 1.0
HD1 A:HIS100 4.8 77.3 1.0
HA3 A:GLY121 4.8 76.0 1.0
HD13 A:ILE206 4.8 82.2 1.0
CD1 A:ILE206 4.8 68.5 1.0
HA2 A:GLY121 4.9 76.0 1.0
HD1 A:HIS202 4.9 67.6 1.0
HA3 A:GLY37 4.9 76.8 1.0
HA2 A:GLY37 5.0 76.8 1.0

Iron binding site 3 out of 4 in 4i7z

Go back to Iron Binding Sites List in 4i7z
Iron binding site 3 out of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe303

b:71.7
occ:1.00
FE A:HEM303 0.0 71.7 1.0
NA A:HEM303 2.1 78.9 1.0
NB A:HEM303 2.1 73.4 1.0
NC A:HEM303 2.1 64.2 1.0
ND A:HEM303 2.1 69.9 1.0
O A:HOH401 2.2 47.4 1.0
C1B A:HEM303 3.0 77.8 1.0
C4A A:HEM303 3.1 80.2 1.0
C4B A:HEM303 3.1 73.7 1.0
C1A A:HEM303 3.1 78.1 1.0
C1D A:HEM303 3.1 68.3 1.0
C4C A:HEM303 3.1 61.5 1.0
C4D A:HEM303 3.1 72.9 1.0
C1C A:HEM303 3.1 65.5 1.0
HE2 B:PHE40 3.3 92.0 1.0
CHB A:HEM303 3.4 80.5 1.0
CHD A:HEM303 3.4 64.2 1.0
CHA A:HEM303 3.5 74.9 1.0
CHC A:HEM303 3.5 69.6 1.0
HZ B:PHE40 3.6 92.1 1.0
HA3 A:GLY38 3.8 74.5 1.0
CE2 B:PHE40 3.8 76.7 1.0
CZ B:PHE40 3.9 76.7 1.0
C2B A:HEM303 4.2 77.6 1.0
C3B A:HEM303 4.2 75.9 1.0
C3A A:HEM303 4.3 81.8 1.0
C2A A:HEM303 4.3 81.8 1.0
H A:GLY38 4.3 79.0 1.0
C2D A:HEM303 4.3 70.7 1.0
C3C A:HEM303 4.3 59.2 1.0
C3D A:HEM303 4.3 74.0 1.0
C2C A:HEM303 4.3 62.9 1.0
O A:TYR34 4.3 66.9 1.0
CMA A:HEM302 4.4 56.6 1.0
O2A A:HEM302 4.4 68.4 1.0
CA A:GLY38 4.5 62.1 1.0
HA A:CYS35 4.5 72.6 1.0
HA2 A:GLY38 4.6 74.5 1.0
CAA A:HEM302 4.7 56.7 1.0
N A:GLY38 4.7 65.8 1.0
CD2 B:PHE40 4.9 76.5 1.0
CGA A:HEM302 4.9 64.9 1.0

Iron binding site 4 out of 4 in 4i7z

Go back to Iron Binding Sites List in 4i7z
Iron binding site 4 out of 4 in the Crystal Structure of Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain


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 Cytochrome B6F in Dopg, with Disordered Rieske Iron-Sulfur Protein Soluble Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:79.8
occ:1.00
FE C:HEM301 0.0 79.8 1.0
H1 C:TYR1 1.5 98.4 1.0
NC C:HEM301 2.0 78.5 1.0
ND C:HEM301 2.0 83.5 1.0
NA C:HEM301 2.1 81.8 1.0
NB C:HEM301 2.1 77.4 1.0
N C:TYR1 2.2 82.0 1.0
NE2 C:HIS26 2.2 86.6 1.0
H2 C:TYR1 2.3 98.4 1.0
H3 C:TYR1 2.9 98.4 1.0
C4C C:HEM301 2.9 81.0 1.0
HA C:TYR1 3.0 96.5 1.0
C1D C:HEM301 3.0 83.4 1.0
C1C C:HEM301 3.0 78.1 1.0
C1A C:HEM301 3.1 84.0 1.0
C4D C:HEM301 3.1 85.9 1.0
C4A C:HEM301 3.1 81.4 1.0
CA C:TYR1 3.1 80.5 1.0
C1B C:HEM301 3.1 78.0 1.0
C4B C:HEM301 3.1 76.2 1.0
CE1 C:HIS26 3.2 88.3 1.0
CD2 C:HIS26 3.2 84.9 1.0
CHD C:HEM301 3.3 80.9 1.0
HE1 C:HIS26 3.3 0.9 1.0
HD2 C:HIS26 3.4 0.9 1.0
CHA C:HEM301 3.4 85.8 1.0
CHC C:HEM301 3.5 76.1 1.0
CHB C:HEM301 3.5 79.2 1.0
C C:TYR1 3.8 79.3 1.0
O C:TYR1 4.0 79.4 1.0
HE3 C:TRP4 4.1 0.2 1.0
C3C C:HEM301 4.1 83.0 1.0
C2C C:HEM301 4.2 80.2 1.0
C2D C:HEM301 4.3 86.3 1.0
C3D C:HEM301 4.3 88.2 1.0
C2A C:HEM301 4.3 84.1 1.0
C3A C:HEM301 4.3 82.7 1.0
ND1 C:HIS26 4.3 87.9 1.0
C2B C:HEM301 4.4 77.8 1.0
C3B C:HEM301 4.4 77.6 1.0
CG C:HIS26 4.4 86.2 1.0
CB C:TYR1 4.5 81.7 1.0
HD3 C:PRO2 4.5 96.4 1.0
HG C:CYS22 4.6 0.7 1.0
HA3 C:GLY158 4.6 0.6 1.0
N C:PRO2 4.7 79.1 1.0
CG C:TYR1 4.7 82.5 1.0
H C:GLY158 4.8 0.1 1.0
CE3 C:TRP4 4.9 84.3 1.0
HB2 C:TYR1 4.9 98.1 1.0
HZ3 C:TRP4 4.9 0.8 1.0
OD1 C:ASN154 4.9 91.5 1.0
HB2 C:TRP4 4.9 0.2 1.0

Reference:

S.S.Hasan, J.T.Stofleth, E.Yamashita, W.A.Cramer. Lipid-Induced Conformational Changes Within the Cytochrome B6F Complex of Oxygenic Photosynthesis. Biochemistry V. 52 2649 2013.
ISSN: ISSN 0006-2960
PubMed: 23514009
DOI: 10.1021/BI301638H
Page generated: Mon Aug 5 03:53:36 2024

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