Atomistry » Iron » PDB 4hm7-4ies » 4i7z
Atomistry »
  Iron »
    PDB 4hm7-4ies »
      4i7z »

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: Sun Dec 13 15:37:13 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy