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Iron in PDB 2ibz: Yeast Cytochrome BC1 Complex with Stigmatellin

Enzymatic activity of Yeast Cytochrome BC1 Complex with Stigmatellin

All present enzymatic activity of Yeast Cytochrome BC1 Complex with Stigmatellin:
1.10.2.2;

Protein crystallography data

The structure of Yeast Cytochrome BC1 Complex with Stigmatellin, PDB code: 2ibz was solved by C.Hunte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.96 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.473, 163.921, 147.276, 90.00, 117.50, 90.00
R / Rfree (%) 22.2 / 25.6

Iron Binding Sites:

The binding sites of Iron atom in the Yeast Cytochrome BC1 Complex with Stigmatellin (pdb code 2ibz). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Yeast Cytochrome BC1 Complex with Stigmatellin, PDB code: 2ibz:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 2ibz

Go back to Iron Binding Sites List in 2ibz
Iron binding site 1 out of 5 in the Yeast Cytochrome BC1 Complex with Stigmatellin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Yeast Cytochrome BC1 Complex with Stigmatellin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:29.1
occ:1.00
 FE C:HEM401 0.0 29.1 1.0
NA C:HEM401 2.0 25.3 1.0
NE2 C:HIS82 2.0 26.2 1.0
NB C:HEM401 2.0 25.5 1.0
NE2 C:HIS183 2.0 26.7 1.0
NC C:HEM401 2.0 26.3 1.0
ND C:HEM401 2.0 27.8 1.0
CE1 C:HIS183 2.9 24.6 1.0
CE1 C:HIS82 2.9 25.2 1.0
C1A C:HEM401 3.0 29.5 1.0
C4B C:HEM401 3.0 24.8 1.0
C4D C:HEM401 3.0 28.4 1.0
C1C C:HEM401 3.0 28.0 1.0
C4A C:HEM401 3.1 27.3 1.0
C1B C:HEM401 3.1 26.0 1.0
C1D C:HEM401 3.1 28.5 1.0
C4C C:HEM401 3.1 26.9 1.0
CD2 C:HIS82 3.1 26.0 1.0
CD2 C:HIS183 3.1 25.8 1.0
CHA C:HEM401 3.4 24.8 1.0
CHC C:HEM401 3.4 26.6 1.0
CHB C:HEM401 3.5 26.8 1.0
CHD C:HEM401 3.5 28.4 1.0
ND1 C:HIS183 4.1 27.4 1.0
ND1 C:HIS82 4.1 26.1 1.0
CG C:HIS82 4.2 30.9 1.0
CG C:HIS183 4.2 24.2 1.0
C2A C:HEM401 4.2 26.0 1.0
C3B C:HEM401 4.2 27.5 1.0
C3A C:HEM401 4.3 24.4 1.0
C2C C:HEM401 4.3 25.9 1.0
C3D C:HEM401 4.3 27.1 1.0
C2B C:HEM401 4.3 26.0 1.0
C3C C:HEM401 4.3 27.1 1.0
C2D C:HEM401 4.3 28.3 1.0
CA C:GLY131 4.7 30.5 1.0

Iron binding site 2 out of 5 in 2ibz

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Iron binding site 2 out of 5 in the Yeast Cytochrome BC1 Complex with Stigmatellin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Yeast Cytochrome BC1 Complex with Stigmatellin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:28.4
occ:1.00
 FE C:HEM402 0.0 28.4 1.0
NE2 C:HIS96 2.0 26.8 1.0
ND C:HEM402 2.0 30.4 1.0
NE2 C:HIS197 2.0 28.2 1.0
NA C:HEM402 2.0 29.4 1.0
NC C:HEM402 2.0 31.2 1.0
NB C:HEM402 2.1 30.9 1.0
CE1 C:HIS96 2.9 27.4 1.0
CE1 C:HIS197 3.0 27.8 1.0
C1D C:HEM402 3.0 29.6 1.0
C4D C:HEM402 3.0 31.7 1.0
C4C C:HEM402 3.0 29.6 1.0
CD2 C:HIS96 3.1 26.3 1.0
C4A C:HEM402 3.1 28.1 1.0
C1B C:HEM402 3.1 29.1 1.0
C1A C:HEM402 3.1 29.2 1.0
C4B C:HEM402 3.1 31.8 1.0
C1C C:HEM402 3.1 32.4 1.0
CD2 C:HIS197 3.1 25.8 1.0
CHD C:HEM402 3.4 31.1 1.0
CHB C:HEM402 3.4 26.9 1.0
CHA C:HEM402 3.4 29.1 1.0
CHC C:HEM402 3.5 30.1 1.0
ND1 C:HIS96 4.1 25.3 1.0
ND1 C:HIS197 4.1 26.8 1.0
CG C:HIS96 4.2 25.6 1.0
C2D C:HEM402 4.2 30.5 1.0
CG C:HIS197 4.2 29.9 1.0
C3D C:HEM402 4.2 32.4 1.0
C3C C:HEM402 4.3 31.2 1.0
C2A C:HEM402 4.3 28.4 1.0
C3A C:HEM402 4.3 28.9 1.0
C2B C:HEM402 4.3 29.7 1.0
C2C C:HEM402 4.3 32.0 1.0
C3B C:HEM402 4.3 30.5 1.0
O C:HOH514 4.8 36.5 1.0

Iron binding site 3 out of 5 in 2ibz

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Iron binding site 3 out of 5 in the Yeast Cytochrome BC1 Complex with Stigmatellin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Yeast Cytochrome BC1 Complex with Stigmatellin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe3

b:49.2
occ:1.00
 FE D:HEM3 0.0 49.2 1.0
NE2 D:HIS105 2.0 50.3 1.0
ND D:HEM3 2.0 46.3 1.0
NB D:HEM3 2.0 48.4 1.0
NC D:HEM3 2.0 51.0 1.0
NA D:HEM3 2.0 47.6 1.0
SD D:MET225 2.2 53.1 1.0
CE1 D:HIS105 2.9 53.0 1.0
C4D D:HEM3 3.0 46.8 1.0
C1D D:HEM3 3.0 47.8 1.0
CD2 D:HIS105 3.0 53.0 1.0
C4B D:HEM3 3.0 48.1 1.0
C4C D:HEM3 3.0 50.7 1.0
C1C D:HEM3 3.1 48.7 1.0
C1B D:HEM3 3.1 47.2 1.0
C1A D:HEM3 3.1 45.6 1.0
C4A D:HEM3 3.1 44.9 1.0
CHA D:HEM3 3.4 47.5 1.0
CHD D:HEM3 3.4 49.5 1.0
CHC D:HEM3 3.4 47.2 1.0
CHB D:HEM3 3.4 45.3 1.0
CE D:MET225 3.5 49.2 1.0
CG D:MET225 3.6 50.3 1.0
ND1 D:HIS105 4.1 53.6 1.0
CG D:HIS105 4.1 53.1 1.0
CB D:MET225 4.2 53.1 1.0
C2D D:HEM3 4.2 47.7 1.0
C3D D:HEM3 4.2 47.0 1.0
C3C D:HEM3 4.3 51.7 1.0
C2C D:HEM3 4.3 50.2 1.0
C2B D:HEM3 4.3 47.0 1.0
C3B D:HEM3 4.3 48.8 1.0
C2A D:HEM3 4.3 44.2 1.0
C3A D:HEM3 4.3 44.4 1.0

Iron binding site 4 out of 5 in 2ibz

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Iron binding site 4 out of 5 in the Yeast Cytochrome BC1 Complex with Stigmatellin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Yeast Cytochrome BC1 Complex with Stigmatellin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe4

b:40.9
occ:1.00
 FE1 E:FES4 0.0 40.9 1.0
S1 E:FES4 2.1 35.8 1.0
S2 E:FES4 2.2 36.5 1.0
SG E:CYS178 2.2 40.9 1.0
SG E:CYS159 2.2 37.4 1.0
FE2 E:FES4 2.9 37.1 1.0
CB E:CYS178 3.1 42.2 1.0
CB E:CYS159 3.1 38.5 1.0
CB E:HIS161 4.0 35.9 1.0
CB E:CYS180 4.3 36.6 1.0
CB E:SER183 4.4 39.6 1.0
OG E:SER183 4.5 39.2 1.0
ND1 E:HIS161 4.5 34.4 1.0
CA E:CYS178 4.5 40.5 1.0
CB E:CYS164 4.5 36.0 1.0
N E:HIS181 4.5 41.1 1.0
CA E:CYS159 4.6 38.1 1.0
ND1 E:HIS181 4.6 35.0 1.0
N E:LEU162 4.7 35.1 1.0
CG E:HIS161 4.8 33.1 1.0
N E:CYS164 4.8 34.4 1.0
O E:CYS178 4.8 39.9 1.0
C E:CYS178 4.8 40.2 1.0
N E:CYS180 5.0 39.4 1.0
N E:HIS161 5.0 35.8 1.0

Iron binding site 5 out of 5 in 2ibz

Go back to Iron Binding Sites List in 2ibz
Iron binding site 5 out of 5 in the Yeast Cytochrome BC1 Complex with Stigmatellin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Yeast Cytochrome BC1 Complex with Stigmatellin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe4

b:37.1
occ:1.00
 FE2 E:FES4 0.0 37.1 1.0
ND1 E:HIS161 2.1 34.4 1.0
ND1 E:HIS181 2.1 35.0 1.0
S2 E:FES4 2.2 36.5 1.0
S1 E:FES4 2.2 35.8 1.0
FE1 E:FES4 2.9 40.9 1.0
CG E:HIS181 3.0 36.6 1.0
CG E:HIS161 3.0 33.1 1.0
CE1 E:HIS161 3.1 31.6 1.0
CE1 E:HIS181 3.1 28.9 1.0
CB E:HIS181 3.2 37.6 1.0
CB E:HIS161 3.3 35.9 1.0
N E:HIS181 3.8 41.1 1.0
N E:LEU162 4.0 35.1 1.0
CA E:HIS181 4.1 40.3 1.0
CB E:CYS180 4.1 36.6 1.0
CD2 E:HIS181 4.2 35.5 1.0
CD2 E:HIS161 4.2 34.7 1.0
NE2 E:HIS161 4.2 35.6 1.0
NE2 E:HIS181 4.2 34.3 1.0
CB E:LEU162 4.3 31.1 1.0
C E:CYS180 4.4 40.2 1.0
SG E:CYS159 4.5 37.4 1.0
CG E:LEU162 4.5 29.7 1.0
SG E:CYS178 4.6 40.9 1.0
CA E:HIS161 4.6 36.1 1.0
CG E:PRO195 4.6 40.9 1.0
CA E:LEU162 4.7 34.9 1.0
C E:HIS161 4.7 35.9 1.0
CD1 E:LEU162 4.8 25.9 1.0
CA E:CYS180 4.8 39.1 1.0
C E:HIS181 4.8 40.9 1.0

Reference:

C.R.Lancaster, C.Hunte, J.Kelley, B.L.Trumpower, R.Ditchfield. A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex. J.Mol.Biol. V. 368 197 2007.
ISSN: ISSN 0022-2836
PubMed: 17337272
DOI: 10.1016/J.JMB.2007.02.013
Page generated: Sun Dec 13 14:46:53 2020

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