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Iron in PDB 1kb9: Yeast Cytochrome BC1 Complex

Enzymatic activity of Yeast Cytochrome BC1 Complex

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

Protein crystallography data

The structure of Yeast Cytochrome BC1 Complex, PDB code: 1kb9 was solved by C.Lange, J.H.Nett, B.L.Trumpower, 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 (%) 21.8 / 24.9

Iron Binding Sites:

The binding sites of Iron atom in the Yeast Cytochrome BC1 Complex (pdb code 1kb9). 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, PDB code: 1kb9:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1kb9

Go back to Iron Binding Sites List in 1kb9
Iron binding site 1 out of 5 in the Yeast Cytochrome BC1 Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:27.8
occ:1.00
 FE C:HEM501 0.0 27.8 1.0
NA C:HEM501 2.0 25.6 1.0
NE2 C:HIS82 2.0 26.5 1.0
NE2 C:HIS183 2.0 27.2 1.0
NB C:HEM501 2.0 25.2 1.0
NC C:HEM501 2.0 26.4 1.0
ND C:HEM501 2.0 27.6 1.0
CE1 C:HIS183 2.9 24.6 1.0
CE1 C:HIS82 2.9 25.8 1.0
C1A C:HEM501 3.0 29.4 1.0
C4B C:HEM501 3.0 24.9 1.0
C1C C:HEM501 3.0 28.4 1.0
C4D C:HEM501 3.0 28.1 1.0
C4A C:HEM501 3.1 27.0 1.0
C1B C:HEM501 3.1 26.1 1.0
C1D C:HEM501 3.1 28.1 1.0
C4C C:HEM501 3.1 26.8 1.0
CD2 C:HIS82 3.1 26.4 1.0
CD2 C:HIS183 3.1 25.8 1.0
CHC C:HEM501 3.4 26.9 1.0
CHA C:HEM501 3.4 24.7 1.0
CHB C:HEM501 3.5 27.2 1.0
CHD C:HEM501 3.5 27.9 1.0
ND1 C:HIS183 4.1 27.2 1.0
ND1 C:HIS82 4.1 26.7 1.0
CG C:HIS82 4.2 31.0 1.0
CG C:HIS183 4.2 25.1 1.0
C2A C:HEM501 4.2 26.0 1.0
C3B C:HEM501 4.2 27.4 1.0
C3A C:HEM501 4.3 24.4 1.0
C3D C:HEM501 4.3 26.4 1.0
C2C C:HEM501 4.3 26.1 1.0
C2B C:HEM501 4.3 25.7 1.0
C2D C:HEM501 4.3 27.1 1.0
C3C C:HEM501 4.3 26.9 1.0
CA C:GLY131 4.7 30.8 1.0

Iron binding site 2 out of 5 in 1kb9

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:28.4
occ:1.00
 FE C:HEM502 0.0 28.4 1.0
NE2 C:HIS96 2.0 27.3 1.0
ND C:HEM502 2.0 30.4 1.0
NE2 C:HIS197 2.0 28.6 1.0
NC C:HEM502 2.0 31.0 1.0
NA C:HEM502 2.0 29.8 1.0
NB C:HEM502 2.0 30.9 1.0
CE1 C:HIS197 3.0 27.6 1.0
CE1 C:HIS96 3.0 27.6 1.0
C1D C:HEM502 3.0 29.6 1.0
C4D C:HEM502 3.0 31.1 1.0
C4C C:HEM502 3.0 29.1 1.0
CD2 C:HIS96 3.0 26.9 1.0
C4A C:HEM502 3.1 28.0 1.0
C1A C:HEM502 3.1 29.5 1.0
C1B C:HEM502 3.1 28.7 1.0
C1C C:HEM502 3.1 31.6 1.0
C4B C:HEM502 3.1 31.3 1.0
CD2 C:HIS197 3.1 26.1 1.0
CHD C:HEM502 3.4 30.9 1.0
CHA C:HEM502 3.4 29.7 1.0
CHB C:HEM502 3.4 26.4 1.0
CHC C:HEM502 3.5 30.5 1.0
ND1 C:HIS96 4.1 26.4 1.0
ND1 C:HIS197 4.1 27.1 1.0
CG C:HIS96 4.2 26.4 1.0
CG C:HIS197 4.2 29.8 1.0
C2D C:HEM502 4.2 30.3 1.0
C3D C:HEM502 4.3 32.3 1.0
C3C C:HEM502 4.3 30.8 1.0
C2A C:HEM502 4.3 28.9 1.0
C2C C:HEM502 4.3 31.4 1.0
C3A C:HEM502 4.3 29.2 1.0
C2B C:HEM502 4.3 28.8 1.0
C3B C:HEM502 4.3 29.7 1.0
O C:HOH522 4.8 36.0 1.0

Iron binding site 3 out of 5 in 1kb9

Go back to Iron Binding Sites List in 1kb9
Iron binding site 3 out of 5 in the Yeast Cytochrome BC1 Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe503

b:47.7
occ:1.00
 FE D:HEM503 0.0 47.7 1.0
NE2 D:HIS105 2.0 50.4 1.0
ND D:HEM503 2.0 46.5 1.0
NC D:HEM503 2.0 50.8 1.0
NB D:HEM503 2.0 48.2 1.0
NA D:HEM503 2.0 47.5 1.0
SD D:MET225 2.1 52.9 1.0
CE1 D:HIS105 2.9 53.2 1.0
CD2 D:HIS105 3.0 53.1 1.0
C1D D:HEM503 3.0 47.7 1.0
C4D D:HEM503 3.0 46.8 1.0
C4C D:HEM503 3.0 50.2 1.0
C4B D:HEM503 3.0 47.5 1.0
C1C D:HEM503 3.0 48.7 1.0
C1B D:HEM503 3.1 46.6 1.0
C1A D:HEM503 3.1 45.8 1.0
C4A D:HEM503 3.1 44.6 1.0
CHD D:HEM503 3.4 49.4 1.0
CHA D:HEM503 3.4 47.3 1.0
CHC D:HEM503 3.4 46.9 1.0
CHB D:HEM503 3.4 44.8 1.0
CE D:MET225 3.5 49.5 1.0
CG D:MET225 3.6 50.7 1.0
ND1 D:HIS105 4.1 53.6 1.0
CG D:HIS105 4.1 53.2 1.0
CB D:MET225 4.2 52.8 1.0
C2D D:HEM503 4.3 47.7 1.0
C3D D:HEM503 4.3 47.1 1.0
C3C D:HEM503 4.3 51.5 1.0
C2C D:HEM503 4.3 50.1 1.0
C2B D:HEM503 4.3 46.0 1.0
C3B D:HEM503 4.3 48.0 1.0
C2A D:HEM503 4.3 44.0 1.0
C3A D:HEM503 4.3 44.2 1.0

Iron binding site 4 out of 5 in 1kb9

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe504

b:40.6
occ:1.00
 FE1 E:FES504 0.0 40.6 1.0
S1 E:FES504 2.1 35.9 1.0
S2 E:FES504 2.2 37.4 1.0
SG E:CYS178 2.2 40.2 1.0
SG E:CYS159 2.2 38.4 1.0
FE2 E:FES504 2.9 37.6 1.0
CB E:CYS178 3.1 41.1 1.0
CB E:CYS159 3.1 38.1 1.0
CB E:HIS161 4.1 36.2 1.0
CB E:CYS180 4.4 36.9 1.0
CB E:SER183 4.4 39.4 1.0
CB E:CYS164 4.5 35.8 1.0
CA E:CYS178 4.5 39.8 1.0
OG E:SER183 4.5 39.2 1.0
ND1 E:HIS161 4.5 34.1 1.0
CA E:CYS159 4.5 38.0 1.0
N E:HIS181 4.6 40.8 1.0
ND1 E:HIS181 4.7 35.4 1.0
N E:LEU162 4.7 35.2 1.0
N E:CYS164 4.8 34.1 1.0
CG E:HIS161 4.8 33.2 1.0
O E:CYS178 4.8 39.5 1.0
C E:CYS178 4.8 39.6 1.0
N E:HIS161 5.0 36.1 1.0

Iron binding site 5 out of 5 in 1kb9

Go back to Iron Binding Sites List in 1kb9
Iron binding site 5 out of 5 in the Yeast Cytochrome BC1 Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe504

b:37.6
occ:1.00
 FE2 E:FES504 0.0 37.6 1.0
ND1 E:HIS161 2.1 34.1 1.0
ND1 E:HIS181 2.1 35.4 1.0
S2 E:FES504 2.2 37.4 1.0
S1 E:FES504 2.2 35.9 1.0
FE1 E:FES504 2.9 40.6 1.0
CG E:HIS181 3.0 36.6 1.0
CG E:HIS161 3.1 33.2 1.0
CE1 E:HIS161 3.1 31.8 1.0
CE1 E:HIS181 3.2 29.7 1.0
CB E:HIS181 3.2 38.2 1.0
CB E:HIS161 3.3 36.2 1.0
N E:HIS181 3.8 40.8 1.0
N E:LEU162 4.0 35.2 1.0
CA E:HIS181 4.1 40.3 1.0
CB E:CYS180 4.1 36.9 1.0
CD2 E:HIS181 4.2 36.6 1.0
CD2 E:HIS161 4.2 34.9 1.0
NE2 E:HIS161 4.2 35.7 1.0
NE2 E:HIS181 4.3 35.5 1.0
CB E:LEU162 4.3 30.5 1.0
C E:CYS180 4.4 39.6 1.0
SG E:CYS159 4.5 38.4 1.0
CG E:LEU162 4.5 29.6 1.0
CG E:PRO195 4.6 41.5 1.0
CA E:HIS161 4.6 36.3 1.0
SG E:CYS178 4.6 40.2 1.0
CA E:LEU162 4.7 34.9 1.0
C E:HIS161 4.7 36.0 1.0
CD1 E:LEU162 4.7 25.1 1.0
CA E:CYS180 4.8 38.7 1.0
C E:HIS181 4.9 40.7 1.0

Reference:

C.Lange, J.H.Nett, B.L.Trumpower, C.Hunte. Specific Roles of Protein-Phospholipid Interactions in the Yeast Cytochrome BC1 Complex Structure Embo J. V. 20 6591 2001.
ISSN: ISSN 0261-4189
PubMed: 11726495
DOI: 10.1093/EMBOJ/20.23.6591
Page generated: Sat Aug 3 09:07:44 2024

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