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Iron in PDB 1ezv: Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment

Enzymatic activity of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment

All present enzymatic activity of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment:
1.10.2.2;

Protein crystallography data

The structure of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment, PDB code: 1ezv was solved by C.Hunte, J.Koepke, C.Lange, T.Rossmanith, H.Michel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 214.470, 163.920, 147.270, 90.00, 117.50, 90.00
R / Rfree (%) 22.2 / 25.4

Iron Binding Sites:

The binding sites of Iron atom in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment (pdb code 1ezv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment, PDB code: 1ezv:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1ezv

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Iron binding site 1 out of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:28.3
occ:1.00
FE C:HEM401 0.0 28.3 1.0
NE2 C:HIS82 2.0 26.6 1.0
NA C:HEM401 2.0 26.2 1.0
NE2 C:HIS183 2.0 27.2 1.0
ND C:HEM401 2.0 28.9 1.0
NB C:HEM401 2.0 25.9 1.0
NC C:HEM401 2.0 27.1 1.0
CE1 C:HIS183 2.9 24.3 1.0
CE1 C:HIS82 2.9 25.6 1.0
C1A C:HEM401 3.0 29.4 1.0
C4D C:HEM401 3.0 29.6 1.0
C4B C:HEM401 3.0 25.6 1.0
C4A C:HEM401 3.0 28.1 1.0
C1C C:HEM401 3.1 28.8 1.0
CD2 C:HIS82 3.1 26.7 1.0
C1D C:HEM401 3.1 29.8 1.0
C1B C:HEM401 3.1 26.1 1.0
C4C C:HEM401 3.1 27.4 1.0
CD2 C:HIS183 3.1 26.3 1.0
CHA C:HEM401 3.4 26.0 1.0
CHC C:HEM401 3.4 27.5 1.0
CHB C:HEM401 3.5 27.3 1.0
CHD C:HEM401 3.5 28.8 1.0
ND1 C:HIS82 4.1 26.7 1.0
ND1 C:HIS183 4.1 27.3 1.0
CG C:HIS82 4.2 31.0 1.0
CG C:HIS183 4.2 25.2 1.0
C2A C:HEM401 4.2 26.0 1.0
C3A C:HEM401 4.3 24.4 1.0
C3D C:HEM401 4.3 28.3 1.0
C3B C:HEM401 4.3 28.5 1.0
C2C C:HEM401 4.3 27.1 1.0
C2D C:HEM401 4.3 29.1 1.0
C2B C:HEM401 4.3 26.6 1.0
C3C C:HEM401 4.3 27.9 1.0
CA C:GLY131 4.7 31.2 1.0

Iron binding site 2 out of 5 in 1ezv

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Iron binding site 2 out of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:28.7
occ:1.00
FE C:HEM402 0.0 28.7 1.0
ND C:HEM402 2.0 31.0 1.0
NE2 C:HIS96 2.0 27.8 1.0
NE2 C:HIS197 2.0 28.3 1.0
NA C:HEM402 2.0 29.8 1.0
NC C:HEM402 2.0 31.4 1.0
NB C:HEM402 2.1 31.4 1.0
CE1 C:HIS197 2.9 28.4 1.0
CE1 C:HIS96 3.0 28.0 1.0
C1D C:HEM402 3.0 29.8 1.0
CD2 C:HIS96 3.0 27.6 1.0
C4D C:HEM402 3.0 31.9 1.0
C4C C:HEM402 3.0 29.8 1.0
C1A C:HEM402 3.1 30.1 1.0
C4A C:HEM402 3.1 28.7 1.0
CD2 C:HIS197 3.1 26.7 1.0
C1B C:HEM402 3.1 29.6 1.0
C1C C:HEM402 3.1 32.5 1.0
C4B C:HEM402 3.1 32.0 1.0
CHD C:HEM402 3.4 31.5 1.0
CHA C:HEM402 3.4 30.2 1.0
CHB C:HEM402 3.4 27.2 1.0
CHC C:HEM402 3.5 29.9 1.0
ND1 C:HIS197 4.1 27.1 1.0
ND1 C:HIS96 4.1 25.1 1.0
CG C:HIS96 4.2 26.7 1.0
CG C:HIS197 4.2 29.7 1.0
C2D C:HEM402 4.2 31.6 1.0
C3D C:HEM402 4.2 33.1 1.0
C2A C:HEM402 4.3 28.8 1.0
C3C C:HEM402 4.3 31.6 1.0
C3A C:HEM402 4.3 29.8 1.0
C2C C:HEM402 4.3 32.1 1.0
C2B C:HEM402 4.3 30.7 1.0
C3B C:HEM402 4.3 31.2 1.0
O C:HOH515 4.8 36.8 1.0

Iron binding site 3 out of 5 in 1ezv

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Iron binding site 3 out of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe3

b:49.0
occ:1.00
FE D:HEM3 0.0 49.0 1.0
NE2 D:HIS105 2.0 51.3 1.0
ND D:HEM3 2.0 46.6 1.0
NB D:HEM3 2.0 48.1 1.0
NC D:HEM3 2.0 51.1 1.0
NA D:HEM3 2.0 47.6 1.0
SD D:MET225 2.2 53.5 1.0
CE1 D:HIS105 3.0 53.9 1.0
CD2 D:HIS105 3.0 54.2 1.0
C1D D:HEM3 3.0 48.5 1.0
C4D D:HEM3 3.0 47.7 1.0
C4C D:HEM3 3.0 50.2 1.0
C1B D:HEM3 3.1 46.7 1.0
C4B D:HEM3 3.1 47.3 1.0
C1C D:HEM3 3.1 48.1 1.0
C1A D:HEM3 3.1 46.5 1.0
C4A D:HEM3 3.1 44.6 1.0
CHD D:HEM3 3.4 49.3 1.0
CHA D:HEM3 3.4 48.1 1.0
CHC D:HEM3 3.4 46.7 1.0
CHB D:HEM3 3.4 44.7 1.0
CE D:MET225 3.5 49.9 1.0
CG D:MET225 3.6 51.4 1.0
ND1 D:HIS105 4.1 54.8 1.0
CG D:HIS105 4.1 54.2 1.0
CB D:MET225 4.2 53.4 1.0
C2D D:HEM3 4.2 48.2 1.0
C3D D:HEM3 4.2 47.7 1.0
C3C D:HEM3 4.3 51.4 1.0
C2B D:HEM3 4.3 46.2 1.0
C2C D:HEM3 4.3 50.1 1.0
C3B D:HEM3 4.3 47.9 1.0
C2A D:HEM3 4.3 45.1 1.0
C3A D:HEM3 4.3 45.1 1.0

Iron binding site 4 out of 5 in 1ezv

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Iron binding site 4 out of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe4

b:40.6
occ:1.00
FE1 E:FES4 0.0 40.6 1.0
S1 E:FES4 2.1 36.8 1.0
S2 E:FES4 2.2 37.8 1.0
SG E:CYS178 2.2 41.3 1.0
SG E:CYS159 2.2 38.5 1.0
FE2 E:FES4 2.9 38.0 1.0
CB E:CYS178 3.1 41.5 1.0
CB E:CYS159 3.1 38.3 1.0
CB E:HIS161 4.1 35.0 1.0
CB E:CYS180 4.4 36.6 1.0
CB E:SER183 4.5 39.2 1.0
CB E:CYS164 4.5 36.6 1.0
OG E:SER183 4.5 39.0 1.0
ND1 E:HIS161 4.5 33.5 1.0
CA E:CYS178 4.5 40.3 1.0
N E:HIS181 4.5 41.6 1.0
CA E:CYS159 4.6 38.1 1.0
ND1 E:HIS181 4.7 36.1 1.0
N E:LEU162 4.8 34.4 1.0
N E:CYS164 4.8 34.1 1.0
CG E:HIS161 4.8 32.5 1.0
O E:CYS178 4.8 40.0 1.0
C E:CYS178 4.8 40.1 1.0
C E:CYS159 5.0 39.8 1.0

Iron binding site 5 out of 5 in 1ezv

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Iron binding site 5 out of 5 in the Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of the Yeast Cytochrome BC1 Complex Co- Crystallized with An Antibody Fv-Fragment within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe4

b:38.0
occ:1.00
FE2 E:FES4 0.0 38.0 1.0
ND1 E:HIS161 2.1 33.5 1.0
ND1 E:HIS181 2.1 36.1 1.0
S2 E:FES4 2.2 37.8 1.0
S1 E:FES4 2.2 36.8 1.0
FE1 E:FES4 2.9 40.6 1.0
CG E:HIS161 3.0 32.5 1.0
CG E:HIS181 3.1 38.1 1.0
CE1 E:HIS161 3.1 30.3 1.0
CE1 E:HIS181 3.1 30.7 1.0
CB E:HIS161 3.3 35.0 1.0
CB E:HIS181 3.3 38.5 1.0
N E:HIS181 3.7 41.6 1.0
N E:LEU162 4.0 34.4 1.0
CA E:HIS181 4.1 41.0 1.0
CB E:CYS180 4.2 36.6 1.0
CD2 E:HIS161 4.2 33.9 1.0
CD2 E:HIS181 4.2 37.6 1.0
NE2 E:HIS161 4.3 35.1 1.0
NE2 E:HIS181 4.3 35.8 1.0
CB E:LEU162 4.3 30.0 1.0
C E:CYS180 4.4 40.4 1.0
SG E:CYS159 4.5 38.5 1.0
CG E:LEU162 4.5 30.3 1.0
CA E:HIS161 4.6 35.5 1.0
SG E:CYS178 4.6 41.3 1.0
CG E:PRO195 4.7 40.8 1.0
CD1 E:LEU162 4.7 25.9 1.0
CA E:LEU162 4.7 34.1 1.0
C E:HIS161 4.7 35.2 1.0
C E:HIS181 4.8 41.2 1.0
CA E:CYS180 4.9 39.4 1.0

Reference:

C.Hunte, J.Koepke, C.Lange, T.Rossmanith, H.Michel. Structure at 2.3 A Resolution of the Cytochrome Bc(1) Complex From the Yeast Saccharomyces Cerevisiae Co-Crystallized with An Antibody Fv Fragment. Structure Fold.Des. V. 8 669 2000.
ISSN: ISSN 0969-2126
PubMed: 10873857
DOI: 10.1016/S0969-2126(00)00152-0
Page generated: Sun Dec 13 14:13:03 2020

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