Iron in PDB 6ymx: CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae

Enzymatic activity of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae

All present enzymatic activity of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae:
1.9.3.1; 7.1.1.8;

Other elements in 6ymx:

The structure of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Copper (Cu) 3 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Iron atom in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae (pdb code 6ymx). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 12 binding sites of Iron where determined in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae, PDB code: 6ymx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 12 in 6ymx

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Iron binding site 1 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:0.4
occ:1.00
FE a:HEA602 0.0 0.4 1.0
ND a:HEA602 1.9 0.4 1.0
NB a:HEA602 2.0 0.4 1.0
NA a:HEA602 2.0 0.4 1.0
NC a:HEA602 2.0 0.4 1.0
NE2 a:HIS62 2.7 0.1 1.0
NE2 a:HIS378 2.8 0.3 1.0
C4D a:HEA602 2.9 0.4 1.0
CE1 a:HIS378 3.0 0.3 1.0
C1D a:HEA602 3.0 0.4 1.0
C1B a:HEA602 3.0 0.4 1.0
C1A a:HEA602 3.0 0.4 1.0
C4C a:HEA602 3.0 0.4 1.0
C4B a:HEA602 3.0 0.4 1.0
C4A a:HEA602 3.0 0.4 1.0
C1C a:HEA602 3.1 0.4 1.0
CHD a:HEA602 3.3 0.4 1.0
CHA a:HEA602 3.3 0.4 1.0
CHB a:HEA602 3.4 0.4 1.0
CHC a:HEA602 3.4 0.4 1.0
CE1 a:HIS62 3.5 0.1 1.0
CD2 a:HIS62 3.7 0.1 1.0
CD2 a:HIS378 4.0 0.3 1.0
ND1 a:HIS378 4.2 0.3 1.0
C3D a:HEA602 4.2 0.4 1.0
C2D a:HEA602 4.2 0.4 1.0
C2B a:HEA602 4.2 0.4 1.0
C2A a:HEA602 4.3 0.4 1.0
C3B a:HEA602 4.3 0.4 1.0
C3A a:HEA602 4.3 0.4 1.0
C3C a:HEA602 4.3 0.4 1.0
C2C a:HEA602 4.3 0.4 1.0
ND1 a:HIS62 4.7 0.1 1.0
CG a:HIS378 4.7 0.3 1.0
CG a:HIS62 4.8 0.1 1.0

Iron binding site 2 out of 12 in 6ymx

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Iron binding site 2 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


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Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe603

b:0.2
occ:1.00
FE a:HEA603 0.0 0.2 1.0
ND a:HEA603 1.9 0.2 1.0
NB a:HEA603 2.0 0.2 1.0
NA a:HEA603 2.0 0.2 1.0
NC a:HEA603 2.0 0.2 1.0
NE2 a:HIS376 2.8 0.0 1.0
C4D a:HEA603 2.9 0.2 1.0
C1D a:HEA603 3.0 0.2 1.0
C1B a:HEA603 3.0 0.2 1.0
C1A a:HEA603 3.0 0.2 1.0
C4B a:HEA603 3.0 0.2 1.0
C4C a:HEA603 3.0 0.2 1.0
C4A a:HEA603 3.1 0.2 1.0
C1C a:HEA603 3.1 0.2 1.0
CHD a:HEA603 3.3 0.2 1.0
CHA a:HEA603 3.3 0.2 1.0
CHB a:HEA603 3.4 0.2 1.0
CHC a:HEA603 3.4 0.2 1.0
CE1 a:HIS376 3.7 0.0 1.0
CD2 a:HIS376 3.7 0.0 1.0
CU a:CU601 4.0 0.3 1.0
C3D a:HEA603 4.2 0.2 1.0
C2D a:HEA603 4.2 0.2 1.0
C2B a:HEA603 4.2 0.2 1.0
C2A a:HEA603 4.3 0.2 1.0
C3A a:HEA603 4.3 0.2 1.0
C3B a:HEA603 4.3 0.2 1.0
C2C a:HEA603 4.3 0.2 1.0
C3C a:HEA603 4.3 0.2 1.0
ND1 a:HIS376 4.9 0.0 1.0
CG a:HIS376 4.9 0.0 1.0

Iron binding site 3 out of 12 in 6ymx

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Iron binding site 3 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:60.1
occ:1.00
FE C:HEM402 0.0 60.1 1.0
NB C:HEM402 1.9 60.1 1.0
NA C:HEM402 2.0 60.1 1.0
NC C:HEM402 2.0 60.1 1.0
ND C:HEM402 2.1 60.1 1.0
NE2 C:HIS183 2.7 57.3 1.0
NE2 C:HIS82 2.7 59.1 1.0
C1B C:HEM402 2.9 60.1 1.0
C4B C:HEM402 2.9 60.1 1.0
C4A C:HEM402 3.0 60.1 1.0
CE1 C:HIS82 3.0 59.1 1.0
CE1 C:HIS183 3.0 57.3 1.0
C1C C:HEM402 3.0 60.1 1.0
C4C C:HEM402 3.0 60.1 1.0
C1A C:HEM402 3.0 60.1 1.0
C1D C:HEM402 3.1 60.1 1.0
C4D C:HEM402 3.2 60.1 1.0
CHB C:HEM402 3.3 60.1 1.0
CHC C:HEM402 3.3 60.1 1.0
CHD C:HEM402 3.4 60.1 1.0
CHA C:HEM402 3.4 60.1 1.0
CD2 C:HIS82 3.9 59.1 1.0
CD2 C:HIS183 4.0 57.3 1.0
C2B C:HEM402 4.1 60.1 1.0
C3B C:HEM402 4.1 60.1 1.0
C3A C:HEM402 4.2 60.1 1.0
C2A C:HEM402 4.2 60.1 1.0
C3C C:HEM402 4.2 60.1 1.0
C2C C:HEM402 4.2 60.1 1.0
ND1 C:HIS82 4.2 59.1 1.0
ND1 C:HIS183 4.3 57.3 1.0
C2D C:HEM402 4.3 60.1 1.0
C3D C:HEM402 4.4 60.1 1.0
CG C:HIS82 4.7 59.1 1.0
CG C:HIS183 4.8 57.3 1.0

Iron binding site 4 out of 12 in 6ymx

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Iron binding site 4 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:58.4
occ:1.00
FE C:HEM403 0.0 58.4 1.0
NB C:HEM403 1.9 58.4 1.0
NC C:HEM403 2.0 58.4 1.0
NA C:HEM403 2.0 58.4 1.0
ND C:HEM403 2.0 58.4 1.0
NE2 C:HIS197 2.7 58.7 1.0
NE2 C:HIS96 2.7 59.1 1.0
C1B C:HEM403 2.9 58.4 1.0
C4A C:HEM403 2.9 58.4 1.0
C4C C:HEM403 3.0 58.4 1.0
C4B C:HEM403 3.0 58.4 1.0
C1C C:HEM403 3.0 58.4 1.0
C1D C:HEM403 3.0 58.4 1.0
C1A C:HEM403 3.0 58.4 1.0
C4D C:HEM403 3.1 58.4 1.0
CHB C:HEM403 3.3 58.4 1.0
CD2 C:HIS197 3.4 58.7 1.0
CHD C:HEM403 3.4 58.4 1.0
CHC C:HEM403 3.4 58.4 1.0
CD2 C:HIS96 3.4 59.1 1.0
CHA C:HEM403 3.5 58.4 1.0
CE1 C:HIS197 3.5 58.7 1.0
CE1 C:HIS96 3.7 59.1 1.0
C3A C:HEM403 4.2 58.4 1.0
C2B C:HEM403 4.2 58.4 1.0
C3B C:HEM403 4.2 58.4 1.0
C2A C:HEM403 4.2 58.4 1.0
C3C C:HEM403 4.2 58.4 1.0
C2C C:HEM403 4.2 58.4 1.0
C2D C:HEM403 4.2 58.4 1.0
C3D C:HEM403 4.3 58.4 1.0
CG C:HIS197 4.3 58.7 1.0
ND1 C:HIS197 4.4 58.7 1.0
CG C:HIS96 4.5 59.1 1.0
ND1 C:HIS96 4.6 59.1 1.0

Iron binding site 5 out of 12 in 6ymx

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Iron binding site 5 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:69.2
occ:1.00
FE D:HEM401 0.0 69.2 1.0
NA D:HEM401 1.9 69.2 1.0
ND D:HEM401 2.0 69.2 1.0
NB D:HEM401 2.0 69.2 1.0
NC D:HEM401 2.0 69.2 1.0
NE2 D:HIS105 2.7 64.6 1.0
C1A D:HEM401 2.9 69.2 1.0
C4D D:HEM401 3.0 69.2 1.0
SD D:MET225 3.0 71.2 1.0
C4A D:HEM401 3.0 69.2 1.0
CE1 D:HIS105 3.0 64.6 1.0
C4B D:HEM401 3.0 69.2 1.0
C1C D:HEM401 3.0 69.2 1.0
C1B D:HEM401 3.0 69.2 1.0
C1D D:HEM401 3.1 69.2 1.0
C4C D:HEM401 3.1 69.2 1.0
CHA D:HEM401 3.3 69.2 1.0
CHC D:HEM401 3.4 69.2 1.0
CHB D:HEM401 3.4 69.2 1.0
CHD D:HEM401 3.5 69.2 1.0
CE D:MET225 3.9 71.2 1.0
CD2 D:HIS105 3.9 64.6 1.0
CG D:MET225 3.9 71.2 1.0
CB D:MET225 4.1 71.2 1.0
C2A D:HEM401 4.2 69.2 1.0
C3A D:HEM401 4.2 69.2 1.0
C3D D:HEM401 4.2 69.2 1.0
ND1 D:HIS105 4.2 64.6 1.0
C2B D:HEM401 4.2 69.2 1.0
C3B D:HEM401 4.2 69.2 1.0
C2D D:HEM401 4.2 69.2 1.0
C2C D:HEM401 4.3 69.2 1.0
C3C D:HEM401 4.3 69.2 1.0
CG D:HIS105 4.7 64.6 1.0

Iron binding site 6 out of 12 in 6ymx

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Iron binding site 6 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:0.0
occ:1.00
FE1 E:FES302 0.0 0.0 1.0
S2 E:FES302 2.2 0.0 1.0
S1 E:FES302 2.2 0.0 1.0
FE2 E:FES302 3.1 0.0 1.0
CB E:CYS159 3.2 0.1 1.0
OH E:TYR185 3.3 0.5 1.0
SG E:CYS178 3.4 0.7 1.0
SG E:CYS159 3.6 0.1 1.0
CB E:CYS178 3.8 0.7 1.0
CB E:HIS161 4.1 1.0 1.0
OG E:SER183 4.1 0.9 1.0
CB E:SER183 4.3 0.9 1.0
CZ E:TYR185 4.3 0.5 1.0
CE2 E:TYR185 4.5 0.5 1.0
N E:HIS161 4.6 1.0 1.0
CA E:CYS159 4.6 0.1 1.0
N E:LEU162 4.8 0.8 1.0
CA E:HIS161 4.9 1.0 1.0
C E:CYS159 4.9 0.1 1.0
N E:THR160 5.0 0.4 1.0

Iron binding site 7 out of 12 in 6ymx

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Iron binding site 7 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe302

b:0.0
occ:1.00
FE2 E:FES302 0.0 0.0 1.0
S1 E:FES302 2.2 0.0 1.0
S2 E:FES302 2.2 0.0 1.0
CD1 E:LEU162 3.1 0.8 1.0
ND1 E:HIS181 3.1 0.3 1.0
FE1 E:FES302 3.1 0.0 1.0
CB E:HIS181 3.2 0.3 1.0
SG E:CYS178 3.4 0.7 1.0
CG E:HIS181 3.5 0.3 1.0
N E:HIS181 3.5 0.3 1.0
CB E:CYS180 3.6 0.0 1.0
CA E:HIS181 3.9 0.3 1.0
ND1 E:HIS161 4.0 1.0 1.0
C E:CYS180 4.1 0.0 1.0
CB E:HIS161 4.1 1.0 1.0
CE1 E:HIS181 4.2 0.3 1.0
CG E:LEU162 4.4 0.8 1.0
CA E:CYS180 4.4 0.0 1.0
CG E:HIS161 4.5 1.0 1.0
CB E:LEU162 4.6 0.8 1.0
N E:LEU162 4.7 0.8 1.0
CD2 E:HIS181 4.7 0.3 1.0
SG E:CYS164 4.8 0.6 1.0
C E:HIS181 4.8 0.3 1.0
CB E:CYS164 4.9 0.6 1.0
CB E:CYS178 4.9 0.7 1.0
OG E:SER183 4.9 0.9 1.0
O E:CYS180 4.9 0.0 1.0
N E:CYS180 5.0 0.0 1.0
SG E:CYS180 5.0 0.0 1.0

Iron binding site 8 out of 12 in 6ymx

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Iron binding site 8 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe401

b:57.8
occ:1.00
FE N:HEM401 0.0 57.8 1.0
NA N:HEM401 1.9 57.8 1.0
NB N:HEM401 2.0 57.8 1.0
ND N:HEM401 2.0 57.8 1.0
NC N:HEM401 2.1 57.8 1.0
NE2 N:HIS82 2.7 57.5 1.0
NE2 N:HIS183 2.7 54.3 1.0
C1A N:HEM401 2.9 57.8 1.0
C4A N:HEM401 3.0 57.8 1.0
CE1 N:HIS183 3.0 54.3 1.0
C4B N:HEM401 3.0 57.8 1.0
C1B N:HEM401 3.0 57.8 1.0
C4D N:HEM401 3.0 57.8 1.0
C1C N:HEM401 3.0 57.8 1.0
CD2 N:HIS82 3.1 57.5 1.0
C1D N:HEM401 3.1 57.8 1.0
C4C N:HEM401 3.1 57.8 1.0
CHA N:HEM401 3.3 57.8 1.0
CHB N:HEM401 3.4 57.8 1.0
CHC N:HEM401 3.4 57.8 1.0
CHD N:HEM401 3.5 57.8 1.0
CE1 N:HIS82 3.9 57.5 1.0
CD2 N:HIS183 4.0 54.3 1.0
C2A N:HEM401 4.1 57.8 1.0
C3A N:HEM401 4.1 57.8 1.0
C3B N:HEM401 4.2 57.8 1.0
C2B N:HEM401 4.2 57.8 1.0
C3D N:HEM401 4.3 57.8 1.0
C2C N:HEM401 4.3 57.8 1.0
ND1 N:HIS183 4.3 54.3 1.0
C2D N:HEM401 4.3 57.8 1.0
C3C N:HEM401 4.3 57.8 1.0
CG N:HIS82 4.4 57.5 1.0
ND1 N:HIS82 4.8 57.5 1.0
CA N:GLY131 4.8 59.4 1.0
CG N:HIS183 4.8 54.3 1.0

Iron binding site 9 out of 12 in 6ymx

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Iron binding site 9 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe402

b:57.0
occ:1.00
FE N:HEM402 0.0 57.0 1.0
NB N:HEM402 1.9 57.0 1.0
NA N:HEM402 2.0 57.0 1.0
NC N:HEM402 2.0 57.0 1.0
ND N:HEM402 2.0 57.0 1.0
NE2 N:HIS197 2.7 57.1 1.0
NE2 N:HIS96 2.7 56.8 1.0
C1B N:HEM402 2.9 57.0 1.0
C4B N:HEM402 3.0 57.0 1.0
C4A N:HEM402 3.0 57.0 1.0
C1C N:HEM402 3.0 57.0 1.0
C1A N:HEM402 3.0 57.0 1.0
C4D N:HEM402 3.0 57.0 1.0
C4C N:HEM402 3.0 57.0 1.0
C1D N:HEM402 3.1 57.0 1.0
CD2 N:HIS197 3.3 57.1 1.0
CHB N:HEM402 3.3 57.0 1.0
CD2 N:HIS96 3.3 56.8 1.0
CHC N:HEM402 3.3 57.0 1.0
CHA N:HEM402 3.4 57.0 1.0
CHD N:HEM402 3.4 57.0 1.0
CE1 N:HIS96 3.6 56.8 1.0
CE1 N:HIS197 3.9 57.1 1.0
C2B N:HEM402 4.2 57.0 1.0
C3A N:HEM402 4.2 57.0 1.0
C3B N:HEM402 4.2 57.0 1.0
C2A N:HEM402 4.2 57.0 1.0
C2C N:HEM402 4.2 57.0 1.0
C3C N:HEM402 4.2 57.0 1.0
C3D N:HEM402 4.2 57.0 1.0
C2D N:HEM402 4.3 57.0 1.0
CG N:HIS96 4.3 56.8 1.0
ND1 N:HIS96 4.4 56.8 1.0
CG N:HIS197 4.6 57.1 1.0
ND1 N:HIS197 4.8 57.1 1.0

Iron binding site 10 out of 12 in 6ymx

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Iron binding site 10 out of 12 in the CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of CIII2/Civ Respiratory Supercomplex From Saccharomyces Cerevisiae within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe402

b:66.5
occ:1.00
FE O:HEM402 0.0 66.5 1.0
NC O:HEM402 2.0 66.5 1.0
ND O:HEM402 2.0 66.5 1.0
NA O:HEM402 2.0 66.5 1.0
NB O:HEM402 2.0 66.5 1.0
NE2 O:HIS105 2.7 62.9 1.0
SD O:MET225 3.0 70.9 1.0
C1C O:HEM402 3.0 66.5 1.0
C1B O:HEM402 3.0 66.5 1.0
C1D O:HEM402 3.0 66.5 1.0
C4A O:HEM402 3.0 66.5 1.0
C4C O:HEM402 3.0 66.5 1.0
C4B O:HEM402 3.0 66.5 1.0
C4D O:HEM402 3.0 66.5 1.0
C1A O:HEM402 3.0 66.5 1.0
CHC O:HEM402 3.4 66.5 1.0
CHD O:HEM402 3.4 66.5 1.0
CD2 O:HIS105 3.4 62.9 1.0
CHB O:HEM402 3.4 66.5 1.0
CHA O:HEM402 3.4 66.5 1.0
CE O:MET225 3.5 70.9 1.0
CE1 O:HIS105 3.8 62.9 1.0
CG O:MET225 3.8 70.9 1.0
CB O:MET225 4.0 70.9 1.0
C2C O:HEM402 4.2 66.5 1.0
C2B O:HEM402 4.2 66.5 1.0
C3A O:HEM402 4.2 66.5 1.0
C3C O:HEM402 4.2 66.5 1.0
C2D O:HEM402 4.2 66.5 1.0
C3D O:HEM402 4.2 66.5 1.0
C2A O:HEM402 4.2 66.5 1.0
C3B O:HEM402 4.2 66.5 1.0
CG O:HIS105 4.6 62.9 1.0
ND1 O:HIS105 4.8 62.9 1.0

Reference:

J.Berndtsson, A.Aufschnaiter, S.Rathore, L.Marin-Buera, H.Dawitz, J.Diessl, V.Kohler, A.Barrientos, S.Buttner, F.Fontanesi, M.Ott. Mitochondrial Respiratory Supercomplex Formation Improves Bioenergetics and Confers A Selectable Fitness Advantage To Be Published.
Page generated: Sun Dec 13 17:38:07 2020

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