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Iron in PDB 5luf: Cryo-Em of Bovine Respirasome

Enzymatic activity of Cryo-Em of Bovine Respirasome

All present enzymatic activity of Cryo-Em of Bovine Respirasome:
1.10.2.2; 1.9.3.1;

Other elements in 5luf:

The structure of Cryo-Em of Bovine Respirasome also contains other interesting chemical elements:

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

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 38;

Binding sites:

The binding sites of Iron atom in the Cryo-Em of Bovine Respirasome (pdb code 5luf). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 38 binding sites of Iron where determined in the Cryo-Em of Bovine Respirasome, PDB code: 5luf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 38 in 5luf

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Iron binding site 1 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Fe401

b:3.5
occ:1.00
FE b:HEM401 0.0 3.5 1.0
NA b:HEM401 2.0 4.2 1.0
NC b:HEM401 2.0 6.7 1.0
ND b:HEM401 2.0 5.9 1.0
NB b:HEM401 2.0 3.5 1.0
NE2 b:HIS83 2.1 22.2 1.0
NE2 b:HIS182 2.1 7.0 1.0
CE1 b:HIS83 2.6 30.3 1.0
CE1 b:HIS182 2.8 2.2 1.0
C1A b:HEM401 3.0 11.5 1.0
C1C b:HEM401 3.0 2.2 1.0
C4A b:HEM401 3.0 4.8 1.0
C4C b:HEM401 3.0 6.2 1.0
C4D b:HEM401 3.1 6.3 1.0
C4B b:HEM401 3.1 2.4 1.0
C1D b:HEM401 3.1 5.0 1.0
C1B b:HEM401 3.1 5.3 1.0
CD2 b:HIS182 3.3 5.4 1.0
CD2 b:HIS83 3.3 26.9 1.0
CHA b:HEM401 3.4 10.7 1.0
CHD b:HEM401 3.4 4.4 1.0
CHB b:HEM401 3.4 3.2 1.0
CHC b:HEM401 3.5 2.2 1.0
ND1 b:HIS83 3.9 28.5 1.0
ND1 b:HIS182 4.0 7.6 1.0
C3A b:HEM401 4.2 6.0 1.0
C2C b:HEM401 4.2 2.2 1.0
CG b:HIS83 4.2 24.3 1.0
C2A b:HEM401 4.2 7.4 1.0
C3C b:HEM401 4.3 3.5 1.0
C3B b:HEM401 4.3 5.6 1.0
CG b:HIS182 4.3 2.2 1.0
C3D b:HEM401 4.3 8.5 1.0
C2B b:HEM401 4.3 2.2 1.0
C2D b:HEM401 4.3 2.2 1.0
CA b:GLY48 5.0 6.4 1.0

Iron binding site 2 out of 38 in 5luf

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Iron binding site 2 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Fe402

b:2.6
occ:1.00
FE b:HEM402 0.0 2.6 1.0
NA b:HEM402 2.0 4.5 1.0
NB b:HEM402 2.0 6.7 1.0
ND b:HEM402 2.0 2.2 1.0
NC b:HEM402 2.0 2.2 1.0
NE2 b:HIS97 2.1 8.9 1.0
NE2 b:HIS196 2.2 2.2 1.0
CD2 b:HIS97 2.9 5.7 1.0
CE1 b:HIS196 2.9 7.3 1.0
C1A b:HEM402 3.0 6.7 1.0
C4A b:HEM402 3.0 2.2 1.0
C1D b:HEM402 3.0 5.9 1.0
C4D b:HEM402 3.0 6.0 1.0
C1B b:HEM402 3.0 4.8 1.0
C4B b:HEM402 3.1 5.5 1.0
C4C b:HEM402 3.1 6.0 1.0
C1C b:HEM402 3.1 6.2 1.0
CE1 b:HIS97 3.2 4.0 1.0
CHB b:HEM402 3.3 2.2 1.0
CD2 b:HIS196 3.3 6.5 1.0
CHA b:HEM402 3.4 7.2 1.0
CHC b:HEM402 3.4 5.7 1.0
CHD b:HEM402 3.4 5.8 1.0
ND1 b:HIS196 4.1 6.3 1.0
CG b:HIS97 4.1 2.2 1.0
C2A b:HEM402 4.2 6.3 1.0
C3A b:HEM402 4.2 5.7 1.0
ND1 b:HIS97 4.2 4.4 1.0
C2D b:HEM402 4.2 2.2 1.0
C3D b:HEM402 4.2 6.3 1.0
C2B b:HEM402 4.3 2.2 1.0
C3B b:HEM402 4.3 5.9 1.0
C3C b:HEM402 4.3 2.2 1.0
CG b:HIS196 4.4 6.7 1.0
C2C b:HEM402 4.4 2.2 1.0
CD1 b:LEU37 4.6 10.1 1.0

Iron binding site 3 out of 38 in 5luf

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Iron binding site 3 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Fe301

b:37.1
occ:1.00
FE d:HEC301 0.0 37.1 1.0
NE2 d:HIS41 1.9 43.2 1.0
NB d:HEC301 2.0 34.0 1.0
NC d:HEC301 2.0 37.2 1.0
ND d:HEC301 2.0 43.2 1.0
NA d:HEC301 2.0 40.5 1.0
SD d:MET160 2.4 23.4 1.0
CE1 d:HIS41 2.5 52.7 1.0
C1A d:HEC301 3.0 44.7 1.0
C1B d:HEC301 3.0 33.9 1.0
C4A d:HEC301 3.0 40.6 1.0
C4C d:HEC301 3.0 35.5 1.0
C1C d:HEC301 3.0 36.1 1.0
C4B d:HEC301 3.0 34.3 1.0
C4D d:HEC301 3.0 44.4 1.0
C1D d:HEC301 3.0 41.4 1.0
CD2 d:HIS41 3.1 52.3 1.0
CHC d:HEC301 3.4 36.2 1.0
CHD d:HEC301 3.4 36.0 1.0
CHB d:HEC301 3.4 36.3 1.0
CHA d:HEC301 3.4 45.1 1.0
CE d:MET160 3.6 36.2 1.0
ND1 d:HIS41 3.8 54.9 1.0
CG d:MET160 3.8 35.9 1.0
CG d:HIS41 4.1 48.6 1.0
C2A d:HEC301 4.2 44.0 1.0
C3A d:HEC301 4.2 41.4 1.0
C3C d:HEC301 4.2 35.5 1.0
C2C d:HEC301 4.2 36.1 1.0
C2B d:HEC301 4.2 34.4 1.0
C3B d:HEC301 4.3 35.5 1.0
C2D d:HEC301 4.3 44.4 1.0
C3D d:HEC301 4.3 45.5 1.0
CB d:MET160 4.9 38.1 1.0

Iron binding site 4 out of 38 in 5luf

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Iron binding site 4 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Fe401

b:2.5
occ:1.00
FE o:HEM401 0.0 2.5 1.0
NC o:HEM401 2.0 4.8 1.0
ND o:HEM401 2.0 7.8 1.0
NA o:HEM401 2.0 6.9 1.0
NE2 o:HIS182 2.0 7.8 1.0
NB o:HEM401 2.0 6.0 1.0
NE2 o:HIS83 2.1 8.6 1.0
CE1 o:HIS182 2.7 5.2 1.0
CE1 o:HIS83 2.8 16.0 1.0
C4C o:HEM401 3.0 2.2 1.0
C1D o:HEM401 3.0 8.2 1.0
C4A o:HEM401 3.0 6.0 1.0
C1C o:HEM401 3.1 2.2 1.0
C4D o:HEM401 3.1 5.1 1.0
C1A o:HEM401 3.1 8.0 1.0
C4B o:HEM401 3.1 6.6 1.0
C1B o:HEM401 3.1 11.1 1.0
CD2 o:HIS182 3.2 2.2 1.0
CHD o:HEM401 3.3 3.3 1.0
CD2 o:HIS83 3.4 10.9 1.0
CHB o:HEM401 3.4 10.3 1.0
CHA o:HEM401 3.4 6.6 1.0
CHC o:HEM401 3.4 3.9 1.0
ND1 o:HIS182 3.9 8.6 1.0
ND1 o:HIS83 4.0 13.0 1.0
CG o:HIS182 4.2 2.2 1.0
C3C o:HEM401 4.2 4.9 1.0
C2C o:HEM401 4.2 4.0 1.0
C2D o:HEM401 4.3 2.6 1.0
C3A o:HEM401 4.3 6.2 1.0
C3D o:HEM401 4.3 2.2 1.0
C3B o:HEM401 4.3 7.6 1.0
C2A o:HEM401 4.3 2.2 1.0
CG o:HIS83 4.4 7.4 1.0
C2B o:HEM401 4.4 2.2 1.0
CA o:GLY48 5.0 3.8 1.0

Iron binding site 5 out of 38 in 5luf

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Iron binding site 5 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
o:Fe402

b:3.2
occ:1.00
FE o:HEM402 0.0 3.2 1.0
ND o:HEM402 2.0 6.7 1.0
NB o:HEM402 2.0 2.2 1.0
NC o:HEM402 2.1 2.2 1.0
NE2 o:HIS97 2.1 5.8 1.0
NA o:HEM402 2.1 2.2 1.0
NE2 o:HIS196 2.1 4.7 1.0
CD2 o:HIS97 2.8 9.1 1.0
CE1 o:HIS196 3.0 6.6 1.0
C1D o:HEM402 3.0 9.5 1.0
C4B o:HEM402 3.0 5.2 1.0
C4D o:HEM402 3.0 5.9 1.0
C4A o:HEM402 3.0 6.4 1.0
C4C o:HEM402 3.1 6.9 1.0
C1B o:HEM402 3.1 5.0 1.0
C1C o:HEM402 3.1 6.7 1.0
C1A o:HEM402 3.1 2.2 1.0
CE1 o:HIS97 3.2 8.4 1.0
CD2 o:HIS196 3.3 3.4 1.0
CHB o:HEM402 3.3 3.9 1.0
CHD o:HEM402 3.4 9.2 1.0
CHA o:HEM402 3.4 6.1 1.0
CHC o:HEM402 3.4 2.2 1.0
CG o:HIS97 4.1 2.2 1.0
ND1 o:HIS196 4.2 4.1 1.0
ND1 o:HIS97 4.2 5.4 1.0
C3A o:HEM402 4.2 5.8 1.0
C2D o:HEM402 4.2 7.8 1.0
C2B o:HEM402 4.3 2.2 1.0
C3D o:HEM402 4.3 7.0 1.0
C3C o:HEM402 4.3 5.8 1.0
C3B o:HEM402 4.3 5.1 1.0
C2A o:HEM402 4.3 4.1 1.0
C2C o:HEM402 4.3 5.5 1.0
CG o:HIS196 4.3 2.2 1.0
CD1 o:LEU37 4.6 13.1 1.0

Iron binding site 6 out of 38 in 5luf

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Iron binding site 6 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
p:Fe301

b:33.0
occ:1.00
FE p:HEC301 0.0 33.0 1.0
NE2 p:HIS41 2.0 38.7 1.0
NA p:HEC301 2.0 34.4 1.0
NB p:HEC301 2.0 31.5 1.0
NC p:HEC301 2.0 35.3 1.0
ND p:HEC301 2.0 37.0 1.0
SD p:MET160 2.4 46.5 1.0
CE1 p:HIS41 2.7 45.5 1.0
C4A p:HEC301 3.0 36.6 1.0
C1A p:HEC301 3.0 34.9 1.0
C1B p:HEC301 3.0 31.4 1.0
C4B p:HEC301 3.0 31.7 1.0
C4C p:HEC301 3.0 36.7 1.0
C1C p:HEC301 3.0 36.1 1.0
C4D p:HEC301 3.0 37.4 1.0
C1D p:HEC301 3.1 36.9 1.0
CD2 p:HIS41 3.1 42.8 1.0
CHB p:HEC301 3.4 34.0 1.0
CHA p:HEC301 3.4 35.4 1.0
CHC p:HEC301 3.4 33.7 1.0
CHD p:HEC301 3.4 37.6 1.0
CG p:MET160 3.7 43.3 1.0
CE p:MET160 3.8 40.0 1.0
ND1 p:HIS41 3.9 46.4 1.0
CG p:HIS41 4.1 40.8 1.0
C3A p:HEC301 4.2 37.8 1.0
C2A p:HEC301 4.2 36.9 1.0
C2B p:HEC301 4.2 33.0 1.0
C3B p:HEC301 4.2 31.8 1.0
C3C p:HEC301 4.2 37.2 1.0
C2C p:HEC301 4.3 36.6 1.0
C3D p:HEC301 4.3 38.5 1.0
C2D p:HEC301 4.3 38.1 1.0
CB p:MET160 4.9 37.8 1.0

Iron binding site 7 out of 38 in 5luf

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Iron binding site 7 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
q:Fe201

b:4.2
occ:1.00
FE1 q:FES201 0.0 4.2 1.0
SG q:CYS158 2.2 17.3 1.0
SG q:CYS139 2.3 26.5 1.0
S1 q:FES201 2.3 5.5 1.0
S2 q:FES201 2.3 5.7 1.0
FE2 q:FES201 2.7 7.0 1.0
CB q:CYS158 3.2 3.0 1.0
CB q:CYS139 3.4 20.6 1.0
CB q:HIS141 4.0 22.7 1.0
CB q:CYS160 4.1 32.4 1.0
O q:CYS144 4.2 12.9 1.0
ND1 q:HIS141 4.3 16.9 1.0
O q:CYS158 4.4 15.9 1.0
CA q:CYS158 4.6 13.8 1.0
ND1 q:HIS161 4.6 9.8 1.0
CG q:HIS141 4.7 26.2 1.0
N q:LEU142 4.7 15.6 1.0
N q:HIS161 4.7 14.7 1.0
C q:CYS158 4.7 12.9 1.0
N q:GLY143 4.8 21.9 1.0
CA q:CYS139 4.8 21.8 1.0
N q:CYS144 4.8 15.6 1.0
CB q:SER163 4.9 12.6 1.0
CA q:CYS160 4.9 21.1 1.0
SG q:CYS144 5.0 35.5 1.0
OG q:SER163 5.0 7.7 1.0

Iron binding site 8 out of 38 in 5luf

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Iron binding site 8 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
q:Fe201

b:7.0
occ:1.00
FE2 q:FES201 0.0 7.0 1.0
ND1 q:HIS161 2.1 9.8 1.0
ND1 q:HIS141 2.2 16.9 1.0
S1 q:FES201 2.2 5.5 1.0
S2 q:FES201 2.3 5.7 1.0
FE1 q:FES201 2.7 4.2 1.0
CG q:HIS161 3.0 10.6 1.0
CG q:HIS141 3.1 26.2 1.0
CB q:HIS161 3.1 7.1 1.0
CE1 q:HIS161 3.2 5.9 1.0
CE1 q:HIS141 3.2 12.5 1.0
CB q:HIS141 3.3 22.7 1.0
N q:HIS161 3.9 14.7 1.0
SG q:CYS158 4.1 17.3 1.0
CA q:HIS161 4.1 13.6 1.0
SG q:CYS139 4.1 26.5 1.0
N q:LEU142 4.2 15.6 1.0
CD2 q:HIS161 4.2 5.1 1.0
NE2 q:HIS161 4.2 6.1 1.0
CB q:CYS160 4.2 32.4 1.0
CD2 q:HIS141 4.3 20.0 1.0
NE2 q:HIS141 4.3 10.9 1.0
C q:CYS160 4.3 20.2 1.0
CB q:LEU142 4.7 26.5 1.0
O q:CYS160 4.7 23.6 1.0
CA q:HIS141 4.8 20.7 1.0
CA q:CYS160 4.9 21.1 1.0
OG q:SER163 4.9 7.7 1.0
CG q:LEU142 4.9 26.9 1.0
C q:HIS141 4.9 21.2 1.0
C q:HIS161 5.0 17.5 1.0
CA q:LEU142 5.0 19.8 1.0

Iron binding site 9 out of 38 in 5luf

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Iron binding site 9 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
x:Fe603

b:9.8
occ:1.00
FE x:HEA603 0.0 9.8 1.0
NE2 x:HIS61 1.8 7.0 1.0
NE2 x:HIS378 1.9 7.0 1.0
NB x:HEA603 1.9 13.1 1.0
NA x:HEA603 1.9 20.1 1.0
ND x:HEA603 2.0 9.7 1.0
NC x:HEA603 2.0 22.6 1.0
CE1 x:HIS378 2.6 7.0 1.0
CE1 x:HIS61 2.7 13.2 1.0
C1B x:HEA603 2.9 12.2 1.0
CD2 x:HIS61 2.9 9.3 1.0
C4A x:HEA603 3.0 15.2 1.0
C1D x:HEA603 3.0 14.3 1.0
C4C x:HEA603 3.0 17.6 1.0
C4B x:HEA603 3.0 19.0 1.0
C1A x:HEA603 3.1 10.3 1.0
C4D x:HEA603 3.1 15.1 1.0
C1C x:HEA603 3.1 17.1 1.0
CD2 x:HIS378 3.1 8.6 1.0
CHB x:HEA603 3.3 11.5 1.0
CHD x:HEA603 3.4 16.3 1.0
CHA x:HEA603 3.5 9.4 1.0
CHC x:HEA603 3.5 13.9 1.0
ND1 x:HIS378 3.9 11.0 1.0
ND1 x:HIS61 4.0 13.6 1.0
CG x:HIS61 4.1 8.7 1.0
C2B x:HEA603 4.2 16.0 1.0
C3A x:HEA603 4.2 13.5 1.0
CG x:HIS378 4.2 7.0 1.0
C2A x:HEA603 4.2 9.1 1.0
C2D x:HEA603 4.3 18.3 1.0
C3B x:HEA603 4.3 17.7 1.0
C3C x:HEA603 4.3 18.0 1.0
C3D x:HEA603 4.3 18.0 1.0
C2C x:HEA603 4.3 18.8 1.0

Iron binding site 10 out of 38 in 5luf

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Iron binding site 10 out of 38 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
x:Fe604

b:8.0
occ:1.00
FE x:HEA604 0.0 8.0 1.0
ND x:HEA604 1.9 7.6 1.0
NB x:HEA604 2.0 10.9 1.0
NC x:HEA604 2.0 16.3 1.0
NA x:HEA604 2.0 14.8 1.0
NE2 x:HIS376 2.1 7.0 1.0
C1D x:HEA604 3.0 11.3 1.0
C4D x:HEA604 3.0 14.8 1.0
CE1 x:HIS376 3.0 10.5 1.0
C1B x:HEA604 3.0 14.2 1.0
C4B x:HEA604 3.0 14.2 1.0
C4C x:HEA604 3.1 13.7 1.0
C4A x:HEA604 3.1 14.3 1.0
C1C x:HEA604 3.1 13.1 1.0
C1A x:HEA604 3.1 7.0 1.0
CD2 x:HIS376 3.2 9.2 1.0
CHD x:HEA604 3.4 12.9 1.0
CHB x:HEA604 3.4 17.8 1.0
CHA x:HEA604 3.4 8.6 1.0
CHC x:HEA604 3.4 10.2 1.0
C3D x:HEA604 4.2 13.9 1.0
C2D x:HEA604 4.2 12.4 1.0
C2B x:HEA604 4.3 11.5 1.0
ND1 x:HIS376 4.3 7.0 1.0
C3B x:HEA604 4.3 16.1 1.0
C3A x:HEA604 4.3 7.0 1.0
C3C x:HEA604 4.3 14.3 1.0
CG x:HIS376 4.3 7.0 1.0
C2C x:HEA604 4.3 15.4 1.0
C2A x:HEA604 4.4 7.0 1.0
CU x:CU601 4.7 15.3 1.0
CE1 x:HIS240 4.9 27.2 1.0

Reference:

J.S.Sousa, D.J.Mills, J.Vonck, W.Kuhlbrandt. Functional Asymmetry and Electron Flow in the Bovine Respirasome. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27830641
DOI: 10.7554/ELIFE.21290
Page generated: Sun Dec 13 16:07:41 2020

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