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Iron in PDB 29yb: Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position

Enzymatic activity of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position

All present enzymatic activity of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position:
7.1.1.8;

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position (pdb code 29yb). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position, PDB code: 29yb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 29yb

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Iron binding site 1 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:121.1
occ:1.00
 FE1 A:FES501 0.0 121.1 1.0
S2 A:FES501 2.2 103.4 1.0
S1 A:FES501 2.2 125.2 1.0
SG A:CYS133 2.3 106.8 1.0
SG A:CYS153 2.3 113.7 1.0
FE2 A:FES501 2.7 124.2 1.0
CB A:CYS133 2.8 100.0 1.0
CB A:CYS153 3.6 107.7 1.0
CB A:HIS135 3.8 99.2 1.0
CB A:CYS138 4.1 93.5 1.0
ND1 A:HIS135 4.3 100.2 1.0
CA A:CYS133 4.3 96.4 1.0
N A:CYS138 4.3 89.6 1.0
N A:LEU136 4.4 95.2 1.0
OG A:SER158 4.5 117.0 1.0
ND1 A:HIS156 4.5 104.1 1.0
CG A:HIS135 4.5 99.9 1.0
CB A:CYS155 4.6 113.6 1.0
N A:HIS135 4.6 94.8 1.0
CA A:HIS135 4.7 93.4 1.0
CA A:CYS138 4.7 89.3 1.0
C A:CYS133 4.7 93.9 1.0
SG A:CYS138 4.8 110.9 1.0
N A:GLY137 4.8 88.7 1.0
CB A:SER158 4.9 117.9 1.0
CA A:CYS153 4.9 108.7 1.0
N A:HIS156 5.0 111.0 1.0
O A:CYS138 5.0 94.9 1.0

Iron binding site 2 out of 10 in 29yb

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Iron binding site 2 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:124.2
occ:1.00
 FE2 A:FES501 0.0 124.2 1.0
ND1 A:HIS135 2.1 100.2 1.0
ND1 A:HIS156 2.1 104.1 1.0
S2 A:FES501 2.2 103.4 1.0
S1 A:FES501 2.2 125.2 1.0
FE1 A:FES501 2.7 121.1 1.0
CG A:HIS156 2.9 103.6 1.0
CG A:HIS135 3.1 99.9 1.0
CE1 A:HIS135 3.1 99.0 1.0
CB A:HIS156 3.2 108.1 1.0
CE1 A:HIS156 3.2 104.6 1.0
CB A:HIS135 3.4 99.2 1.0
N A:HIS156 3.8 111.0 1.0
CA A:HIS156 4.0 107.8 1.0
SG A:CYS153 4.1 113.7 1.0
CD2 A:HIS156 4.1 102.0 1.0
CB A:CYS155 4.1 113.6 1.0
NE2 A:HIS156 4.2 101.6 1.0
NE2 A:HIS135 4.2 96.0 1.0
CD2 A:HIS135 4.2 96.3 1.0
N A:LEU136 4.3 95.2 1.0
SG A:CYS133 4.4 106.8 1.0
C A:CYS155 4.4 108.3 1.0
OG A:SER158 4.5 117.0 1.0
CA A:HIS135 4.7 93.4 1.0
CB A:LEU136 4.7 84.4 1.0
C A:HIS156 4.8 110.6 1.0
C A:HIS135 4.8 94.2 1.0
CA A:CYS155 4.9 105.8 1.0
CG A:LEU136 4.9 89.7 1.0
CG A:PRO170 4.9 114.5 1.0

Iron binding site 3 out of 10 in 29yb

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Iron binding site 3 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:95.5
occ:1.00
 FE B:HEM501 0.0 95.5 1.0
ND B:HEM501 2.0 70.1 1.0
NB B:HEM501 2.0 71.8 1.0
NC B:HEM501 2.0 66.9 1.0
NA B:HEM501 2.0 69.9 1.0
NE2 B:HIS198 2.2 66.7 1.0
NE2 B:HIS97 2.2 67.5 1.0
C1B B:HEM501 3.0 68.0 1.0
C4A B:HEM501 3.0 66.3 1.0
CE1 B:HIS198 3.0 65.4 1.0
C1D B:HEM501 3.0 69.0 1.0
C4C B:HEM501 3.0 63.6 1.0
C4D B:HEM501 3.1 67.8 1.0
C4B B:HEM501 3.1 66.6 1.0
C1C B:HEM501 3.1 63.5 1.0
C1A B:HEM501 3.1 63.3 1.0
CE1 B:HIS97 3.2 66.2 1.0
CD2 B:HIS97 3.3 68.7 1.0
CD2 B:HIS198 3.4 69.7 1.0
CHB B:HEM501 3.4 64.0 1.0
CHD B:HEM501 3.4 68.2 1.0
CHC B:HEM501 3.4 63.2 1.0
CHA B:HEM501 3.4 67.9 1.0
ND1 B:HIS198 4.2 67.9 1.0
C2B B:HEM501 4.2 65.9 1.0
C3A B:HEM501 4.2 63.9 1.0
C2D B:HEM501 4.3 70.4 1.0
C3D B:HEM501 4.3 70.5 1.0
C3B B:HEM501 4.3 65.5 1.0
C3C B:HEM501 4.3 59.4 1.0
C2C B:HEM501 4.3 62.6 1.0
C2A B:HEM501 4.3 61.6 1.0
ND1 B:HIS97 4.3 70.2 1.0
CG B:HIS97 4.4 72.2 1.0
CG B:HIS198 4.4 71.3 1.0

Iron binding site 4 out of 10 in 29yb

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Iron binding site 4 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe502

b:94.2
occ:1.00
 FE B:HEM502 0.0 94.2 1.0
ND B:HEM502 2.0 74.9 1.0
NB B:HEM502 2.0 79.5 1.0
NC B:HEM502 2.0 74.5 1.0
NA B:HEM502 2.0 78.6 1.0
NE2 B:HIS212 2.3 75.4 1.0
NE2 B:HIS111 2.3 77.5 1.0
C4C B:HEM502 3.0 68.5 1.0
C1D B:HEM502 3.0 71.4 1.0
C4D B:HEM502 3.0 72.3 1.0
C1C B:HEM502 3.0 72.2 1.0
C1B B:HEM502 3.1 73.6 1.0
C4A B:HEM502 3.1 79.5 1.0
C1A B:HEM502 3.1 73.6 1.0
C4B B:HEM502 3.1 76.3 1.0
CD2 B:HIS212 3.1 72.4 1.0
CD2 B:HIS111 3.1 74.9 1.0
CE1 B:HIS212 3.4 78.0 1.0
CHD B:HEM502 3.4 69.0 1.0
CHB B:HEM502 3.4 73.4 1.0
CHA B:HEM502 3.4 73.5 1.0
CHC B:HEM502 3.4 70.6 1.0
CE1 B:HIS111 3.4 77.0 1.0
C3C B:HEM502 4.2 67.7 1.0
C2C B:HEM502 4.2 70.3 1.0
C3D B:HEM502 4.3 73.2 1.0
C2D B:HEM502 4.3 73.6 1.0
C3A B:HEM502 4.3 78.9 1.0
C2A B:HEM502 4.3 77.4 1.0
C2B B:HEM502 4.3 65.2 1.0
C3B B:HEM502 4.3 71.2 1.0
CG B:HIS212 4.3 75.2 1.0
CG B:HIS111 4.3 75.0 1.0
ND1 B:HIS212 4.4 82.1 1.0
ND1 B:HIS111 4.4 80.5 1.0

Iron binding site 5 out of 10 in 29yb

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Iron binding site 5 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:91.0
occ:1.00
 FE C:HEC501 0.0 91.0 1.0
NA C:HEC501 2.0 61.9 1.0
NC C:HEC501 2.0 70.2 1.0
NB C:HEC501 2.1 67.6 1.0
ND C:HEC501 2.1 67.1 1.0
SD C:MET183 2.2 74.9 1.0
NE2 C:HIS38 2.2 61.6 1.0
CE1 C:HIS38 3.0 57.5 1.0
C1A C:HEC501 3.0 64.5 1.0
C1C C:HEC501 3.0 64.7 1.0
C4C C:HEC501 3.0 64.3 1.0
C4D C:HEC501 3.1 57.5 1.0
C4A C:HEC501 3.1 59.2 1.0
C4B C:HEC501 3.1 68.5 1.0
C1D C:HEC501 3.1 65.5 1.0
C1B C:HEC501 3.1 62.1 1.0
CE C:MET183 3.2 66.9 1.0
CD2 C:HIS38 3.4 63.8 1.0
CG C:MET183 3.4 74.3 1.0
CHA C:HEC501 3.4 61.9 1.0
CHC C:HEC501 3.4 65.5 1.0
CHD C:HEC501 3.4 63.8 1.0
CHB C:HEC501 3.5 58.8 1.0
CB C:MET183 4.2 72.0 1.0
ND1 C:HIS38 4.2 51.9 1.0
C2C C:HEC501 4.2 66.1 1.0
C3C C:HEC501 4.2 65.5 1.0
C2A C:HEC501 4.3 65.3 1.0
C3A C:HEC501 4.3 62.0 1.0
C3B C:HEC501 4.3 62.3 1.0
C2B C:HEC501 4.3 59.4 1.0
C3D C:HEC501 4.3 61.0 1.0
C2D C:HEC501 4.3 64.7 1.0
CG C:HIS38 4.4 54.6 1.0

Iron binding site 6 out of 10 in 29yb

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Iron binding site 6 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:125.7
occ:1.00
 FE1 D:FES501 0.0 125.7 1.0
S2 D:FES501 2.2 101.6 1.0
S1 D:FES501 2.2 134.0 1.0
SG D:CYS133 2.3 112.0 1.0
SG D:CYS153 2.3 113.2 1.0
FE2 D:FES501 2.7 128.0 1.0
CB D:CYS133 2.8 102.4 1.0
CB D:CYS153 3.6 108.2 1.0
CB D:HIS135 3.8 102.2 1.0
CB D:CYS138 4.1 92.4 1.0
ND1 D:HIS135 4.3 103.2 1.0
CA D:CYS133 4.3 99.5 1.0
N D:CYS138 4.3 90.2 1.0
N D:LEU136 4.4 99.5 1.0
OG D:SER158 4.5 115.0 1.0
ND1 D:HIS156 4.5 103.4 1.0
CG D:HIS135 4.5 103.4 1.0
CB D:CYS155 4.6 113.8 1.0
N D:HIS135 4.6 98.4 1.0
CA D:HIS135 4.7 96.3 1.0
CA D:CYS138 4.7 88.8 1.0
C D:CYS133 4.7 97.4 1.0
SG D:CYS138 4.8 110.5 1.0
N D:GLY137 4.8 92.5 1.0
CB D:SER158 4.9 117.8 1.0
CA D:CYS153 4.9 108.8 1.0
N D:HIS156 5.0 112.7 1.0
O D:CYS138 5.0 99.0 1.0

Iron binding site 7 out of 10 in 29yb

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Iron binding site 7 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:128.0
occ:1.00
 FE2 D:FES501 0.0 128.0 1.0
ND1 D:HIS135 2.1 103.2 1.0
ND1 D:HIS156 2.1 103.4 1.0
S1 D:FES501 2.2 134.0 1.0
S2 D:FES501 2.2 101.6 1.0
FE1 D:FES501 2.7 125.7 1.0
CG D:HIS156 2.9 104.1 1.0
CG D:HIS135 3.1 103.4 1.0
CE1 D:HIS135 3.1 100.0 1.0
CB D:HIS156 3.2 109.2 1.0
CE1 D:HIS156 3.2 103.7 1.0
CB D:HIS135 3.4 102.2 1.0
N D:HIS156 3.8 112.7 1.0
CA D:HIS156 4.0 108.3 1.0
SG D:CYS153 4.1 113.2 1.0
CD2 D:HIS156 4.1 100.2 1.0
CB D:CYS155 4.1 113.8 1.0
NE2 D:HIS156 4.2 99.7 1.0
NE2 D:HIS135 4.2 96.7 1.0
CD2 D:HIS135 4.2 98.7 1.0
N D:LEU136 4.3 99.5 1.0
SG D:CYS133 4.4 112.0 1.0
C D:CYS155 4.4 107.1 1.0
OG D:SER158 4.5 115.0 1.0
CA D:HIS135 4.7 96.3 1.0
CB D:LEU136 4.7 85.1 1.0
C D:HIS156 4.8 110.8 1.0
C D:HIS135 4.8 96.6 1.0
CA D:CYS155 4.9 105.0 1.0
CG D:LEU136 4.9 91.8 1.0
CG D:PRO170 4.9 116.9 1.0

Iron binding site 8 out of 10 in 29yb

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Iron binding site 8 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:97.0
occ:1.00
 FE E:HEM501 0.0 97.0 1.0
ND E:HEM501 2.0 69.7 1.0
NB E:HEM501 2.0 71.4 1.0
NC E:HEM501 2.0 67.7 1.0
NA E:HEM501 2.0 70.0 1.0
NE2 E:HIS198 2.2 67.2 1.0
NE2 E:HIS97 2.2 67.2 1.0
C1B E:HEM501 3.0 67.6 1.0
C4A E:HEM501 3.0 66.4 1.0
CE1 E:HIS198 3.0 66.7 1.0
C1D E:HEM501 3.0 68.4 1.0
C4C E:HEM501 3.0 64.1 1.0
C4D E:HEM501 3.1 67.1 1.0
C4B E:HEM501 3.1 66.3 1.0
C1C E:HEM501 3.1 64.4 1.0
C1A E:HEM501 3.1 62.6 1.0
CE1 E:HIS97 3.2 65.7 1.0
CD2 E:HIS97 3.3 68.2 1.0
CD2 E:HIS198 3.4 70.3 1.0
CHB E:HEM501 3.4 63.5 1.0
CHD E:HEM501 3.4 68.5 1.0
CHC E:HEM501 3.4 62.8 1.0
CHA E:HEM501 3.4 66.5 1.0
ND1 E:HIS198 4.2 69.1 1.0
C2B E:HEM501 4.2 65.2 1.0
C3A E:HEM501 4.2 64.0 1.0
C2D E:HEM501 4.2 69.2 1.0
C3D E:HEM501 4.3 70.0 1.0
C3B E:HEM501 4.3 64.9 1.0
C3C E:HEM501 4.3 60.0 1.0
C2C E:HEM501 4.3 64.0 1.0
C2A E:HEM501 4.3 61.6 1.0
ND1 E:HIS97 4.3 70.5 1.0
CG E:HIS97 4.4 72.7 1.0
CG E:HIS198 4.4 71.6 1.0

Iron binding site 9 out of 10 in 29yb

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Iron binding site 9 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe502

b:93.8
occ:1.00
 FE E:HEM502 0.0 93.8 1.0
ND E:HEM502 2.0 75.8 1.0
NB E:HEM502 2.0 78.0 1.0
NC E:HEM502 2.0 75.9 1.0
NA E:HEM502 2.0 80.3 1.0
NE2 E:HIS212 2.3 72.9 1.0
NE2 E:HIS111 2.3 77.2 1.0
C4C E:HEM502 3.0 68.0 1.0
C1D E:HEM502 3.0 71.5 1.0
C4D E:HEM502 3.0 72.8 1.0
C1C E:HEM502 3.0 71.9 1.0
C1B E:HEM502 3.1 72.0 1.0
C4A E:HEM502 3.1 79.8 1.0
C1A E:HEM502 3.1 74.6 1.0
C4B E:HEM502 3.1 76.1 1.0
CD2 E:HIS212 3.1 70.5 1.0
CD2 E:HIS111 3.1 75.5 1.0
CE1 E:HIS212 3.4 78.5 1.0
CHD E:HEM502 3.4 67.7 1.0
CHB E:HEM502 3.4 72.9 1.0
CHA E:HEM502 3.4 74.9 1.0
CHC E:HEM502 3.4 69.3 1.0
CE1 E:HIS111 3.4 76.5 1.0
C3C E:HEM502 4.2 67.4 1.0
C2C E:HEM502 4.2 70.6 1.0
C3D E:HEM502 4.3 71.5 1.0
C2D E:HEM502 4.3 73.3 1.0
C3A E:HEM502 4.3 78.5 1.0
C2A E:HEM502 4.3 77.6 1.0
C2B E:HEM502 4.3 63.5 1.0
C3B E:HEM502 4.3 70.3 1.0
CG E:HIS212 4.3 74.8 1.0
CG E:HIS111 4.3 75.8 1.0
ND1 E:HIS212 4.4 84.1 1.0
ND1 E:HIS111 4.4 80.7 1.0

Iron binding site 10 out of 10 in 29yb

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Iron binding site 10 out of 10 in the Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cryo-Em Structure of Rhodobacter Capsulatus Cytochrome BC1 Dimer with Both Rieske Proteins in the B Position within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe501

b:92.1
occ:1.00
 FE F:HEC501 0.0 92.1 1.0
NA F:HEC501 2.0 64.3 1.0
NC F:HEC501 2.0 72.8 1.0
NB F:HEC501 2.1 68.9 1.0
ND F:HEC501 2.1 68.9 1.0
SD F:MET183 2.2 78.1 1.0
NE2 F:HIS38 2.2 64.1 1.0
CE1 F:HIS38 3.0 60.3 1.0
C1A F:HEC501 3.0 66.3 1.0
C4C F:HEC501 3.0 67.0 1.0
C1C F:HEC501 3.0 67.1 1.0
C4D F:HEC501 3.1 59.6 1.0
C4A F:HEC501 3.1 61.1 1.0
C4B F:HEC501 3.1 70.6 1.0
C1D F:HEC501 3.1 67.2 1.0
C1B F:HEC501 3.1 63.5 1.0
CE F:MET183 3.2 68.5 1.0
CD2 F:HIS38 3.4 65.5 1.0
CG F:MET183 3.4 76.2 1.0
CHA F:HEC501 3.4 63.5 1.0
CHC F:HEC501 3.4 67.5 1.0
CHD F:HEC501 3.4 66.1 1.0
CHB F:HEC501 3.5 60.6 1.0
CB F:MET183 4.2 73.9 1.0
ND1 F:HIS38 4.2 54.0 1.0
C2C F:HEC501 4.2 67.8 1.0
C3C F:HEC501 4.2 67.3 1.0
C2A F:HEC501 4.3 67.1 1.0
C3A F:HEC501 4.3 63.5 1.0
C3B F:HEC501 4.3 63.8 1.0
C2B F:HEC501 4.3 60.2 1.0
C3D F:HEC501 4.3 62.7 1.0
C2D F:HEC501 4.3 66.4 1.0
CG F:HIS38 4.4 56.0 1.0

Reference:

R.Pietras, A.Wojcik-Augustyn, B.Mielecki, M.Sarewicz, M.Jaciuk, L.Koziej, S.Glatt, A.Osyczka. Distinct Ubiquinone Binding at the Oxidation and Reduction Sites of Cytochrome Bc 1. Proc.Natl.Acad.Sci.Usa V. 123 42123 2026.
ISSN: ESSN 1091-6490
PubMed: 42679026
DOI: 10.1073/PNAS.2618242123
Page generated: Sun Oct 4 09:43:25 2026

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