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Iron in PDB 8ab8: Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced

Enzymatic activity of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced

All present enzymatic activity of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced:
7.1.1.8;

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced (pdb code 8ab8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced, PDB code: 8ab8:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8ab8

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Iron binding site 1 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:26.0
occ:1.00
 FE C:HEM501 0.0 26.0 1.0
ND C:HEM501 1.9 27.7 1.0
NA C:HEM501 2.0 27.5 1.0
NE2 C:HIS183 2.0 26.9 1.0
NC C:HEM501 2.1 28.5 1.0
NB C:HEM501 2.1 28.1 1.0
NE2 C:HIS82 2.1 24.1 1.0
C1D C:HEM501 2.9 27.4 1.0
C4D C:HEM501 2.9 27.8 1.0
C1A C:HEM501 3.0 27.5 1.0
CE1 C:HIS183 3.0 25.2 1.0
C4A C:HEM501 3.0 28.6 1.0
CE1 C:HIS82 3.1 23.9 1.0
C4B C:HEM501 3.1 29.9 1.0
C4C C:HEM501 3.1 29.0 1.0
CD2 C:HIS183 3.1 26.9 1.0
C1B C:HEM501 3.1 29.4 1.0
C1C C:HEM501 3.1 29.9 1.0
CD2 C:HIS82 3.1 23.7 1.0
CHA C:HEM501 3.4 26.7 1.0
CHD C:HEM501 3.4 28.2 1.0
CHB C:HEM501 3.5 28.9 1.0
CHC C:HEM501 3.5 30.7 1.0
ND1 C:HIS183 4.1 25.5 1.0
C2A C:HEM501 4.2 29.6 1.0
ND1 C:HIS82 4.2 24.6 1.0
CG C:HIS183 4.2 26.8 1.0
C3A C:HEM501 4.2 28.7 1.0
C3D C:HEM501 4.2 29.1 1.0
C2D C:HEM501 4.2 28.6 1.0
CG C:HIS82 4.2 25.1 1.0
C3C C:HEM501 4.3 31.8 1.0
C2C C:HEM501 4.3 32.0 1.0
C3B C:HEM501 4.3 30.5 1.0
C2B C:HEM501 4.3 29.7 1.0
CA C:GLY131 4.7 31.8 1.0
NE2 C:GLN43 4.9 33.1 1.0

Iron binding site 2 out of 8 in 8ab8

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Iron binding site 2 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:26.9
occ:1.00
 FE C:HEM502 0.0 26.9 1.0
ND C:HEM502 1.9 26.7 1.0
NA C:HEM502 2.0 27.1 1.0
NC C:HEM502 2.1 26.4 1.0
NB C:HEM502 2.1 26.3 1.0
NE2 C:HIS197 2.2 29.4 1.0
NE2 C:HIS96 2.2 27.0 1.0
C4D C:HEM502 2.9 26.9 1.0
C1D C:HEM502 2.9 28.0 1.0
C4C C:HEM502 3.0 27.4 1.0
C1A C:HEM502 3.0 27.2 1.0
CE1 C:HIS197 3.0 27.9 1.0
C4A C:HEM502 3.1 27.0 1.0
C1B C:HEM502 3.1 25.8 1.0
C4B C:HEM502 3.1 26.6 1.0
C1C C:HEM502 3.1 27.5 1.0
CD2 C:HIS96 3.2 28.2 1.0
CE1 C:HIS96 3.2 27.8 1.0
CD2 C:HIS197 3.2 29.1 1.0
CHA C:HEM502 3.4 27.2 1.0
CHD C:HEM502 3.4 27.3 1.0
CHB C:HEM502 3.5 25.7 1.0
CHC C:HEM502 3.5 27.0 1.0
C3D C:HEM502 4.1 28.4 1.0
C3C C:HEM502 4.2 27.8 1.0
C2D C:HEM502 4.2 27.7 1.0
C2A C:HEM502 4.2 27.4 1.0
ND1 C:HIS197 4.2 29.3 1.0
C2C C:HEM502 4.2 27.1 1.0
C3A C:HEM502 4.3 26.9 1.0
ND1 C:HIS96 4.3 29.8 1.0
CG C:HIS96 4.3 28.1 1.0
C2B C:HEM502 4.3 26.7 1.0
CG C:HIS197 4.3 28.6 1.0
C3B C:HEM502 4.3 26.9 1.0

Iron binding site 3 out of 8 in 8ab8

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Iron binding site 3 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:83.6
occ:1.00
 FE1 P:FES301 0.0 83.6 1.0
S2 P:FES301 2.2 73.7 1.0
SG P:CYS187 2.2 92.1 1.0
S1 P:FES301 2.2 87.9 1.0
SG P:CYS168 2.3 94.0 1.0
CB P:CYS168 2.9 84.1 1.0
FE2 P:FES301 3.0 80.4 1.0
CB P:CYS187 3.1 105.5 1.0
OG P:SER192 3.7 136.1 1.0
CB P:HIS170 3.8 76.5 1.0
CA P:CYS168 4.3 77.4 1.0
N P:LEU171 4.5 77.2 1.0
ND1 P:HIS170 4.5 81.5 1.0
ND1 P:HIS190 4.5 109.3 1.0
CB P:CYS173 4.5 85.6 1.0
CA P:CYS187 4.6 114.0 1.0
CB P:CYS189 4.6 120.8 1.0
N P:HIS170 4.6 72.6 1.0
CG P:HIS170 4.7 79.4 1.0
C P:CYS168 4.7 78.3 1.0
CA P:HIS170 4.7 73.8 1.0
N P:CYS173 4.7 69.2 1.0
CB P:SER192 4.8 135.5 1.0
N P:GLY172 4.9 71.3 1.0
N P:HIS190 4.9 114.6 1.0
O P:CYS168 4.9 82.5 1.0
SG P:CYS173 5.0 99.0 1.0

Iron binding site 4 out of 8 in 8ab8

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Iron binding site 4 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:80.4
occ:1.00
 FE2 P:FES301 0.0 80.4 1.0
ND1 P:HIS190 2.1 109.3 1.0
ND1 P:HIS170 2.1 81.5 1.0
S2 P:FES301 2.2 73.7 1.0
S1 P:FES301 2.2 87.9 1.0
CG P:HIS190 2.8 109.0 1.0
FE1 P:FES301 3.0 83.6 1.0
CG P:HIS170 3.0 79.4 1.0
CB P:HIS190 3.0 111.2 1.0
CE1 P:HIS190 3.1 107.2 1.0
CE1 P:HIS170 3.1 83.4 1.0
CB P:HIS170 3.3 76.5 1.0
N P:HIS190 3.7 114.6 1.0
CD2 P:HIS190 3.9 103.9 1.0
CA P:HIS190 3.9 109.9 1.0
NE2 P:HIS190 4.0 107.4 1.0
CD2 P:HIS170 4.2 81.8 1.0
NE2 P:HIS170 4.2 82.1 1.0
N P:LEU171 4.2 77.2 1.0
CB P:CYS189 4.3 120.8 1.0
SG P:CYS187 4.4 92.1 1.0
CB P:LEU171 4.5 83.3 1.0
C P:CYS189 4.5 122.4 1.0
CG P:LEU171 4.6 89.9 1.0
CA P:HIS170 4.6 73.8 1.0
SG P:CYS168 4.7 94.0 1.0
C P:HIS190 4.7 109.6 1.0
CG P:PRO204 4.8 111.1 1.0
CD1 P:LEU171 4.8 96.2 1.0
C P:HIS170 4.8 73.0 1.0
CA P:CYS189 4.9 123.0 1.0
CA P:LEU171 5.0 78.0 1.0

Iron binding site 5 out of 8 in 8ab8

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Iron binding site 5 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:37.8
occ:1.00
 FE D:HEC401 0.0 37.8 1.0
NE2 D:HIS128 2.0 33.7 1.0
NB D:HEC401 2.1 37.0 1.0
ND D:HEC401 2.1 37.2 1.0
NA D:HEC401 2.1 37.9 1.0
NC D:HEC401 2.1 40.0 1.0
SD D:MET248 2.2 43.5 1.0
CE1 D:HIS128 2.9 34.3 1.0
CD2 D:HIS128 3.0 33.2 1.0
C4B D:HEC401 3.0 38.2 1.0
C4D D:HEC401 3.1 38.1 1.0
C1B D:HEC401 3.1 37.7 1.0
C1C D:HEC401 3.1 40.1 1.0
C4A D:HEC401 3.1 37.5 1.0
C4C D:HEC401 3.1 40.0 1.0
C1A D:HEC401 3.1 38.6 1.0
C1D D:HEC401 3.1 37.7 1.0
CE D:MET248 3.3 38.9 1.0
CHA D:HEC401 3.4 38.7 1.0
CHB D:HEC401 3.4 36.5 1.0
CHC D:HEC401 3.4 37.7 1.0
CG D:MET248 3.5 42.4 1.0
CHD D:HEC401 3.5 37.1 1.0
ND1 D:HIS128 4.1 33.9 1.0
CB D:MET248 4.1 43.5 1.0
CG D:HIS128 4.1 33.5 1.0
C3B D:HEC401 4.3 39.2 1.0
C3C D:HEC401 4.3 41.7 1.0
C3D D:HEC401 4.4 37.5 1.0
C2D D:HEC401 4.4 37.7 1.0
C3A D:HEC401 4.4 36.8 1.0
C2A D:HEC401 4.4 36.7 1.0
C2C D:HEC401 4.4 41.2 1.0
C2B D:HEC401 4.4 39.6 1.0

Iron binding site 6 out of 8 in 8ab8

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Iron binding site 6 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe501

b:26.8
occ:1.00
 FE N:HEM501 0.0 26.8 1.0
ND N:HEM501 1.9 27.1 1.0
NA N:HEM501 2.0 28.0 1.0
NE2 N:HIS183 2.0 26.3 1.0
NE2 N:HIS82 2.1 24.0 1.0
NC N:HEM501 2.1 28.4 1.0
NB N:HEM501 2.1 28.9 1.0
C4D N:HEM501 2.9 27.3 1.0
C1D N:HEM501 2.9 26.7 1.0
C1A N:HEM501 3.0 27.6 1.0
CE1 N:HIS183 3.0 24.1 1.0
CE1 N:HIS82 3.0 23.8 1.0
C4A N:HEM501 3.0 29.5 1.0
C4B N:HEM501 3.1 30.8 1.0
C4C N:HEM501 3.1 29.2 1.0
CD2 N:HIS183 3.1 26.0 1.0
C1C N:HEM501 3.1 29.4 1.0
C1B N:HEM501 3.1 30.4 1.0
CD2 N:HIS82 3.1 24.3 1.0
CHA N:HEM501 3.4 27.2 1.0
CHD N:HEM501 3.4 27.0 1.0
CHC N:HEM501 3.5 31.0 1.0
CHB N:HEM501 3.5 29.8 1.0
ND1 N:HIS183 4.1 24.1 1.0
ND1 N:HIS82 4.2 23.9 1.0
C3D N:HEM501 4.2 28.4 1.0
C2D N:HEM501 4.2 27.1 1.0
C2A N:HEM501 4.2 28.3 1.0
CG N:HIS183 4.2 26.1 1.0
C3A N:HEM501 4.2 28.3 1.0
CG N:HIS82 4.2 25.7 1.0
C2C N:HEM501 4.3 31.4 1.0
C3C N:HEM501 4.3 32.0 1.0
C3B N:HEM501 4.3 31.6 1.0
C2B N:HEM501 4.3 30.8 1.0
CA N:GLY131 4.8 32.2 1.0
NE2 N:GLN43 4.9 32.8 1.0

Iron binding site 7 out of 8 in 8ab8

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Iron binding site 7 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe502

b:27.2
occ:1.00
 FE N:HEM502 0.0 27.2 1.0
ND N:HEM502 1.9 27.4 1.0
NA N:HEM502 2.0 27.1 1.0
NC N:HEM502 2.0 27.4 1.0
NE2 N:HIS96 2.1 25.4 1.0
NB N:HEM502 2.1 27.6 1.0
NE2 N:HIS197 2.2 26.4 1.0
C4D N:HEM502 2.9 27.1 1.0
C1D N:HEM502 2.9 28.0 1.0
CE1 N:HIS96 2.9 24.1 1.0
C4C N:HEM502 3.0 28.6 1.0
C1A N:HEM502 3.0 26.2 1.0
C4A N:HEM502 3.0 28.2 1.0
C1B N:HEM502 3.0 28.0 1.0
C4B N:HEM502 3.0 29.0 1.0
CE1 N:HIS197 3.1 25.1 1.0
C1C N:HEM502 3.1 28.2 1.0
CD2 N:HIS96 3.1 25.8 1.0
CD2 N:HIS197 3.3 26.9 1.0
CHA N:HEM502 3.4 26.4 1.0
CHD N:HEM502 3.4 28.5 1.0
CHB N:HEM502 3.4 27.8 1.0
CHC N:HEM502 3.5 28.0 1.0
ND1 N:HIS96 4.1 26.1 1.0
C3D N:HEM502 4.1 28.0 1.0
C3C N:HEM502 4.2 28.9 1.0
C2D N:HEM502 4.2 28.1 1.0
C2A N:HEM502 4.2 28.7 1.0
CG N:HIS96 4.2 26.5 1.0
ND1 N:HIS197 4.2 25.3 1.0
C2C N:HEM502 4.2 28.7 1.0
C3A N:HEM502 4.2 28.3 1.0
C3B N:HEM502 4.3 29.4 1.0
C2B N:HEM502 4.3 29.1 1.0
CG N:HIS197 4.3 25.9 1.0

Iron binding site 8 out of 8 in 8ab8

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Iron binding site 8 out of 8 in the Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex III2, B-Position, with Decylubiquinone and Ascorbate-Reduced within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe401

b:37.4
occ:1.00
 FE O:HEC401 0.0 37.4 1.0
NE2 O:HIS128 2.0 37.2 1.0
NB O:HEC401 2.1 37.4 1.0
NA O:HEC401 2.1 37.5 1.0
NC O:HEC401 2.1 38.5 1.0
ND O:HEC401 2.1 39.2 1.0
SD O:MET248 2.2 38.8 1.0
CE1 O:HIS128 2.9 38.6 1.0
CD2 O:HIS128 3.0 37.2 1.0
C4D O:HEC401 3.1 39.4 1.0
C4B O:HEC401 3.1 37.6 1.0
C4C O:HEC401 3.1 38.5 1.0
C1B O:HEC401 3.1 38.0 1.0
C1A O:HEC401 3.1 37.4 1.0
C1C O:HEC401 3.1 39.5 1.0
C4A O:HEC401 3.1 37.5 1.0
C1D O:HEC401 3.1 39.0 1.0
CE O:MET248 3.3 35.7 1.0
CHA O:HEC401 3.4 38.6 1.0
CHB O:HEC401 3.4 37.4 1.0
CHC O:HEC401 3.4 36.7 1.0
CHD O:HEC401 3.5 38.5 1.0
CG O:MET248 3.5 39.5 1.0
ND1 O:HIS128 4.0 37.1 1.0
CB O:MET248 4.1 42.9 1.0
CG O:HIS128 4.1 36.8 1.0
C3B O:HEC401 4.3 39.8 1.0
C3C O:HEC401 4.3 40.7 1.0
C3D O:HEC401 4.4 40.4 1.0
C2A O:HEC401 4.4 36.0 1.0
C2C O:HEC401 4.4 39.2 1.0
C3A O:HEC401 4.4 37.2 1.0
C2D O:HEC401 4.4 39.5 1.0
C2B O:HEC401 4.4 38.6 1.0

Reference:

J.P.Wieferig, W.Kuhlbrandt. Analysis of the Conformational Heterogeneity of the Rieske Iron-Sulfur Protein in Complex III2 By Cryo-Em Iucrj 2023.
ISSN: ESSN 2052-2525
Page generated: Fri Aug 9 16:15:27 2024

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