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Iron in PDB 8abl: Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement

All present enzymatic activity of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement:
7.1.1.8;

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement (pdb code 8abl). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement, PDB code: 8abl:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 8abl

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Iron binding site 1 out of 6 in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:10.2
occ:1.00
 FE C:HEM501 0.0 10.2 1.0
ND C:HEM501 1.9 10.9 1.0
NA C:HEM501 2.0 10.7 1.0
NE2 C:HIS183 2.0 9.2 1.0
NE2 C:HIS82 2.1 8.2 1.0
NC C:HEM501 2.1 10.7 1.0
NB C:HEM501 2.1 10.6 1.0
C4D C:HEM501 2.9 10.8 1.0
C1D C:HEM501 2.9 10.8 1.0
C1A C:HEM501 3.0 10.9 1.0
CE1 C:HIS183 3.0 9.1 1.0
CE1 C:HIS82 3.0 8.1 1.0
C4A C:HEM501 3.0 10.7 1.0
CD2 C:HIS183 3.1 9.4 1.0
C4C C:HEM501 3.1 10.9 1.0
C4B C:HEM501 3.1 10.5 1.0
C1C C:HEM501 3.1 10.9 1.0
CD2 C:HIS82 3.1 8.3 1.0
C1B C:HEM501 3.1 10.6 1.0
CHA C:HEM501 3.4 10.8 1.0
CHD C:HEM501 3.4 11.0 1.0
CHB C:HEM501 3.5 10.7 1.0
CHC C:HEM501 3.5 10.6 1.0
ND1 C:HIS183 4.1 9.5 1.0
ND1 C:HIS82 4.1 8.4 1.0
C2A C:HEM501 4.2 11.4 1.0
CG C:HIS183 4.2 9.8 1.0
C3A C:HEM501 4.2 11.0 1.0
C2D C:HEM501 4.2 11.4 1.0
C3D C:HEM501 4.2 11.6 1.0
CG C:HIS82 4.2 8.7 1.0
C2C C:HEM501 4.3 11.3 1.0
C3C C:HEM501 4.3 11.3 1.0
C2B C:HEM501 4.3 10.7 1.0
C3B C:HEM501 4.3 10.7 1.0
CA C:GLY131 4.7 14.3 1.0
NE2 C:GLN43 4.9 12.2 1.0

Iron binding site 2 out of 6 in 8abl

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Iron binding site 2 out of 6 in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:8.3
occ:1.00
 FE C:HEM502 0.0 8.3 1.0
ND C:HEM502 1.9 8.6 1.0
NA C:HEM502 2.0 8.6 1.0
NC C:HEM502 2.1 8.4 1.0
NB C:HEM502 2.1 8.5 1.0
NE2 C:HIS197 2.1 9.6 1.0
NE2 C:HIS96 2.2 8.9 1.0
C4D C:HEM502 2.9 8.6 1.0
C1D C:HEM502 2.9 8.5 1.0
C4C C:HEM502 3.0 8.4 1.0
C1A C:HEM502 3.0 8.6 1.0
CE1 C:HIS197 3.0 9.8 1.0
C4A C:HEM502 3.0 8.7 1.0
C4B C:HEM502 3.1 8.4 1.0
C1B C:HEM502 3.1 8.4 1.0
C1C C:HEM502 3.1 8.4 1.0
CD2 C:HIS96 3.2 9.1 1.0
CE1 C:HIS96 3.2 9.1 1.0
CD2 C:HIS197 3.2 9.8 1.0
CHA C:HEM502 3.4 8.6 1.0
CHD C:HEM502 3.4 8.4 1.0
CHB C:HEM502 3.5 8.5 1.0
CHC C:HEM502 3.5 8.4 1.0
C3D C:HEM502 4.1 9.2 1.0
C2D C:HEM502 4.2 8.7 1.0
C3C C:HEM502 4.2 8.5 1.0
ND1 C:HIS197 4.2 9.9 1.0
C2A C:HEM502 4.2 8.9 1.0
C2C C:HEM502 4.2 8.5 1.0
C3A C:HEM502 4.2 8.8 1.0
ND1 C:HIS96 4.3 9.2 1.0
CG C:HIS96 4.3 9.2 1.0
C2B C:HEM502 4.3 8.6 1.0
CG C:HIS197 4.3 10.3 1.0
C3B C:HEM502 4.3 8.7 1.0

Iron binding site 3 out of 6 in 8abl

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Iron binding site 3 out of 6 in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:18.6
occ:1.00
 FE D:HEC401 0.0 18.6 1.0
NE2 D:HIS128 2.0 15.3 1.0
NC D:HEC401 2.1 19.3 1.0
NB D:HEC401 2.1 18.9 1.0
ND D:HEC401 2.1 19.5 1.0
NA D:HEC401 2.1 18.9 1.0
SD D:MET248 2.3 20.9 1.0
CE1 D:HIS128 2.9 15.2 1.0
C4C D:HEC401 3.0 19.7 1.0
C4D D:HEC401 3.0 19.6 1.0
C4B D:HEC401 3.0 19.1 1.0
CD2 D:HIS128 3.0 15.3 1.0
C1B D:HEC401 3.0 18.7 1.0
C1A D:HEC401 3.0 19.2 1.0
C1C D:HEC401 3.1 19.8 1.0
C4A D:HEC401 3.1 18.5 1.0
C1D D:HEC401 3.1 19.7 1.0
CHA D:HEC401 3.4 19.4 1.0
CHB D:HEC401 3.4 18.3 1.0
CE D:MET248 3.4 20.8 1.0
CHC D:HEC401 3.4 19.3 1.0
CHD D:HEC401 3.5 19.7 1.0
CG D:MET248 3.5 22.1 1.0
ND1 D:HIS128 4.1 15.4 1.0
CB D:MET248 4.1 23.3 1.0
CG D:HIS128 4.1 15.7 1.0
C3C D:HEC401 4.3 20.3 1.0
C3B D:HEC401 4.3 19.9 1.0
C3D D:HEC401 4.3 20.1 1.0
C2A D:HEC401 4.4 19.3 1.0
C2C D:HEC401 4.4 20.3 1.0
C2B D:HEC401 4.4 19.8 1.0
C3A D:HEC401 4.4 19.1 1.0
C2D D:HEC401 4.4 20.0 1.0

Iron binding site 4 out of 6 in 8abl

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Iron binding site 4 out of 6 in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe501

b:10.2
occ:1.00
 FE N:HEM501 0.0 10.2 1.0
ND N:HEM501 1.9 10.9 1.0
NA N:HEM501 2.0 10.7 1.0
NE2 N:HIS82 2.1 8.2 1.0
NE2 N:HIS183 2.1 9.2 1.0
NC N:HEM501 2.1 10.8 1.0
NB N:HEM501 2.1 10.6 1.0
C4D N:HEM501 2.9 10.9 1.0
C1D N:HEM501 2.9 10.9 1.0
C1A N:HEM501 3.0 10.9 1.0
CE1 N:HIS82 3.0 8.1 1.0
CE1 N:HIS183 3.0 9.1 1.0
C4A N:HEM501 3.0 10.7 1.0
C4C N:HEM501 3.1 11.0 1.0
CD2 N:HIS82 3.1 8.3 1.0
C4B N:HEM501 3.1 10.6 1.0
CD2 N:HIS183 3.1 9.4 1.0
C1C N:HEM501 3.1 10.9 1.0
C1B N:HEM501 3.1 10.6 1.0
CHA N:HEM501 3.4 10.9 1.0
CHD N:HEM501 3.4 11.1 1.0
CHB N:HEM501 3.5 10.7 1.0
CHC N:HEM501 3.5 10.7 1.0
ND1 N:HIS183 4.1 9.5 1.0
ND1 N:HIS82 4.1 8.4 1.0
C2A N:HEM501 4.2 11.5 1.0
CG N:HIS82 4.2 8.8 1.0
C2D N:HEM501 4.2 11.5 1.0
CG N:HIS183 4.2 9.8 1.0
C3A N:HEM501 4.2 11.1 1.0
C3D N:HEM501 4.2 11.6 1.0
C2C N:HEM501 4.3 11.4 1.0
C3C N:HEM501 4.3 11.4 1.0
C3B N:HEM501 4.3 10.8 1.0
C2B N:HEM501 4.3 10.7 1.0
CA N:GLY131 4.7 14.5 1.0
NE2 N:GLN43 4.9 12.3 1.0

Iron binding site 5 out of 6 in 8abl

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Iron binding site 5 out of 6 in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe502

b:8.1
occ:1.00
 FE N:HEM502 0.0 8.1 1.0
ND N:HEM502 1.9 8.4 1.0
NA N:HEM502 2.0 8.4 1.0
NC N:HEM502 2.0 8.3 1.0
NE2 N:HIS96 2.1 8.8 1.0
NB N:HEM502 2.1 8.4 1.0
NE2 N:HIS197 2.2 9.6 1.0
C4D N:HEM502 2.9 8.4 1.0
C1D N:HEM502 2.9 8.3 1.0
CE1 N:HIS96 2.9 8.8 1.0
C4C N:HEM502 3.0 8.3 1.0
C1A N:HEM502 3.0 8.5 1.0
C4A N:HEM502 3.0 8.6 1.0
CE1 N:HIS197 3.1 9.9 1.0
C4B N:HEM502 3.1 8.3 1.0
C1B N:HEM502 3.1 8.3 1.0
C1C N:HEM502 3.1 8.3 1.0
CD2 N:HIS96 3.2 9.1 1.0
CD2 N:HIS197 3.2 9.9 1.0
CHA N:HEM502 3.4 8.4 1.0
CHD N:HEM502 3.4 8.3 1.0
CHB N:HEM502 3.5 8.4 1.0
CHC N:HEM502 3.5 8.3 1.0
ND1 N:HIS96 4.1 8.9 1.0
C3D N:HEM502 4.1 9.0 1.0
C2D N:HEM502 4.2 8.6 1.0
C3C N:HEM502 4.2 8.4 1.0
C2A N:HEM502 4.2 8.8 1.0
C3A N:HEM502 4.2 8.7 1.0
ND1 N:HIS197 4.2 10.0 1.0
C2C N:HEM502 4.2 8.4 1.0
CG N:HIS96 4.2 9.1 1.0
C2B N:HEM502 4.3 8.4 1.0
C3B N:HEM502 4.3 8.5 1.0
CG N:HIS197 4.3 10.3 1.0

Iron binding site 6 out of 6 in 8abl

Go back to Iron Binding Sites List in 8abl
Iron binding site 6 out of 6 in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol and Antimycin A, Consensus Refinement within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe401

b:18.7
occ:1.00
 FE O:HEC401 0.0 18.7 1.0
NE2 O:HIS128 2.0 15.3 1.0
NB O:HEC401 2.1 18.9 1.0
NC O:HEC401 2.1 19.3 1.0
ND O:HEC401 2.1 19.5 1.0
NA O:HEC401 2.1 19.0 1.0
SD O:MET248 2.3 20.9 1.0
CE1 O:HIS128 3.0 15.2 1.0
C4B O:HEC401 3.0 19.2 1.0
C4D O:HEC401 3.0 19.7 1.0
C4C O:HEC401 3.0 19.7 1.0
C1B O:HEC401 3.0 18.7 1.0
C1A O:HEC401 3.0 19.2 1.0
C1C O:HEC401 3.1 19.9 1.0
CD2 O:HIS128 3.1 15.2 1.0
C4A O:HEC401 3.1 18.5 1.0
C1D O:HEC401 3.1 19.7 1.0
CE O:MET248 3.4 20.8 1.0
CHA O:HEC401 3.4 19.4 1.0
CHB O:HEC401 3.4 18.3 1.0
CHC O:HEC401 3.4 19.3 1.0
CG O:MET248 3.5 22.0 1.0
CHD O:HEC401 3.5 19.7 1.0
CB O:MET248 4.1 23.3 1.0
ND1 O:HIS128 4.1 15.3 1.0
CG O:HIS128 4.2 15.7 1.0
C3B O:HEC401 4.3 19.9 1.0
C3C O:HEC401 4.3 20.4 1.0
C3D O:HEC401 4.3 20.1 1.0
C2A O:HEC401 4.4 19.3 1.0
C2C O:HEC401 4.4 20.3 1.0
C2B O:HEC401 4.4 19.8 1.0
C3A O:HEC401 4.4 19.1 1.0
C2D O:HEC401 4.4 20.0 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: Thu Aug 7 12:51:22 2025

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