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Iron in PDB 8abb: Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position

All present enzymatic activity of Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position:
7.1.1.8;

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position (pdb code 8abb). 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 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position, PDB code: 8abb:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8abb

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Iron binding site 1 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


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, Ascorbate-Reduced, C-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:31.2
occ:1.00
 FE C:HEM501 0.0 31.2 1.0
ND C:HEM501 1.9 31.6 1.0
NA C:HEM501 1.9 33.1 1.0
NE2 C:HIS183 2.0 34.9 1.0
NC C:HEM501 2.1 33.0 1.0
NE2 C:HIS82 2.1 35.1 1.0
NB C:HEM501 2.1 31.7 1.0
C1D C:HEM501 2.9 33.0 1.0
C4D C:HEM501 2.9 30.3 1.0
C1A C:HEM501 2.9 34.4 1.0
CE1 C:HIS183 3.0 34.8 1.0
C4A C:HEM501 3.0 34.9 1.0
C4B C:HEM501 3.0 33.1 1.0
CE1 C:HIS82 3.0 34.8 1.0
C4C C:HEM501 3.0 33.2 1.0
C1B C:HEM501 3.0 33.7 1.0
C1C C:HEM501 3.1 34.9 1.0
CD2 C:HIS82 3.1 35.7 1.0
CD2 C:HIS183 3.1 34.9 1.0
CHA C:HEM501 3.3 31.6 1.0
CHD C:HEM501 3.4 32.8 1.0
CHB C:HEM501 3.4 34.0 1.0
CHC C:HEM501 3.5 33.5 1.0
ND1 C:HIS183 4.1 35.2 1.0
C2A C:HEM501 4.1 36.1 1.0
C3A C:HEM501 4.1 35.1 1.0
ND1 C:HIS82 4.1 36.9 1.0
C3D C:HEM501 4.1 32.7 1.0
C2D C:HEM501 4.2 33.8 1.0
CG C:HIS183 4.2 33.8 1.0
CG C:HIS82 4.2 35.0 1.0
C3B C:HEM501 4.3 34.2 1.0
C2C C:HEM501 4.3 37.4 1.0
C3C C:HEM501 4.3 37.5 1.0
C2B C:HEM501 4.3 33.5 1.0
CA C:GLY131 4.7 42.8 1.0
NE2 C:GLN43 4.9 45.8 1.0

Iron binding site 2 out of 8 in 8abb

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Iron binding site 2 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


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, Ascorbate-Reduced, C-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:31.9
occ:1.00
 FE C:HEM502 0.0 31.9 1.0
ND C:HEM502 1.9 35.0 1.0
NA C:HEM502 2.0 36.9 1.0
NC C:HEM502 2.0 34.6 1.0
NB C:HEM502 2.1 36.4 1.0
NE2 C:HIS197 2.2 34.3 1.0
NE2 C:HIS96 2.2 36.2 1.0
C4D C:HEM502 2.9 35.9 1.0
C1D C:HEM502 2.9 34.2 1.0
C4C C:HEM502 3.0 34.7 1.0
C1A C:HEM502 3.0 37.9 1.0
CE1 C:HIS197 3.0 36.4 1.0
C4A C:HEM502 3.0 35.8 1.0
C4B C:HEM502 3.0 37.5 1.0
C1B C:HEM502 3.1 37.2 1.0
C1C C:HEM502 3.1 36.3 1.0
CD2 C:HIS96 3.1 38.0 1.0
CE1 C:HIS96 3.2 40.1 1.0
CD2 C:HIS197 3.3 36.4 1.0
CHA C:HEM502 3.4 36.2 1.0
CHD C:HEM502 3.4 32.4 1.0
CHB C:HEM502 3.4 36.7 1.0
CHC C:HEM502 3.5 36.0 1.0
C3C C:HEM502 4.1 35.8 1.0
C2D C:HEM502 4.2 34.5 1.0
C3D C:HEM502 4.2 37.7 1.0
C2A C:HEM502 4.2 38.1 1.0
C2C C:HEM502 4.2 35.9 1.0
C3A C:HEM502 4.2 34.8 1.0
ND1 C:HIS197 4.2 37.9 1.0
CG C:HIS96 4.3 40.4 1.0
C3B C:HEM502 4.3 38.0 1.0
C2B C:HEM502 4.3 36.6 1.0
ND1 C:HIS96 4.3 44.4 1.0
CG C:HIS197 4.3 37.8 1.0

Iron binding site 3 out of 8 in 8abb

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Iron binding site 3 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


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, Ascorbate-Reduced, C-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:116.8
occ:1.00
 FE1 P:FES301 0.0 116.8 1.0
SG P:CYS168 2.2 127.3 1.0
S2 P:FES301 2.2 118.7 1.0
S1 P:FES301 2.2 121.9 1.0
SG P:CYS187 2.2 131.5 1.0
CB P:CYS168 2.8 118.8 1.0
FE2 P:FES301 3.0 105.7 1.0
CB P:CYS187 3.1 127.2 1.0
OG P:SER192 3.7 123.3 1.0
CB P:HIS170 3.7 124.6 1.0
CA P:CYS168 4.2 118.6 1.0
N P:LEU171 4.4 155.4 1.0
ND1 P:HIS170 4.4 119.1 1.0
ND1 P:HIS190 4.5 134.8 1.0
CB P:CYS173 4.5 145.5 1.0
N P:CYS173 4.6 129.0 1.0
CG P:HIS170 4.6 123.7 1.0
CA P:CYS187 4.6 126.3 1.0
N P:HIS170 4.6 128.8 1.0
C P:CYS168 4.6 116.5 1.0
CB P:CYS189 4.6 156.6 1.0
CA P:HIS170 4.7 135.0 1.0
N P:GLY172 4.7 138.9 1.0
CB P:SER192 4.9 130.0 1.0
O P:CYS168 4.9 116.6 1.0
N P:HIS190 4.9 141.2 1.0
O P:CYS173 5.0 139.4 1.0
SG P:CYS173 5.0 175.6 1.0

Iron binding site 4 out of 8 in 8abb

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Iron binding site 4 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


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, Ascorbate-Reduced, C-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:105.7
occ:1.00
 FE2 P:FES301 0.0 105.7 1.0
ND1 P:HIS170 2.0 119.1 1.0
ND1 P:HIS190 2.1 134.8 1.0
S1 P:FES301 2.2 121.9 1.0
S2 P:FES301 2.2 118.7 1.0
CG P:HIS190 2.7 126.5 1.0
CB P:HIS190 2.9 130.9 1.0
FE1 P:FES301 3.0 116.8 1.0
CG P:HIS170 3.0 123.7 1.0
CE1 P:HIS170 3.0 119.5 1.0
CE1 P:HIS190 3.1 137.6 1.0
CB P:HIS170 3.3 124.6 1.0
N P:HIS190 3.7 141.2 1.0
CA P:HIS190 3.9 136.4 1.0
CD2 P:HIS190 3.9 115.7 1.0
NE2 P:HIS190 4.0 121.2 1.0
CD2 P:HIS170 4.1 132.4 1.0
NE2 P:HIS170 4.1 127.2 1.0
SG P:CYS187 4.2 131.5 1.0
CB P:CYS189 4.3 156.6 1.0
N P:LEU171 4.3 155.4 1.0
C P:CYS189 4.5 149.8 1.0
CG P:LEU171 4.5 163.0 1.0
CB P:LEU171 4.6 139.9 1.0
SG P:CYS168 4.6 127.3 1.0
CA P:HIS170 4.7 135.0 1.0
C P:HIS190 4.7 136.3 1.0
CG P:PRO204 4.8 124.9 1.0
CD1 P:LEU171 4.8 180.8 1.0
C P:HIS170 4.9 152.8 1.0
CB P:PRO204 4.9 133.4 1.0
CA P:CYS189 5.0 141.6 1.0

Iron binding site 5 out of 8 in 8abb

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Iron binding site 5 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


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, Ascorbate-Reduced, C-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:38.4
occ:1.00
 FE D:HEC401 0.0 38.4 1.0
NE2 D:HIS128 2.0 41.5 1.0
NB D:HEC401 2.0 43.6 1.0
NA D:HEC401 2.0 38.8 1.0
NC D:HEC401 2.1 42.1 1.0
ND D:HEC401 2.1 44.8 1.0
SD D:MET248 2.2 46.6 1.0
CE1 D:HIS128 2.9 41.8 1.0
C4B D:HEC401 3.0 47.5 1.0
C4A D:HEC401 3.0 40.0 1.0
C4C D:HEC401 3.0 44.0 1.0
C1A D:HEC401 3.0 39.5 1.0
C1B D:HEC401 3.0 45.5 1.0
CD2 D:HIS128 3.0 44.6 1.0
C4D D:HEC401 3.1 46.3 1.0
C1C D:HEC401 3.1 44.2 1.0
C1D D:HEC401 3.1 45.4 1.0
CE D:MET248 3.3 43.7 1.0
CHB D:HEC401 3.4 41.5 1.0
CHA D:HEC401 3.4 41.4 1.0
CHC D:HEC401 3.4 45.9 1.0
CHD D:HEC401 3.4 43.5 1.0
CG D:MET248 3.4 47.4 1.0
CB D:MET248 4.0 50.0 1.0
ND1 D:HIS128 4.1 43.6 1.0
CG D:HIS128 4.2 43.5 1.0
C3B D:HEC401 4.3 48.0 1.0
C3C D:HEC401 4.3 47.8 1.0
C3A D:HEC401 4.3 39.8 1.0
C2A D:HEC401 4.3 41.1 1.0
C2B D:HEC401 4.3 47.4 1.0
C2C D:HEC401 4.4 46.2 1.0
C3D D:HEC401 4.4 47.2 1.0
C2D D:HEC401 4.4 45.4 1.0

Iron binding site 6 out of 8 in 8abb

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Iron binding site 6 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


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, Ascorbate-Reduced, C-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe501

b:31.6
occ:1.00
 FE N:HEM501 0.0 31.6 1.0
ND N:HEM501 1.9 32.6 1.0
NA N:HEM501 1.9 33.0 1.0
NE2 N:HIS183 2.0 29.4 1.0
NE2 N:HIS82 2.1 30.7 1.0
NC N:HEM501 2.1 33.3 1.0
NB N:HEM501 2.1 33.7 1.0
C1D N:HEM501 2.9 33.0 1.0
C4D N:HEM501 2.9 31.9 1.0
C1A N:HEM501 2.9 33.6 1.0
CE1 N:HIS183 3.0 29.6 1.0
C4A N:HEM501 3.0 34.4 1.0
CE1 N:HIS82 3.0 33.0 1.0
C4B N:HEM501 3.0 35.8 1.0
C4C N:HEM501 3.0 33.2 1.0
C1B N:HEM501 3.1 36.8 1.0
CD2 N:HIS82 3.1 30.4 1.0
C1C N:HEM501 3.1 36.5 1.0
CD2 N:HIS183 3.1 29.1 1.0
CHA N:HEM501 3.3 31.6 1.0
CHD N:HEM501 3.4 30.8 1.0
CHB N:HEM501 3.4 36.5 1.0
CHC N:HEM501 3.4 36.6 1.0
ND1 N:HIS183 4.1 30.8 1.0
ND1 N:HIS82 4.1 33.2 1.0
C2A N:HEM501 4.1 36.3 1.0
C3A N:HEM501 4.1 35.1 1.0
C3D N:HEM501 4.1 33.4 1.0
C2D N:HEM501 4.2 34.5 1.0
CG N:HIS183 4.2 30.0 1.0
CG N:HIS82 4.2 31.6 1.0
C3C N:HEM501 4.3 39.7 1.0
C3B N:HEM501 4.3 38.8 1.0
C2C N:HEM501 4.3 38.8 1.0
C2B N:HEM501 4.3 37.0 1.0
CA N:GLY131 4.7 41.7 1.0
NE2 N:GLN43 4.9 48.9 1.0

Iron binding site 7 out of 8 in 8abb

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Iron binding site 7 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


Mono view


Stereo pair view

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

b:32.9
occ:1.00
 FE N:HEM502 0.0 32.9 1.0
ND N:HEM502 1.9 36.4 1.0
NA N:HEM502 2.0 36.3 1.0
NC N:HEM502 2.0 33.3 1.0
NE2 N:HIS96 2.0 37.2 1.0
NB N:HEM502 2.1 35.5 1.0
NE2 N:HIS197 2.1 34.4 1.0
C4D N:HEM502 2.9 37.5 1.0
C1D N:HEM502 2.9 36.0 1.0
CE1 N:HIS96 2.9 35.6 1.0
C4C N:HEM502 2.9 33.1 1.0
C1A N:HEM502 2.9 38.0 1.0
C4A N:HEM502 3.0 38.2 1.0
CE1 N:HIS197 3.0 33.9 1.0
C4B N:HEM502 3.0 37.0 1.0
C1B N:HEM502 3.1 37.5 1.0
C1C N:HEM502 3.1 34.9 1.0
CD2 N:HIS96 3.1 39.8 1.0
CD2 N:HIS197 3.2 36.3 1.0
CHA N:HEM502 3.3 38.6 1.0
CHD N:HEM502 3.4 33.6 1.0
CHB N:HEM502 3.4 38.6 1.0
CHC N:HEM502 3.5 35.2 1.0
ND1 N:HIS96 4.1 37.4 1.0
C3C N:HEM502 4.1 35.9 1.0
C2D N:HEM502 4.1 36.8 1.0
C3D N:HEM502 4.1 38.6 1.0
C2A N:HEM502 4.2 39.8 1.0
C3A N:HEM502 4.2 38.2 1.0
ND1 N:HIS197 4.2 36.1 1.0
CG N:HIS96 4.2 37.9 1.0
C2C N:HEM502 4.2 36.3 1.0
C3B N:HEM502 4.3 40.0 1.0
CG N:HIS197 4.3 35.8 1.0
C2B N:HEM502 4.3 37.6 1.0

Iron binding site 8 out of 8 in 8abb

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Iron binding site 8 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, C-Position


Mono view


Stereo pair view

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

b:40.3
occ:1.00
 FE O:HEC401 0.0 40.3 1.0
NE2 O:HIS128 2.0 43.2 1.0
NB O:HEC401 2.0 41.4 1.0
NC O:HEC401 2.1 44.5 1.0
NA O:HEC401 2.1 43.1 1.0
ND O:HEC401 2.1 46.0 1.0
SD O:MET248 2.2 52.5 1.0
CE1 O:HIS128 3.0 41.0 1.0
C4B O:HEC401 3.0 43.3 1.0
C4C O:HEC401 3.0 48.0 1.0
CD2 O:HIS128 3.0 46.2 1.0
C1B O:HEC401 3.0 42.0 1.0
C4A O:HEC401 3.0 44.1 1.0
C4D O:HEC401 3.0 48.6 1.0
C1D O:HEC401 3.1 47.1 1.0
C1C O:HEC401 3.1 46.2 1.0
C1A O:HEC401 3.1 43.9 1.0
CE O:MET248 3.3 49.4 1.0
CHA O:HEC401 3.4 46.6 1.0
CHC O:HEC401 3.4 43.6 1.0
CHB O:HEC401 3.4 41.1 1.0
CHD O:HEC401 3.4 49.0 1.0
CG O:MET248 3.4 56.8 1.0
CB O:MET248 4.0 54.6 1.0
ND1 O:HIS128 4.1 41.6 1.0
CG O:HIS128 4.1 43.3 1.0
C3B O:HEC401 4.2 44.7 1.0
C3C O:HEC401 4.3 50.2 1.0
C3A O:HEC401 4.3 46.7 1.0
C2B O:HEC401 4.3 43.7 1.0
C2A O:HEC401 4.3 45.0 1.0
C2D O:HEC401 4.3 48.5 1.0
C3D O:HEC401 4.3 51.0 1.0
C2C O:HEC401 4.4 47.9 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 16:19:23 2024

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