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Iron in PDB 8abh: Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-Position

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-Position

All present enzymatic activity of Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-Position:
7.1.1.8;

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 8abh

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Iron binding site 1 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:33.2
occ:1.00
 FE C:HEM501 0.0 33.2 1.0
ND C:HEM501 1.9 34.8 1.0
NA C:HEM501 1.9 34.5 1.0
NE2 C:HIS183 2.0 35.7 1.0
NE2 C:HIS82 2.0 40.1 1.0
NB C:HEM501 2.1 33.8 1.0
NC C:HEM501 2.1 36.9 1.0
C4D C:HEM501 2.9 35.3 1.0
C1D C:HEM501 2.9 35.7 1.0
C1A C:HEM501 2.9 34.1 1.0
CE1 C:HIS183 3.0 39.1 1.0
C4A C:HEM501 3.0 37.1 1.0
C4B C:HEM501 3.0 37.0 1.0
CE1 C:HIS82 3.0 41.6 1.0
C1C C:HEM501 3.0 41.0 1.0
C1B C:HEM501 3.0 35.1 1.0
C4C C:HEM501 3.1 36.2 1.0
CD2 C:HIS82 3.1 41.5 1.0
CD2 C:HIS183 3.1 33.8 1.0
CHA C:HEM501 3.3 33.6 1.0
CHD C:HEM501 3.4 34.7 1.0
CHC C:HEM501 3.4 39.2 1.0
CHB C:HEM501 3.5 35.9 1.0
C3D C:HEM501 4.1 36.7 1.0
ND1 C:HIS183 4.1 40.9 1.0
C3A C:HEM501 4.1 35.4 1.0
ND1 C:HIS82 4.1 43.7 1.0
C2A C:HEM501 4.1 36.9 1.0
C2D C:HEM501 4.1 35.5 1.0
CG C:HIS82 4.2 41.9 1.0
CG C:HIS183 4.2 36.0 1.0
C2C C:HEM501 4.2 44.4 1.0
C3B C:HEM501 4.2 39.4 1.0
C3C C:HEM501 4.3 44.7 1.0
C2B C:HEM501 4.3 37.8 1.0
CA C:GLY131 4.8 58.7 1.0
NE2 C:GLN43 4.9 56.1 1.0

Iron binding site 2 out of 8 in 8abh

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Iron binding site 2 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:31.8
occ:1.00
 FE C:HEM502 0.0 31.8 1.0
ND C:HEM502 1.9 36.8 1.0
NA C:HEM502 2.0 33.6 1.0
NC C:HEM502 2.0 35.1 1.0
NB C:HEM502 2.1 32.2 1.0
NE2 C:HIS197 2.1 33.6 1.0
NE2 C:HIS96 2.2 42.3 1.0
C4D C:HEM502 2.9 37.8 1.0
C1D C:HEM502 2.9 36.6 1.0
C4C C:HEM502 2.9 36.3 1.0
C1A C:HEM502 2.9 36.9 1.0
C4A C:HEM502 3.0 35.2 1.0
CE1 C:HIS197 3.0 37.3 1.0
C4B C:HEM502 3.0 32.5 1.0
C1B C:HEM502 3.0 33.5 1.0
C1C C:HEM502 3.1 38.7 1.0
CD2 C:HIS96 3.1 40.7 1.0
CE1 C:HIS96 3.2 45.3 1.0
CD2 C:HIS197 3.2 35.0 1.0
CHA C:HEM502 3.4 38.5 1.0
CHD C:HEM502 3.4 35.6 1.0
CHB C:HEM502 3.4 33.9 1.0
CHC C:HEM502 3.5 36.7 1.0
C3C C:HEM502 4.1 39.3 1.0
C2A C:HEM502 4.1 39.2 1.0
C3A C:HEM502 4.2 35.6 1.0
C3D C:HEM502 4.2 38.8 1.0
C2C C:HEM502 4.2 40.1 1.0
ND1 C:HIS197 4.2 38.2 1.0
C2D C:HEM502 4.2 38.7 1.0
C2B C:HEM502 4.3 31.6 1.0
CG C:HIS96 4.3 39.8 1.0
C3B C:HEM502 4.3 33.7 1.0
ND1 C:HIS96 4.3 45.7 1.0
CG C:HIS197 4.3 38.9 1.0

Iron binding site 3 out of 8 in 8abh

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Iron binding site 3 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:128.8
occ:1.00
 FE1 P:FES301 0.0 128.8 1.0
S2 P:FES301 2.2 117.6 1.0
SG P:CYS187 2.2 117.9 1.0
SG P:CYS168 2.2 152.1 1.0
S1 P:FES301 2.2 137.8 1.0
CB P:CYS168 2.9 146.9 1.0
FE2 P:FES301 3.0 140.0 1.0
CB P:CYS187 3.2 113.7 1.0
OG P:SER192 3.7 180.8 1.0
CB P:HIS170 3.8 126.8 1.0
CB P:CYS173 4.2 126.8 1.0
CA P:CYS168 4.3 140.9 1.0
ND1 P:HIS170 4.5 139.7 1.0
ND1 P:HIS190 4.5 150.4 1.0
N P:LEU171 4.6 126.2 1.0
N P:HIS170 4.6 135.1 1.0
CA P:CYS187 4.6 128.8 1.0
C P:CYS168 4.6 133.7 1.0
CG P:HIS170 4.6 137.2 1.0
CB P:CYS189 4.6 172.1 1.0
SG P:CYS173 4.7 162.3 1.0
CA P:HIS170 4.7 133.6 1.0
N P:CYS173 4.7 103.3 1.0
O P:CYS168 4.9 127.4 1.0
CB P:SER192 4.9 162.9 1.0
O P:CYS173 4.9 108.4 1.0
CA P:CYS173 5.0 102.5 1.0
N P:HIS190 5.0 142.5 1.0

Iron binding site 4 out of 8 in 8abh

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Iron binding site 4 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:140.0
occ:1.00
 FE2 P:FES301 0.0 140.0 1.0
ND1 P:HIS170 2.0 139.7 1.0
ND1 P:HIS190 2.1 150.4 1.0
S1 P:FES301 2.2 137.8 1.0
S2 P:FES301 2.2 117.6 1.0
CG P:HIS190 2.8 149.2 1.0
CG P:HIS170 2.9 137.2 1.0
FE1 P:FES301 3.0 128.8 1.0
CB P:HIS190 3.0 137.7 1.0
CE1 P:HIS170 3.0 147.6 1.0
CE1 P:HIS190 3.2 156.0 1.0
CB P:HIS170 3.2 126.8 1.0
N P:HIS190 3.9 142.5 1.0
CD2 P:HIS190 3.9 157.8 1.0
CA P:HIS190 4.0 137.8 1.0
CD2 P:HIS170 4.1 149.1 1.0
NE2 P:HIS190 4.1 153.4 1.0
NE2 P:HIS170 4.1 152.8 1.0
SG P:CYS187 4.2 117.9 1.0
N P:LEU171 4.3 126.2 1.0
CB P:CYS189 4.3 172.1 1.0
CG P:PRO204 4.5 181.3 1.0
CA P:HIS170 4.5 133.6 1.0
SG P:CYS168 4.6 152.1 1.0
CG P:LEU171 4.6 129.7 1.0
C P:CYS189 4.7 151.9 1.0
CB P:LEU171 4.7 126.5 1.0
CB P:PRO204 4.7 181.7 1.0
C P:HIS170 4.8 134.4 1.0
C P:HIS190 4.8 135.2 1.0
CD1 P:LEU171 4.9 137.7 1.0
OG P:SER192 5.0 180.8 1.0

Iron binding site 5 out of 8 in 8abh

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Iron binding site 5 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:53.3
occ:1.00
 FE D:HEC401 0.0 53.3 1.0
NE2 D:HIS128 2.0 61.5 1.0
ND D:HEC401 2.0 58.9 1.0
NB D:HEC401 2.0 54.6 1.0
NA D:HEC401 2.0 56.4 1.0
NC D:HEC401 2.1 58.7 1.0
SD D:MET248 2.2 60.0 1.0
CE1 D:HIS128 3.0 55.9 1.0
C4B D:HEC401 3.0 54.9 1.0
C4C D:HEC401 3.0 64.1 1.0
C1D D:HEC401 3.0 63.9 1.0
C4D D:HEC401 3.0 59.7 1.0
C1A D:HEC401 3.0 59.9 1.0
CD2 D:HIS128 3.0 67.0 1.0
C1B D:HEC401 3.0 55.3 1.0
C4A D:HEC401 3.0 56.7 1.0
C1C D:HEC401 3.1 63.6 1.0
CE D:MET248 3.3 57.6 1.0
CHA D:HEC401 3.4 56.7 1.0
CHD D:HEC401 3.4 60.0 1.0
CHB D:HEC401 3.4 51.5 1.0
CHC D:HEC401 3.4 62.0 1.0
CG D:MET248 3.4 61.7 1.0
CB D:MET248 4.0 62.5 1.0
ND1 D:HIS128 4.1 54.9 1.0
CG D:HIS128 4.1 57.9 1.0
C3B D:HEC401 4.2 54.4 1.0
C3C D:HEC401 4.3 72.9 1.0
C2D D:HEC401 4.3 67.1 1.0
C2B D:HEC401 4.3 55.9 1.0
C3D D:HEC401 4.3 66.4 1.0
C3A D:HEC401 4.3 58.8 1.0
C2A D:HEC401 4.3 60.9 1.0
C2C D:HEC401 4.4 67.0 1.0

Iron binding site 6 out of 8 in 8abh

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Iron binding site 6 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe501

b:34.2
occ:1.00
 FE N:HEM501 0.0 34.2 1.0
ND N:HEM501 1.9 34.8 1.0
NA N:HEM501 2.0 37.4 1.0
NE2 N:HIS82 2.0 34.4 1.0
NC N:HEM501 2.0 37.6 1.0
NB N:HEM501 2.1 35.2 1.0
NE2 N:HIS183 2.1 36.4 1.0
C4D N:HEM501 2.9 34.3 1.0
C1D N:HEM501 2.9 36.7 1.0
C1A N:HEM501 3.0 36.8 1.0
CE1 N:HIS82 3.0 36.5 1.0
C4A N:HEM501 3.0 39.4 1.0
C4B N:HEM501 3.0 38.9 1.0
CE1 N:HIS183 3.0 36.2 1.0
C1C N:HEM501 3.0 42.0 1.0
C4C N:HEM501 3.0 38.3 1.0
C1B N:HEM501 3.0 38.4 1.0
CD2 N:HIS82 3.1 37.0 1.0
CD2 N:HIS183 3.1 36.8 1.0
CHA N:HEM501 3.4 33.3 1.0
CHD N:HEM501 3.4 36.0 1.0
CHC N:HEM501 3.4 39.4 1.0
CHB N:HEM501 3.5 38.6 1.0
ND1 N:HIS82 4.1 41.1 1.0
C3D N:HEM501 4.1 38.3 1.0
ND1 N:HIS183 4.1 39.2 1.0
C3A N:HEM501 4.1 40.3 1.0
C2D N:HEM501 4.1 37.8 1.0
C2A N:HEM501 4.1 40.0 1.0
CG N:HIS82 4.2 37.1 1.0
CG N:HIS183 4.2 38.7 1.0
C2C N:HEM501 4.2 44.5 1.0
C3C N:HEM501 4.2 45.0 1.0
C3B N:HEM501 4.2 42.8 1.0
C2B N:HEM501 4.3 42.4 1.0
CA N:GLY131 4.8 61.1 1.0
NE2 N:GLN43 4.9 47.3 1.0

Iron binding site 7 out of 8 in 8abh

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Iron binding site 7 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe502

b:36.0
occ:1.00
 FE N:HEM502 0.0 36.0 1.0
ND N:HEM502 1.9 38.3 1.0
NA N:HEM502 2.0 37.4 1.0
NE2 N:HIS96 2.0 43.5 1.0
NC N:HEM502 2.0 38.9 1.0
NB N:HEM502 2.1 38.4 1.0
NE2 N:HIS197 2.2 37.3 1.0
C1D N:HEM502 2.9 36.7 1.0
C4D N:HEM502 2.9 40.7 1.0
C4C N:HEM502 2.9 39.5 1.0
CE1 N:HIS96 2.9 45.1 1.0
C1A N:HEM502 2.9 39.2 1.0
C4A N:HEM502 3.0 38.5 1.0
C4B N:HEM502 3.0 42.4 1.0
C1B N:HEM502 3.0 41.9 1.0
CE1 N:HIS197 3.0 36.7 1.0
C1C N:HEM502 3.0 43.8 1.0
CD2 N:HIS96 3.1 44.1 1.0
CD2 N:HIS197 3.2 40.4 1.0
CHD N:HEM502 3.3 38.1 1.0
CHA N:HEM502 3.3 40.3 1.0
CHB N:HEM502 3.4 40.2 1.0
CHC N:HEM502 3.5 43.2 1.0
ND1 N:HIS96 4.1 41.8 1.0
C3C N:HEM502 4.1 42.3 1.0
C2A N:HEM502 4.1 41.3 1.0
C3A N:HEM502 4.1 37.7 1.0
C2D N:HEM502 4.2 38.0 1.0
C3D N:HEM502 4.2 39.6 1.0
C2C N:HEM502 4.2 42.1 1.0
CG N:HIS96 4.2 39.9 1.0
ND1 N:HIS197 4.2 40.0 1.0
C2B N:HEM502 4.3 44.4 1.0
C3B N:HEM502 4.3 48.7 1.0
CG N:HIS197 4.3 40.4 1.0

Iron binding site 8 out of 8 in 8abh

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Iron binding site 8 out of 8 in the Complex III2 From Yarrowia Lipolytica, Antimycin A Bound, B-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, Antimycin A Bound, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe401

b:55.4
occ:1.00
 FE O:HEC401 0.0 55.4 1.0
NE2 O:HIS128 2.0 60.1 1.0
ND O:HEC401 2.0 60.6 1.0
NB O:HEC401 2.0 59.4 1.0
NC O:HEC401 2.0 62.1 1.0
NA O:HEC401 2.1 56.7 1.0
SD O:MET248 2.3 57.3 1.0
CE1 O:HIS128 2.9 53.7 1.0
C4B O:HEC401 3.0 58.6 1.0
CD2 O:HIS128 3.0 65.2 1.0
C4C O:HEC401 3.0 65.5 1.0
C4D O:HEC401 3.0 59.6 1.0
C1D O:HEC401 3.0 65.3 1.0
C1C O:HEC401 3.0 63.9 1.0
C1A O:HEC401 3.0 57.5 1.0
C1B O:HEC401 3.0 59.9 1.0
C4A O:HEC401 3.1 56.4 1.0
CE O:MET248 3.3 63.6 1.0
CHA O:HEC401 3.4 57.2 1.0
CHD O:HEC401 3.4 60.7 1.0
CHC O:HEC401 3.4 59.0 1.0
CHB O:HEC401 3.4 51.3 1.0
CG O:MET248 3.5 60.1 1.0
ND1 O:HIS128 4.0 53.7 1.0
CB O:MET248 4.1 58.6 1.0
CG O:HIS128 4.1 56.9 1.0
C3B O:HEC401 4.3 56.9 1.0
C3C O:HEC401 4.3 67.7 1.0
C3D O:HEC401 4.3 61.0 1.0
C2B O:HEC401 4.3 56.0 1.0
C2D O:HEC401 4.3 63.6 1.0
C2C O:HEC401 4.3 66.1 1.0
C3A O:HEC401 4.4 56.9 1.0
C2A O:HEC401 4.4 55.5 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 17:11:10 2024

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