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

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

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

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 8abj

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

b:43.0
occ:1.00
 FE C:HEM501 0.0 43.0 1.0
ND C:HEM501 1.9 51.0 1.0
NA C:HEM501 2.0 52.6 1.0
NC C:HEM501 2.0 45.3 1.0
NE2 C:HIS183 2.0 45.1 1.0
NE2 C:HIS82 2.0 46.6 1.0
NB C:HEM501 2.1 48.2 1.0
C4D C:HEM501 2.9 50.4 1.0
C1D C:HEM501 2.9 54.4 1.0
C1A C:HEM501 3.0 55.4 1.0
CE1 C:HIS183 3.0 49.0 1.0
C4A C:HEM501 3.0 58.6 1.0
C4B C:HEM501 3.0 54.1 1.0
CE1 C:HIS82 3.0 48.9 1.0
C1C C:HEM501 3.0 51.4 1.0
C4C C:HEM501 3.0 45.3 1.0
C1B C:HEM501 3.0 56.6 1.0
CD2 C:HIS82 3.1 49.6 1.0
CD2 C:HIS183 3.1 48.1 1.0
CHA C:HEM501 3.4 51.1 1.0
CHD C:HEM501 3.4 47.9 1.0
CHC C:HEM501 3.4 55.3 1.0
CHB C:HEM501 3.5 61.2 1.0
ND1 C:HIS183 4.1 50.0 1.0
ND1 C:HIS82 4.1 45.4 1.0
C3A C:HEM501 4.1 61.3 1.0
C3D C:HEM501 4.1 51.2 1.0
C2A C:HEM501 4.2 60.5 1.0
C2D C:HEM501 4.2 56.2 1.0
C2C C:HEM501 4.2 57.5 1.0
CG C:HIS82 4.2 46.7 1.0
CG C:HIS183 4.2 47.2 1.0
C3C C:HEM501 4.2 56.3 1.0
C3B C:HEM501 4.2 63.7 1.0
C2B C:HEM501 4.3 65.0 1.0
CA C:GLY131 4.8 60.8 1.0
NE2 C:GLN43 4.9 74.2 1.0

Iron binding site 2 out of 8 in 8abj

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

b:39.6
occ:1.00
 FE C:HEM502 0.0 39.6 1.0
ND C:HEM502 1.9 46.0 1.0
NA C:HEM502 2.0 44.7 1.0
NC C:HEM502 2.0 46.4 1.0
NB C:HEM502 2.1 48.5 1.0
NE2 C:HIS96 2.2 49.1 1.0
NE2 C:HIS197 2.2 34.0 1.0
C4D C:HEM502 2.9 48.2 1.0
C1D C:HEM502 2.9 47.7 1.0
C4C C:HEM502 2.9 47.5 1.0
C1A C:HEM502 2.9 46.0 1.0
C4A C:HEM502 3.0 47.9 1.0
C4B C:HEM502 3.0 52.1 1.0
C1B C:HEM502 3.0 52.2 1.0
C1C C:HEM502 3.1 43.4 1.0
CD2 C:HIS96 3.1 45.5 1.0
CE1 C:HIS197 3.1 34.3 1.0
CE1 C:HIS96 3.2 74.9 1.0
CD2 C:HIS197 3.3 38.5 1.0
CHA C:HEM502 3.4 48.1 1.0
CHB C:HEM502 3.4 52.1 1.0
CHD C:HEM502 3.4 44.1 1.0
CHC C:HEM502 3.5 47.6 1.0
C3C C:HEM502 4.1 45.0 1.0
C2A C:HEM502 4.1 45.7 1.0
C3A C:HEM502 4.2 48.1 1.0
C3D C:HEM502 4.2 51.7 1.0
C2C C:HEM502 4.2 40.1 1.0
C2D C:HEM502 4.2 49.7 1.0
CG C:HIS96 4.2 54.3 1.0
ND1 C:HIS96 4.2 69.0 1.0
ND1 C:HIS197 4.2 38.5 1.0
C3B C:HEM502 4.3 52.9 1.0
C2B C:HEM502 4.3 53.7 1.0
CG C:HIS197 4.4 39.4 1.0

Iron binding site 3 out of 8 in 8abj

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

b:230.1
occ:1.00
 FE1 P:FES301 0.0 230.1 1.0
SG P:CYS168 2.2 215.6 1.0
S2 P:FES301 2.2 267.7 1.0
S1 P:FES301 2.2 197.4 1.0
SG P:CYS187 2.2 234.1 1.0
CB P:CYS168 2.8 169.8 1.0
FE2 P:FES301 3.0 250.1 1.0
CB P:CYS187 3.2 220.8 1.0
OG P:SER192 3.7 231.8 1.0
CB P:HIS170 3.8 232.4 1.0
CA P:CYS168 4.2 159.9 1.0
CB P:CYS173 4.3 178.9 1.0
ND1 P:HIS170 4.5 254.1 1.0
N P:LEU171 4.5 200.2 1.0
ND1 P:HIS190 4.5 203.2 1.0
N P:HIS170 4.6 206.9 1.0
C P:CYS168 4.6 159.3 1.0
CA P:CYS187 4.6 220.4 1.0
CB P:CYS189 4.7 223.1 1.0
N P:CYS173 4.7 157.1 1.0
CG P:HIS170 4.7 234.8 1.0
CA P:HIS170 4.7 218.9 1.0
SG P:CYS173 4.8 213.5 1.0
O P:CYS168 4.9 158.7 1.0
CB P:SER192 4.9 222.2 1.0
N P:GLY172 4.9 209.2 1.0
O P:CYS173 4.9 143.6 1.0
CA P:CYS173 5.0 160.9 1.0

Iron binding site 4 out of 8 in 8abj

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

b:250.1
occ:1.00
 FE2 P:FES301 0.0 250.1 1.0
ND1 P:HIS170 2.0 254.1 1.0
ND1 P:HIS190 2.1 203.2 1.0
S2 P:FES301 2.2 267.7 1.0
S1 P:FES301 2.2 197.4 1.0
CG P:HIS190 2.8 199.6 1.0
CG P:HIS170 2.9 234.8 1.0
CB P:HIS190 3.0 188.1 1.0
FE1 P:FES301 3.0 230.1 1.0
CE1 P:HIS170 3.0 266.0 1.0
CE1 P:HIS190 3.2 186.7 1.0
CB P:HIS170 3.2 232.4 1.0
N P:HIS190 3.8 179.1 1.0
CD2 P:HIS190 3.9 200.2 1.0
CA P:HIS190 4.0 169.5 1.0
NE2 P:HIS190 4.1 183.8 1.0
CD2 P:HIS170 4.1 222.4 1.0
NE2 P:HIS170 4.1 222.8 1.0
N P:LEU171 4.3 200.2 1.0
SG P:CYS187 4.3 234.1 1.0
CB P:CYS189 4.3 223.1 1.0
CG P:LEU171 4.6 216.9 1.0
CA P:HIS170 4.6 218.9 1.0
C P:CYS189 4.6 194.5 1.0
SG P:CYS168 4.6 215.6 1.0
CB P:LEU171 4.6 201.4 1.0
CG P:PRO204 4.6 160.8 1.0
C P:HIS190 4.7 162.6 1.0
C P:HIS170 4.8 203.9 1.0
CB P:PRO204 4.8 170.9 1.0
CD1 P:LEU171 4.9 180.8 1.0
OG P:SER192 5.0 231.8 1.0

Iron binding site 5 out of 8 in 8abj

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

b:66.7
occ:1.00
 FE D:HEC401 0.0 66.7 1.0
NE2 D:HIS128 2.0 82.2 1.0
NB D:HEC401 2.0 80.8 1.0
NA D:HEC401 2.0 68.4 1.0
ND D:HEC401 2.0 69.3 1.0
NC D:HEC401 2.1 73.4 1.0
SD D:MET248 2.3 73.6 1.0
CE1 D:HIS128 2.9 82.2 1.0
C4B D:HEC401 3.0 81.2 1.0
C4C D:HEC401 3.0 67.9 1.0
C4D D:HEC401 3.0 73.0 1.0
C1D D:HEC401 3.0 70.8 1.0
CD2 D:HIS128 3.0 84.2 1.0
C1A D:HEC401 3.0 69.7 1.0
C4A D:HEC401 3.0 72.5 1.0
C1B D:HEC401 3.0 84.8 1.0
C1C D:HEC401 3.1 77.2 1.0
CE D:MET248 3.3 79.9 1.0
CHA D:HEC401 3.4 75.9 1.0
CHD D:HEC401 3.4 69.5 1.0
CHB D:HEC401 3.4 79.2 1.0
CHC D:HEC401 3.4 72.9 1.0
CG D:MET248 3.5 78.2 1.0
CB D:MET248 4.0 80.7 1.0
ND1 D:HIS128 4.1 76.3 1.0
CG D:HIS128 4.1 77.7 1.0
C3B D:HEC401 4.3 76.1 1.0
C3C D:HEC401 4.3 80.0 1.0
C3D D:HEC401 4.3 75.7 1.0
C3A D:HEC401 4.3 73.5 1.0
C2D D:HEC401 4.3 76.2 1.0
C2A D:HEC401 4.3 70.6 1.0
C2B D:HEC401 4.3 83.2 1.0
C2C D:HEC401 4.4 83.4 1.0

Iron binding site 6 out of 8 in 8abj

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

b:47.9
occ:1.00
 FE N:HEM501 0.0 47.9 1.0
ND N:HEM501 1.9 54.9 1.0
NA N:HEM501 2.0 48.2 1.0
NC N:HEM501 2.0 46.7 1.0
NE2 N:HIS82 2.0 51.4 1.0
NE2 N:HIS183 2.1 41.6 1.0
NB N:HEM501 2.1 52.4 1.0
C4D N:HEM501 2.9 56.3 1.0
C1D N:HEM501 2.9 55.5 1.0
C1A N:HEM501 3.0 50.8 1.0
CE1 N:HIS82 3.0 54.4 1.0
C4A N:HEM501 3.0 49.1 1.0
C1C N:HEM501 3.0 49.5 1.0
C4C N:HEM501 3.0 49.0 1.0
CE1 N:HIS183 3.0 46.5 1.0
C4B N:HEM501 3.0 55.6 1.0
CD2 N:HIS82 3.1 51.7 1.0
C1B N:HEM501 3.1 55.0 1.0
CD2 N:HIS183 3.1 45.2 1.0
CHA N:HEM501 3.4 52.8 1.0
CHD N:HEM501 3.4 51.3 1.0
CHC N:HEM501 3.4 52.4 1.0
CHB N:HEM501 3.5 52.5 1.0
ND1 N:HIS82 4.1 55.1 1.0
C3D N:HEM501 4.1 55.1 1.0
ND1 N:HIS183 4.1 50.8 1.0
C2A N:HEM501 4.1 56.5 1.0
C3A N:HEM501 4.2 52.2 1.0
C2D N:HEM501 4.2 56.1 1.0
CG N:HIS82 4.2 53.9 1.0
CG N:HIS183 4.2 51.5 1.0
C2C N:HEM501 4.2 53.9 1.0
C3C N:HEM501 4.2 57.0 1.0
C3B N:HEM501 4.3 63.9 1.0
C2B N:HEM501 4.3 56.2 1.0
CA N:GLY131 4.8 57.1 1.0
NE2 N:GLN43 4.9 68.8 1.0

Iron binding site 7 out of 8 in 8abj

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

b:38.5
occ:1.00
 FE N:HEM502 0.0 38.5 1.0
ND N:HEM502 1.9 47.8 1.0
NA N:HEM502 2.0 49.5 1.0
NE2 N:HIS96 2.0 55.7 1.0
NC N:HEM502 2.0 42.7 1.0
NB N:HEM502 2.1 44.5 1.0
NE2 N:HIS197 2.2 40.7 1.0
CE1 N:HIS96 2.9 64.5 1.0
C1D N:HEM502 2.9 48.8 1.0
C4C N:HEM502 2.9 45.4 1.0
C4D N:HEM502 2.9 52.1 1.0
C1A N:HEM502 2.9 52.9 1.0
C4A N:HEM502 3.0 51.2 1.0
C1C N:HEM502 3.0 46.1 1.0
C4B N:HEM502 3.0 46.4 1.0
C1B N:HEM502 3.0 45.3 1.0
CE1 N:HIS197 3.1 45.5 1.0
CD2 N:HIS96 3.1 60.6 1.0
CD2 N:HIS197 3.3 45.1 1.0
CHA N:HEM502 3.4 49.9 1.0
CHD N:HEM502 3.4 43.8 1.0
CHB N:HEM502 3.4 47.2 1.0
CHC N:HEM502 3.5 47.3 1.0
ND1 N:HIS96 4.0 64.8 1.0
C3C N:HEM502 4.1 50.8 1.0
C2A N:HEM502 4.1 55.3 1.0
C2C N:HEM502 4.1 48.3 1.0
CG N:HIS96 4.1 61.0 1.0
C3D N:HEM502 4.1 54.3 1.0
C3A N:HEM502 4.2 53.4 1.0
C2D N:HEM502 4.2 51.8 1.0
ND1 N:HIS197 4.2 50.0 1.0
C2B N:HEM502 4.3 45.5 1.0
C3B N:HEM502 4.3 45.5 1.0
CG N:HIS197 4.3 51.2 1.0

Iron binding site 8 out of 8 in 8abj

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

b:70.3
occ:1.00
 FE O:HEC401 0.0 70.3 1.0
NE2 O:HIS128 2.0 83.5 1.0
NB O:HEC401 2.0 71.0 1.0
NA O:HEC401 2.1 65.4 1.0
NC O:HEC401 2.1 79.9 1.0
ND O:HEC401 2.1 74.1 1.0
SD O:MET248 2.3 80.1 1.0
CE1 O:HIS128 2.9 86.4 1.0
C4B O:HEC401 3.0 74.5 1.0
CD2 O:HIS128 3.0 84.0 1.0
C1B O:HEC401 3.0 75.2 1.0
C4D O:HEC401 3.0 73.8 1.0
C4A O:HEC401 3.0 65.2 1.0
C4C O:HEC401 3.0 83.8 1.0
C1C O:HEC401 3.0 82.3 1.0
C1A O:HEC401 3.1 64.8 1.0
C1D O:HEC401 3.1 78.0 1.0
CE O:MET248 3.3 86.5 1.0
CHA O:HEC401 3.4 70.9 1.0
CHC O:HEC401 3.4 73.8 1.0
CHB O:HEC401 3.4 69.2 1.0
CHD O:HEC401 3.4 76.6 1.0
CG O:MET248 3.5 84.5 1.0
ND1 O:HIS128 4.1 77.6 1.0
CB O:MET248 4.1 70.3 1.0
CG O:HIS128 4.1 75.7 1.0
C3B O:HEC401 4.2 77.3 1.0
C3C O:HEC401 4.3 99.8 1.0
C3D O:HEC401 4.3 85.7 1.0
C2B O:HEC401 4.3 77.8 1.0
C3A O:HEC401 4.3 67.1 1.0
C2C O:HEC401 4.3 102.2 1.0
C2A O:HEC401 4.4 60.7 1.0
C2D O:HEC401 4.4 86.7 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 17:11:09 2024

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