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

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

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

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 8abi

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

b:38.7
occ:1.00
 FE C:HEM501 0.0 38.7 1.0
ND C:HEM501 1.9 38.3 1.0
NA C:HEM501 1.9 39.3 1.0
NC C:HEM501 2.0 35.0 1.0
NE2 C:HIS82 2.0 33.5 1.0
NB C:HEM501 2.1 40.2 1.0
NE2 C:HIS183 2.1 36.7 1.0
C4D C:HEM501 2.9 37.9 1.0
C1D C:HEM501 2.9 38.0 1.0
C1A C:HEM501 3.0 40.5 1.0
C4A C:HEM501 3.0 41.9 1.0
CE1 C:HIS183 3.0 35.1 1.0
C4B C:HEM501 3.0 45.1 1.0
CE1 C:HIS82 3.0 36.7 1.0
C1C C:HEM501 3.0 38.9 1.0
C4C C:HEM501 3.0 35.5 1.0
C1B C:HEM501 3.0 43.1 1.0
CD2 C:HIS82 3.1 32.9 1.0
CD2 C:HIS183 3.1 38.1 1.0
CHA C:HEM501 3.4 37.4 1.0
CHD C:HEM501 3.4 34.8 1.0
CHC C:HEM501 3.4 41.1 1.0
CHB C:HEM501 3.4 42.9 1.0
ND1 C:HIS183 4.1 34.8 1.0
C3D C:HEM501 4.1 42.7 1.0
C3A C:HEM501 4.1 41.2 1.0
ND1 C:HIS82 4.1 34.2 1.0
C2A C:HEM501 4.2 41.4 1.0
C2D C:HEM501 4.2 41.8 1.0
CG C:HIS82 4.2 33.7 1.0
CG C:HIS183 4.2 34.8 1.0
C2C C:HEM501 4.2 41.5 1.0
C3C C:HEM501 4.2 42.4 1.0
C3B C:HEM501 4.3 48.4 1.0
C2B C:HEM501 4.3 45.5 1.0
CA C:GLY131 4.8 60.7 1.0
NE2 C:GLN43 4.9 47.9 1.0

Iron binding site 2 out of 8 in 8abi

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

b:36.5
occ:1.00
 FE C:HEM502 0.0 36.5 1.0
ND C:HEM502 1.9 37.4 1.0
NA C:HEM502 2.0 38.4 1.0
NC C:HEM502 2.0 35.9 1.0
NB C:HEM502 2.1 37.9 1.0
NE2 C:HIS96 2.2 42.0 1.0
NE2 C:HIS197 2.2 38.0 1.0
C4C C:HEM502 2.9 36.1 1.0
C1D C:HEM502 2.9 36.5 1.0
C4D C:HEM502 2.9 36.5 1.0
C1A C:HEM502 3.0 40.1 1.0
C4A C:HEM502 3.0 39.0 1.0
C4B C:HEM502 3.0 38.5 1.0
C1B C:HEM502 3.0 40.9 1.0
C1C C:HEM502 3.0 39.0 1.0
CE1 C:HIS197 3.1 37.6 1.0
CD2 C:HIS96 3.1 41.9 1.0
CE1 C:HIS96 3.2 51.9 1.0
CD2 C:HIS197 3.3 39.2 1.0
CHD C:HEM502 3.4 35.1 1.0
CHA C:HEM502 3.4 37.1 1.0
CHB C:HEM502 3.4 41.2 1.0
CHC C:HEM502 3.5 37.7 1.0
C3C C:HEM502 4.1 41.0 1.0
C2A C:HEM502 4.2 41.2 1.0
C2C C:HEM502 4.2 38.0 1.0
C3D C:HEM502 4.2 38.2 1.0
C2D C:HEM502 4.2 37.6 1.0
C3A C:HEM502 4.2 39.7 1.0
CG C:HIS96 4.2 44.2 1.0
ND1 C:HIS197 4.2 39.1 1.0
C2B C:HEM502 4.3 39.0 1.0
ND1 C:HIS96 4.3 50.1 1.0
C3B C:HEM502 4.3 41.0 1.0
CG C:HIS197 4.4 41.2 1.0

Iron binding site 3 out of 8 in 8abi

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

b:391.0
occ:1.00
 FE1 P:FES301 0.0 391.0 1.0
SG P:CYS187 2.2 298.7 1.0
S2 P:FES301 2.2 389.6 1.0
SG P:CYS168 2.2 345.6 1.0
S1 P:FES301 2.2 336.0 1.0
CB P:CYS168 2.9 287.4 1.0
FE2 P:FES301 3.0 332.2 1.0
CB P:CYS187 3.2 284.2 1.0
OG P:SER192 3.7 309.5 1.0
CB P:HIS170 3.8 204.3 1.0
CB P:CYS173 4.3 231.6 1.0
CA P:CYS168 4.3 264.5 1.0
ND1 P:HIS170 4.5 209.0 1.0
N P:LEU171 4.5 266.0 1.0
ND1 P:HIS190 4.5 248.7 1.0
N P:HIS170 4.6 206.8 1.0
CA P:CYS187 4.6 285.5 1.0
C P:CYS168 4.6 249.7 1.0
CG P:HIS170 4.6 208.3 1.0
CB P:CYS189 4.7 247.5 1.0
N P:CYS173 4.7 227.0 1.0
CA P:HIS170 4.7 215.1 1.0
SG P:CYS173 4.7 246.9 1.0
O P:CYS168 4.9 247.2 1.0
CB P:SER192 4.9 305.0 1.0
N P:GLY172 4.9 219.2 1.0
CA P:CYS173 5.0 224.9 1.0

Iron binding site 4 out of 8 in 8abi

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

b:332.2
occ:1.00
 FE2 P:FES301 0.0 332.2 1.0
ND1 P:HIS170 2.0 209.0 1.0
ND1 P:HIS190 2.1 248.7 1.0
S1 P:FES301 2.2 336.0 1.0
S2 P:FES301 2.2 389.6 1.0
CG P:HIS190 2.8 237.0 1.0
CG P:HIS170 2.9 208.3 1.0
CB P:HIS190 3.0 222.2 1.0
FE1 P:FES301 3.0 391.0 1.0
CE1 P:HIS170 3.0 215.9 1.0
CE1 P:HIS190 3.1 255.7 1.0
CB P:HIS170 3.2 204.3 1.0
N P:HIS190 3.8 242.5 1.0
CD2 P:HIS190 3.9 245.3 1.0
CA P:HIS190 4.0 223.3 1.0
NE2 P:HIS190 4.1 252.5 1.0
CD2 P:HIS170 4.1 212.1 1.0
NE2 P:HIS170 4.1 212.4 1.0
SG P:CYS187 4.3 298.7 1.0
N P:LEU171 4.3 266.0 1.0
CB P:CYS189 4.3 247.5 1.0
CG P:LEU171 4.6 322.8 1.0
CA P:HIS170 4.6 215.1 1.0
C P:CYS189 4.6 252.4 1.0
CG P:PRO204 4.6 235.6 1.0
SG P:CYS168 4.6 345.6 1.0
CB P:LEU171 4.7 294.9 1.0
C P:HIS190 4.8 220.9 1.0
CB P:PRO204 4.8 240.1 1.0
C P:HIS170 4.8 241.2 1.0
CD1 P:LEU171 4.9 324.2 1.0
OG P:SER192 5.0 309.5 1.0

Iron binding site 5 out of 8 in 8abi

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

b:56.2
occ:1.00
 FE D:HEC401 0.0 56.2 1.0
NE2 D:HIS128 2.0 56.1 1.0
NB D:HEC401 2.0 58.4 1.0
NA D:HEC401 2.0 60.0 1.0
ND D:HEC401 2.1 64.7 1.0
NC D:HEC401 2.1 64.5 1.0
SD D:MET248 2.2 64.1 1.0
CE1 D:HIS128 3.0 47.5 1.0
C4B D:HEC401 3.0 61.9 1.0
C4C D:HEC401 3.0 65.2 1.0
C1D D:HEC401 3.0 67.1 1.0
C4A D:HEC401 3.0 61.2 1.0
C1B D:HEC401 3.0 57.6 1.0
CD2 D:HIS128 3.0 58.5 1.0
C4D D:HEC401 3.0 67.7 1.0
C1A D:HEC401 3.0 59.9 1.0
C1C D:HEC401 3.1 68.5 1.0
CE D:MET248 3.3 70.8 1.0
CHD D:HEC401 3.4 61.8 1.0
CHA D:HEC401 3.4 65.7 1.0
CHB D:HEC401 3.4 55.0 1.0
CHC D:HEC401 3.4 63.9 1.0
CG D:MET248 3.4 73.6 1.0
CB D:MET248 4.0 68.4 1.0
ND1 D:HIS128 4.1 48.7 1.0
CG D:HIS128 4.1 54.7 1.0
C3B D:HEC401 4.2 60.0 1.0
C3C D:HEC401 4.3 66.7 1.0
C3A D:HEC401 4.3 58.8 1.0
C2B D:HEC401 4.3 58.1 1.0
C2D D:HEC401 4.3 71.9 1.0
C3D D:HEC401 4.3 65.9 1.0
C2A D:HEC401 4.4 59.7 1.0
C2C D:HEC401 4.4 72.1 1.0

Iron binding site 6 out of 8 in 8abi

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

b:35.4
occ:1.00
 FE N:HEM501 0.0 35.4 1.0
ND N:HEM501 1.9 36.4 1.0
NA N:HEM501 1.9 35.7 1.0
NE2 N:HIS82 2.0 37.2 1.0
NC N:HEM501 2.1 34.6 1.0
NB N:HEM501 2.1 34.3 1.0
NE2 N:HIS183 2.1 35.3 1.0
C4D N:HEM501 2.9 36.7 1.0
C1D N:HEM501 2.9 37.0 1.0
C1A N:HEM501 2.9 37.6 1.0
C4A N:HEM501 3.0 41.2 1.0
CE1 N:HIS82 3.0 36.4 1.0
CE1 N:HIS183 3.0 34.9 1.0
C4B N:HEM501 3.0 36.0 1.0
C1C N:HEM501 3.0 38.1 1.0
C4C N:HEM501 3.0 35.8 1.0
C1B N:HEM501 3.0 36.8 1.0
CD2 N:HIS82 3.1 35.4 1.0
CD2 N:HIS183 3.1 33.1 1.0
CHA N:HEM501 3.4 35.6 1.0
CHD N:HEM501 3.4 35.7 1.0
CHC N:HEM501 3.4 38.8 1.0
CHB N:HEM501 3.4 40.1 1.0
ND1 N:HIS82 4.1 36.0 1.0
C3D N:HEM501 4.1 39.7 1.0
ND1 N:HIS183 4.1 37.2 1.0
C2A N:HEM501 4.1 41.8 1.0
C3A N:HEM501 4.1 42.8 1.0
C2D N:HEM501 4.2 39.6 1.0
CG N:HIS82 4.2 36.8 1.0
CG N:HIS183 4.2 32.4 1.0
C2C N:HEM501 4.2 42.4 1.0
C3B N:HEM501 4.3 36.9 1.0
C3C N:HEM501 4.3 44.0 1.0
C2B N:HEM501 4.3 35.8 1.0
CA N:GLY131 4.8 58.6 1.0
NE2 N:GLN43 4.9 50.9 1.0

Iron binding site 7 out of 8 in 8abi

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

b:36.6
occ:1.00
 FE N:HEM502 0.0 36.6 1.0
ND N:HEM502 1.9 37.9 1.0
NA N:HEM502 1.9 37.6 1.0
NE2 N:HIS96 2.0 42.0 1.0
NC N:HEM502 2.0 35.5 1.0
NB N:HEM502 2.1 35.5 1.0
NE2 N:HIS197 2.2 31.4 1.0
CE1 N:HIS96 2.9 42.5 1.0
C1D N:HEM502 2.9 35.8 1.0
C4D N:HEM502 2.9 38.5 1.0
C4C N:HEM502 2.9 35.4 1.0
C1A N:HEM502 2.9 38.1 1.0
C4A N:HEM502 3.0 42.0 1.0
C1B N:HEM502 3.0 38.0 1.0
C4B N:HEM502 3.0 35.5 1.0
CE1 N:HIS197 3.0 33.6 1.0
C1C N:HEM502 3.0 37.2 1.0
CD2 N:HIS96 3.1 42.1 1.0
CD2 N:HIS197 3.2 33.7 1.0
CHD N:HEM502 3.4 34.9 1.0
CHA N:HEM502 3.4 35.9 1.0
CHB N:HEM502 3.4 39.7 1.0
CHC N:HEM502 3.5 35.8 1.0
ND1 N:HIS96 4.0 43.2 1.0
C3C N:HEM502 4.1 38.2 1.0
C2A N:HEM502 4.1 42.0 1.0
C3A N:HEM502 4.1 41.9 1.0
C3D N:HEM502 4.2 39.1 1.0
C2D N:HEM502 4.2 37.8 1.0
C2C N:HEM502 4.2 38.1 1.0
CG N:HIS96 4.2 40.0 1.0
ND1 N:HIS197 4.2 34.5 1.0
C2B N:HEM502 4.3 35.8 1.0
C3B N:HEM502 4.3 36.9 1.0
CG N:HIS197 4.3 37.5 1.0

Iron binding site 8 out of 8 in 8abi

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

b:53.0
occ:1.00
 FE O:HEC401 0.0 53.0 1.0
NE2 O:HIS128 2.0 62.6 1.0
ND O:HEC401 2.0 55.4 1.0
NB O:HEC401 2.0 53.8 1.0
NC O:HEC401 2.1 56.8 1.0
NA O:HEC401 2.1 56.0 1.0
SD O:MET248 2.3 59.8 1.0
CE1 O:HIS128 2.9 56.6 1.0
CD2 O:HIS128 3.0 62.4 1.0
C4D O:HEC401 3.0 61.2 1.0
C4B O:HEC401 3.0 54.4 1.0
C4C O:HEC401 3.0 56.6 1.0
C1D O:HEC401 3.0 58.0 1.0
C1A O:HEC401 3.0 60.8 1.0
C1C O:HEC401 3.0 61.5 1.0
C4A O:HEC401 3.1 55.4 1.0
C1B O:HEC401 3.1 52.2 1.0
CE O:MET248 3.3 66.3 1.0
CHA O:HEC401 3.4 64.2 1.0
CHD O:HEC401 3.4 57.2 1.0
CHC O:HEC401 3.4 56.5 1.0
CHB O:HEC401 3.4 49.5 1.0
CG O:MET248 3.5 69.9 1.0
ND1 O:HIS128 4.0 53.7 1.0
CB O:MET248 4.1 70.4 1.0
CG O:HIS128 4.1 56.1 1.0
C3B O:HEC401 4.3 52.9 1.0
C3C O:HEC401 4.3 62.2 1.0
C3D O:HEC401 4.3 61.9 1.0
C3A O:HEC401 4.3 57.1 1.0
C2A O:HEC401 4.3 57.3 1.0
C2D O:HEC401 4.3 61.3 1.0
C2B O:HEC401 4.4 50.3 1.0
C2C O:HEC401 4.4 63.9 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 17:11:10 2024

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