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Iron in PDB 8ac3: Complex III2 From Yarrowia Lipolytica, Apo, Int-Position

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, Apo, Int-Position

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

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, Apo, Int-Position (pdb code 8ac3). 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, Apo, Int-Position, PDB code: 8ac3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8ac3

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

b:32.1
occ:1.00
 FE C:HEM501 0.0 32.1 1.0
ND C:HEM501 1.9 32.6 1.0
NA C:HEM501 2.0 32.3 1.0
NE2 C:HIS82 2.0 29.8 1.0
NC C:HEM501 2.0 32.5 1.0
NE2 C:HIS183 2.1 31.9 1.0
NB C:HEM501 2.1 32.8 1.0
C1D C:HEM501 2.9 33.3 1.0
C4D C:HEM501 2.9 33.0 1.0
C1A C:HEM501 3.0 33.3 1.0
C4A C:HEM501 3.0 34.9 1.0
CE1 C:HIS82 3.0 30.8 1.0
C4B C:HEM501 3.0 32.9 1.0
C1C C:HEM501 3.0 34.0 1.0
CE1 C:HIS183 3.0 32.0 1.0
C4C C:HEM501 3.0 34.5 1.0
CD2 C:HIS82 3.1 29.6 1.0
C1B C:HEM501 3.1 33.6 1.0
CD2 C:HIS183 3.1 32.0 1.0
CHD C:HEM501 3.4 33.2 1.0
CHA C:HEM501 3.4 31.6 1.0
CHC C:HEM501 3.4 33.2 1.0
CHB C:HEM501 3.5 33.9 1.0
ND1 C:HIS82 4.1 31.3 1.0
C3D C:HEM501 4.1 36.5 1.0
ND1 C:HIS183 4.2 30.4 1.0
C2D C:HEM501 4.2 36.3 1.0
C3A C:HEM501 4.2 35.9 1.0
CG C:HIS82 4.2 30.8 1.0
C2A C:HEM501 4.2 36.9 1.0
C2C C:HEM501 4.2 35.5 1.0
CG C:HIS183 4.2 32.4 1.0
C3C C:HEM501 4.2 36.9 1.0
C3B C:HEM501 4.3 33.2 1.0
C2B C:HEM501 4.3 32.5 1.0
CA C:GLY131 4.8 43.3 1.0
NE2 C:GLN43 4.9 40.5 1.0

Iron binding site 2 out of 8 in 8ac3

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

b:32.1
occ:1.00
 FE C:HEM502 0.0 32.1 1.0
ND C:HEM502 1.9 32.0 1.0
NA C:HEM502 2.0 32.2 1.0
NC C:HEM502 2.0 31.3 1.0
NB C:HEM502 2.1 32.2 1.0
NE2 C:HIS197 2.2 36.4 1.0
NE2 C:HIS96 2.2 38.5 1.0
C1D C:HEM502 2.9 30.7 1.0
C4C C:HEM502 2.9 32.4 1.0
C4D C:HEM502 2.9 31.7 1.0
C1A C:HEM502 3.0 33.0 1.0
C4A C:HEM502 3.0 35.9 1.0
CE1 C:HIS197 3.0 36.9 1.0
C4B C:HEM502 3.1 32.7 1.0
C1C C:HEM502 3.1 32.9 1.0
C1B C:HEM502 3.1 34.3 1.0
CD2 C:HIS96 3.1 36.4 1.0
CE1 C:HIS96 3.2 39.9 1.0
CD2 C:HIS197 3.2 36.1 1.0
CHD C:HEM502 3.4 32.1 1.0
CHA C:HEM502 3.4 31.6 1.0
CHB C:HEM502 3.5 35.2 1.0
CHC C:HEM502 3.5 34.0 1.0
C3C C:HEM502 4.1 33.5 1.0
C2A C:HEM502 4.2 34.1 1.0
C2D C:HEM502 4.2 32.2 1.0
C2C C:HEM502 4.2 31.6 1.0
C3A C:HEM502 4.2 34.8 1.0
C3D C:HEM502 4.2 32.1 1.0
ND1 C:HIS197 4.2 37.1 1.0
CG C:HIS96 4.3 36.7 1.0
ND1 C:HIS96 4.3 43.9 1.0
C2B C:HEM502 4.3 34.9 1.0
C3B C:HEM502 4.3 34.4 1.0
CG C:HIS197 4.3 39.1 1.0

Iron binding site 3 out of 8 in 8ac3

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

b:217.2
occ:1.00
 FE1 P:FES301 0.0 217.2 1.0
SG P:CYS168 2.2 226.8 1.0
SG P:CYS187 2.2 207.2 1.0
S2 P:FES301 2.2 220.4 1.0
S1 P:FES301 2.2 232.3 1.0
CB P:CYS168 2.9 215.4 1.0
FE2 P:FES301 3.0 240.6 1.0
CB P:CYS187 3.2 222.5 1.0
OG P:SER192 3.7 250.4 1.0
CB P:HIS170 3.8 244.5 1.0
CB P:CYS173 4.3 227.7 1.0
CA P:CYS168 4.3 207.6 1.0
ND1 P:HIS170 4.5 253.7 1.0
ND1 P:HIS190 4.5 277.5 1.0
N P:LEU171 4.5 226.4 1.0
N P:HIS170 4.5 229.2 1.0
C P:CYS168 4.6 206.0 1.0
CB P:CYS189 4.6 236.9 1.0
CA P:CYS187 4.6 236.7 1.0
CG P:HIS170 4.6 253.7 1.0
CA P:HIS170 4.7 236.9 1.0
N P:CYS173 4.7 216.4 1.0
SG P:CYS173 4.7 244.5 1.0
O P:CYS168 4.8 206.0 1.0
CB P:SER192 4.9 250.2 1.0
CA P:CYS173 5.0 206.6 1.0
O P:CYS173 5.0 164.0 1.0
N P:HIS190 5.0 249.6 1.0
N P:GLY172 5.0 228.4 1.0

Iron binding site 4 out of 8 in 8ac3

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

b:240.6
occ:1.00
 FE2 P:FES301 0.0 240.6 1.0
ND1 P:HIS170 2.0 253.7 1.0
ND1 P:HIS190 2.1 277.5 1.0
S1 P:FES301 2.2 232.3 1.0
S2 P:FES301 2.2 220.4 1.0
CG P:HIS190 2.8 274.4 1.0
CG P:HIS170 2.9 253.7 1.0
FE1 P:FES301 3.0 217.2 1.0
CB P:HIS190 3.0 264.8 1.0
CE1 P:HIS170 3.0 253.6 1.0
CE1 P:HIS190 3.1 276.5 1.0
CB P:HIS170 3.2 244.5 1.0
N P:HIS190 3.8 249.6 1.0
CD2 P:HIS190 3.9 276.3 1.0
CA P:HIS190 4.0 257.4 1.0
NE2 P:HIS190 4.1 275.2 1.0
CD2 P:HIS170 4.1 255.6 1.0
NE2 P:HIS170 4.1 254.2 1.0
SG P:CYS187 4.2 207.2 1.0
CB P:CYS189 4.3 236.9 1.0
N P:LEU171 4.3 226.4 1.0
CA P:HIS170 4.6 236.9 1.0
CG P:PRO204 4.6 237.9 1.0
CG P:LEU171 4.6 234.4 1.0
C P:CYS189 4.6 244.2 1.0
SG P:CYS168 4.6 226.8 1.0
CB P:LEU171 4.7 230.4 1.0
CB P:PRO204 4.8 242.5 1.0
C P:HIS190 4.8 256.3 1.0
C P:HIS170 4.8 234.8 1.0
CD1 P:LEU171 4.9 235.5 1.0
OG P:SER192 5.0 250.4 1.0

Iron binding site 5 out of 8 in 8ac3

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

b:50.3
occ:1.00
 FE D:HEC401 0.0 50.3 1.0
NE2 D:HIS128 2.0 48.1 1.0
NB D:HEC401 2.0 49.2 1.0
ND D:HEC401 2.0 52.5 1.0
NC D:HEC401 2.0 54.0 1.0
NA D:HEC401 2.1 51.8 1.0
SD D:MET248 2.2 54.4 1.0
CE1 D:HIS128 2.9 48.3 1.0
C4B D:HEC401 3.0 49.5 1.0
C4C D:HEC401 3.0 57.3 1.0
C1D D:HEC401 3.0 54.6 1.0
C4D D:HEC401 3.0 55.5 1.0
C1B D:HEC401 3.0 50.7 1.0
CD2 D:HIS128 3.0 46.8 1.0
C1A D:HEC401 3.1 54.9 1.0
C1C D:HEC401 3.1 55.1 1.0
C4A D:HEC401 3.1 50.7 1.0
CE D:MET248 3.3 46.7 1.0
CHD D:HEC401 3.4 52.1 1.0
CHC D:HEC401 3.4 50.2 1.0
CHA D:HEC401 3.4 53.9 1.0
CHB D:HEC401 3.4 49.8 1.0
CG D:MET248 3.4 53.4 1.0
CB D:MET248 4.0 55.2 1.0
ND1 D:HIS128 4.1 49.1 1.0
CG D:HIS128 4.1 49.4 1.0
C3B D:HEC401 4.3 50.9 1.0
C3C D:HEC401 4.3 60.5 1.0
C2D D:HEC401 4.3 57.7 1.0
C3D D:HEC401 4.3 61.2 1.0
C2B D:HEC401 4.3 49.9 1.0
C3A D:HEC401 4.4 54.3 1.0
C2A D:HEC401 4.4 54.7 1.0
C2C D:HEC401 4.4 58.8 1.0

Iron binding site 6 out of 8 in 8ac3

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

b:32.7
occ:1.00
 FE N:HEM501 0.0 32.7 1.0
ND N:HEM501 1.9 32.4 1.0
NA N:HEM501 2.0 32.3 1.0
NE2 N:HIS183 2.0 31.2 1.0
NC N:HEM501 2.1 32.9 1.0
NE2 N:HIS82 2.1 32.4 1.0
NB N:HEM501 2.1 31.1 1.0
C4D N:HEM501 2.9 33.3 1.0
C1D N:HEM501 2.9 32.2 1.0
C1A N:HEM501 3.0 34.1 1.0
CE1 N:HIS183 3.0 32.1 1.0
C4A N:HEM501 3.0 34.0 1.0
C4B N:HEM501 3.0 32.6 1.0
CE1 N:HIS82 3.0 30.6 1.0
C1C N:HEM501 3.0 34.2 1.0
C4C N:HEM501 3.1 33.8 1.0
CD2 N:HIS183 3.1 30.9 1.0
C1B N:HEM501 3.1 32.4 1.0
CD2 N:HIS82 3.1 29.7 1.0
CHA N:HEM501 3.4 32.3 1.0
CHD N:HEM501 3.4 32.0 1.0
CHC N:HEM501 3.4 33.6 1.0
CHB N:HEM501 3.5 32.7 1.0
ND1 N:HIS183 4.1 30.0 1.0
C3D N:HEM501 4.1 34.0 1.0
ND1 N:HIS82 4.1 30.8 1.0
C2D N:HEM501 4.2 34.6 1.0
C2A N:HEM501 4.2 35.1 1.0
C3A N:HEM501 4.2 33.7 1.0
CG N:HIS183 4.2 30.4 1.0
CG N:HIS82 4.2 32.2 1.0
C2C N:HEM501 4.2 35.2 1.0
C3C N:HEM501 4.3 37.0 1.0
C3B N:HEM501 4.3 34.0 1.0
C2B N:HEM501 4.3 32.4 1.0
CA N:GLY131 4.8 44.5 1.0
NE2 N:GLN43 4.9 43.5 1.0

Iron binding site 7 out of 8 in 8ac3

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

b:32.2
occ:1.00
 FE N:HEM502 0.0 32.2 1.0
ND N:HEM502 1.9 32.1 1.0
NA N:HEM502 2.0 32.8 1.0
NC N:HEM502 2.0 31.9 1.0
NE2 N:HIS96 2.0 32.6 1.0
NB N:HEM502 2.1 32.4 1.0
NE2 N:HIS197 2.1 31.1 1.0
C4D N:HEM502 2.9 32.1 1.0
C1D N:HEM502 2.9 30.5 1.0
C4C N:HEM502 2.9 31.9 1.0
C1A N:HEM502 2.9 34.9 1.0
CE1 N:HIS96 2.9 31.1 1.0
C4A N:HEM502 3.0 34.6 1.0
CE1 N:HIS197 3.0 32.6 1.0
C1B N:HEM502 3.0 33.6 1.0
C4B N:HEM502 3.0 33.5 1.0
C1C N:HEM502 3.1 33.1 1.0
CD2 N:HIS96 3.1 34.1 1.0
CD2 N:HIS197 3.2 33.9 1.0
CHA N:HEM502 3.4 34.7 1.0
CHD N:HEM502 3.4 31.2 1.0
CHB N:HEM502 3.4 34.8 1.0
CHC N:HEM502 3.5 32.4 1.0
ND1 N:HIS96 4.1 32.6 1.0
C3C N:HEM502 4.1 31.6 1.0
C2A N:HEM502 4.1 34.9 1.0
C3A N:HEM502 4.2 33.2 1.0
C2D N:HEM502 4.2 31.6 1.0
C3D N:HEM502 4.2 32.9 1.0
ND1 N:HIS197 4.2 33.7 1.0
C2C N:HEM502 4.2 32.5 1.0
CG N:HIS96 4.2 31.9 1.0
C2B N:HEM502 4.3 33.8 1.0
C3B N:HEM502 4.3 35.7 1.0
CG N:HIS197 4.3 35.2 1.0

Iron binding site 8 out of 8 in 8ac3

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

b:46.5
occ:1.00
 FE O:HEC401 0.0 46.5 1.0
NE2 O:HIS128 2.0 47.2 1.0
NC O:HEC401 2.0 46.5 1.0
ND O:HEC401 2.0 49.7 1.0
NB O:HEC401 2.0 48.6 1.0
NA O:HEC401 2.1 47.0 1.0
SD O:MET248 2.3 55.2 1.0
CE1 O:HIS128 2.9 46.9 1.0
C4B O:HEC401 3.0 50.4 1.0
C4D O:HEC401 3.0 51.8 1.0
CD2 O:HIS128 3.0 47.5 1.0
C4C O:HEC401 3.0 48.4 1.0
C1C O:HEC401 3.0 49.2 1.0
C1A O:HEC401 3.0 49.1 1.0
C1D O:HEC401 3.1 50.8 1.0
C4A O:HEC401 3.1 47.8 1.0
C1B O:HEC401 3.1 50.5 1.0
CE O:MET248 3.3 52.3 1.0
CHA O:HEC401 3.4 49.9 1.0
CHC O:HEC401 3.4 48.6 1.0
CHD O:HEC401 3.4 47.5 1.0
CHB O:HEC401 3.4 47.5 1.0
CG O:MET248 3.5 55.3 1.0
ND1 O:HIS128 4.0 45.4 1.0
CB O:MET248 4.1 61.0 1.0
CG O:HIS128 4.1 45.3 1.0
C3B O:HEC401 4.3 52.5 1.0
C3C O:HEC401 4.3 52.9 1.0
C3D O:HEC401 4.3 52.7 1.0
C2C O:HEC401 4.3 52.1 1.0
C2D O:HEC401 4.3 52.4 1.0
C2A O:HEC401 4.4 49.6 1.0
C3A O:HEC401 4.4 50.3 1.0
C2B O:HEC401 4.4 51.1 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 17:12:55 2024

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