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Iron in PDB 8ac4: Complex III2 From Yarrowia Lipolytica, Apo, C-Position

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

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

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, Apo, C-Position (pdb code 8ac4). 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, C-Position, PDB code: 8ac4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8ac4

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

b:32.5
occ:1.00
FE C:HEM501 0.0 32.5 1.0
ND C:HEM501 1.9 32.6 1.0
NA C:HEM501 2.0 33.0 1.0
NE2 C:HIS82 2.0 28.6 1.0
NE2 C:HIS183 2.0 32.7 1.0
NC C:HEM501 2.1 32.8 1.0
NB C:HEM501 2.1 32.5 1.0
C4D C:HEM501 2.9 33.2 1.0
C1D C:HEM501 2.9 32.5 1.0
C1A C:HEM501 3.0 34.8 1.0
C4A C:HEM501 3.0 34.4 1.0
CE1 C:HIS183 3.0 31.3 1.0
CE1 C:HIS82 3.0 28.6 1.0
C4B C:HEM501 3.0 34.2 1.0
C4C C:HEM501 3.0 34.0 1.0
C1C C:HEM501 3.0 34.2 1.0
CD2 C:HIS82 3.1 28.1 1.0
CD2 C:HIS183 3.1 32.0 1.0
C1B C:HEM501 3.1 33.2 1.0
CHA C:HEM501 3.4 32.9 1.0
CHD C:HEM501 3.4 32.7 1.0
CHC C:HEM501 3.5 35.1 1.0
CHB C:HEM501 3.5 32.7 1.0
ND1 C:HIS82 4.1 28.8 1.0
ND1 C:HIS183 4.1 30.9 1.0
C3D C:HEM501 4.1 35.0 1.0
C3A C:HEM501 4.2 34.9 1.0
C2A C:HEM501 4.2 36.7 1.0
C2D C:HEM501 4.2 33.1 1.0
CG C:HIS82 4.2 28.8 1.0
CG C:HIS183 4.2 31.8 1.0
C2C C:HEM501 4.2 36.0 1.0
C3C C:HEM501 4.3 37.5 1.0
C3B C:HEM501 4.3 35.5 1.0
C2B C:HEM501 4.3 33.8 1.0
CA C:GLY131 4.8 42.9 1.0
NE2 C:GLN43 4.9 38.5 1.0

Iron binding site 2 out of 8 in 8ac4

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

b:34.3
occ:1.00
FE C:HEM502 0.0 34.3 1.0
ND C:HEM502 1.9 33.4 1.0
NA C:HEM502 2.0 33.4 1.0
NC C:HEM502 2.0 33.6 1.0
NB C:HEM502 2.1 33.0 1.0
NE2 C:HIS197 2.1 35.1 1.0
NE2 C:HIS96 2.2 30.0 1.0
C1D C:HEM502 2.9 32.1 1.0
C4C C:HEM502 2.9 34.5 1.0
C4D C:HEM502 2.9 35.1 1.0
C1A C:HEM502 3.0 33.9 1.0
C4A C:HEM502 3.0 35.7 1.0
CE1 C:HIS197 3.0 33.7 1.0
C4B C:HEM502 3.1 33.6 1.0
C1C C:HEM502 3.1 34.4 1.0
C1B C:HEM502 3.1 34.2 1.0
CD2 C:HIS96 3.1 29.9 1.0
CE1 C:HIS96 3.2 31.3 1.0
CD2 C:HIS197 3.2 36.0 1.0
CHD C:HEM502 3.4 34.3 1.0
CHA C:HEM502 3.4 34.3 1.0
CHB C:HEM502 3.5 34.2 1.0
CHC C:HEM502 3.5 34.2 1.0
C3C C:HEM502 4.1 35.6 1.0
C2A C:HEM502 4.2 34.7 1.0
C3A C:HEM502 4.2 34.9 1.0
C2D C:HEM502 4.2 32.7 1.0
C2C C:HEM502 4.2 34.2 1.0
ND1 C:HIS197 4.2 34.4 1.0
C3D C:HEM502 4.2 35.1 1.0
CG C:HIS96 4.3 31.7 1.0
ND1 C:HIS96 4.3 33.8 1.0
C2B C:HEM502 4.3 35.0 1.0
C3B C:HEM502 4.3 34.9 1.0
CG C:HIS197 4.3 35.7 1.0

Iron binding site 3 out of 8 in 8ac4

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

b:198.7
occ:1.00
FE1 P:FES301 0.0 198.7 1.0
S2 P:FES301 2.2 187.0 1.0
S1 P:FES301 2.2 195.7 1.0
SG P:CYS168 2.2 164.0 1.0
SG P:CYS187 2.3 157.4 1.0
CB P:CYS168 2.8 157.4 1.0
FE2 P:FES301 3.0 192.9 1.0
CB P:CYS187 3.1 163.5 1.0
OG P:SER192 3.7 161.2 1.0
CB P:HIS170 3.8 179.6 1.0
CA P:CYS168 4.3 154.9 1.0
CB P:CYS173 4.4 181.5 1.0
ND1 P:HIS170 4.5 182.3 1.0
N P:LEU171 4.5 191.0 1.0
ND1 P:HIS190 4.6 183.8 1.0
CA P:CYS187 4.6 165.0 1.0
C P:CYS168 4.6 154.0 1.0
N P:HIS170 4.6 174.6 1.0
CB P:CYS189 4.6 187.7 1.0
CG P:HIS170 4.6 184.0 1.0
CA P:HIS170 4.7 180.2 1.0
N P:CYS173 4.7 181.9 1.0
SG P:CYS173 4.8 195.0 1.0
O P:CYS168 4.9 150.6 1.0
CB P:SER192 4.9 164.8 1.0
O P:CYS173 5.0 168.9 1.0
N P:HIS190 5.0 175.5 1.0
N P:GLY172 5.0 189.9 1.0

Iron binding site 4 out of 8 in 8ac4

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

b:192.9
occ:1.00
FE2 P:FES301 0.0 192.9 1.0
ND1 P:HIS170 2.0 182.3 1.0
ND1 P:HIS190 2.1 183.8 1.0
S2 P:FES301 2.2 187.0 1.0
S1 P:FES301 2.2 195.7 1.0
CG P:HIS190 2.8 180.5 1.0
CG P:HIS170 3.0 184.0 1.0
CB P:HIS190 3.0 175.7 1.0
FE1 P:FES301 3.0 198.7 1.0
CE1 P:HIS170 3.0 180.6 1.0
CE1 P:HIS190 3.1 185.1 1.0
CB P:HIS170 3.3 179.6 1.0
N P:HIS190 3.8 175.5 1.0
CD2 P:HIS190 3.9 176.6 1.0
CA P:HIS190 3.9 170.9 1.0
NE2 P:HIS190 4.1 176.7 1.0
CD2 P:HIS170 4.1 189.5 1.0
NE2 P:HIS170 4.1 186.5 1.0
CB P:CYS189 4.3 187.7 1.0
N P:LEU171 4.3 191.0 1.0
SG P:CYS187 4.3 157.4 1.0
C P:CYS189 4.5 179.4 1.0
CG P:LEU171 4.5 201.5 1.0
CA P:HIS170 4.6 180.2 1.0
CB P:LEU171 4.6 196.1 1.0
SG P:CYS168 4.7 164.0 1.0
CG P:PRO204 4.7 170.1 1.0
C P:HIS190 4.7 168.3 1.0
CD1 P:LEU171 4.8 203.3 1.0
C P:HIS170 4.9 184.9 1.0
CB P:PRO204 4.9 170.8 1.0

Iron binding site 5 out of 8 in 8ac4

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

b:49.4
occ:1.00
FE D:HEC401 0.0 49.4 1.0
NE2 D:HIS128 2.0 43.3 1.0
NB D:HEC401 2.0 49.4 1.0
NC D:HEC401 2.1 49.6 1.0
ND D:HEC401 2.1 52.4 1.0
NA D:HEC401 2.1 50.9 1.0
SD D:MET248 2.3 55.1 1.0
CE1 D:HIS128 2.9 44.9 1.0
C4C D:HEC401 3.0 51.3 1.0
C4B D:HEC401 3.0 49.9 1.0
CD2 D:HIS128 3.0 43.9 1.0
C1B D:HEC401 3.0 49.2 1.0
C4D D:HEC401 3.0 54.1 1.0
C1D D:HEC401 3.0 52.4 1.0
C1C D:HEC401 3.0 51.8 1.0
C4A D:HEC401 3.1 51.1 1.0
C1A D:HEC401 3.1 52.3 1.0
CE D:MET248 3.3 53.7 1.0
CHB D:HEC401 3.4 50.6 1.0
CHA D:HEC401 3.4 53.9 1.0
CHD D:HEC401 3.4 50.8 1.0
CHC D:HEC401 3.4 49.3 1.0
CG D:MET248 3.5 52.5 1.0
CB D:MET248 4.0 56.2 1.0
ND1 D:HIS128 4.1 42.9 1.0
CG D:HIS128 4.1 43.6 1.0
C3B D:HEC401 4.3 51.2 1.0
C3C D:HEC401 4.3 52.5 1.0
C3D D:HEC401 4.3 56.5 1.0
C2D D:HEC401 4.3 56.1 1.0
C2B D:HEC401 4.4 51.0 1.0
C3A D:HEC401 4.4 52.1 1.0
C2C D:HEC401 4.4 52.9 1.0
C2A D:HEC401 4.4 53.3 1.0

Iron binding site 6 out of 8 in 8ac4

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

b:32.2
occ:1.00
FE N:HEM501 0.0 32.2 1.0
ND N:HEM501 1.9 31.8 1.0
NA N:HEM501 2.0 31.1 1.0
NE2 N:HIS82 2.0 28.4 1.0
NE2 N:HIS183 2.0 35.0 1.0
NC N:HEM501 2.0 32.8 1.0
NB N:HEM501 2.1 31.6 1.0
C4D N:HEM501 2.9 32.0 1.0
C1D N:HEM501 2.9 32.1 1.0
C1A N:HEM501 3.0 32.6 1.0
CE1 N:HIS82 3.0 29.0 1.0
C4A N:HEM501 3.0 31.6 1.0
CE1 N:HIS183 3.0 33.3 1.0
C4B N:HEM501 3.0 33.5 1.0
C1C N:HEM501 3.0 35.4 1.0
C4C N:HEM501 3.0 33.5 1.0
CD2 N:HIS82 3.1 27.5 1.0
CD2 N:HIS183 3.1 33.8 1.0
C1B N:HEM501 3.1 33.4 1.0
CHA N:HEM501 3.4 31.1 1.0
CHD N:HEM501 3.4 32.6 1.0
CHC N:HEM501 3.4 34.6 1.0
CHB N:HEM501 3.5 31.4 1.0
C3D N:HEM501 4.1 35.0 1.0
ND1 N:HIS82 4.1 29.2 1.0
C2D N:HEM501 4.1 33.3 1.0
ND1 N:HIS183 4.1 32.4 1.0
C3A N:HEM501 4.2 32.0 1.0
C2A N:HEM501 4.2 34.4 1.0
CG N:HIS82 4.2 29.7 1.0
CG N:HIS183 4.2 33.0 1.0
C2C N:HEM501 4.2 36.2 1.0
C3C N:HEM501 4.3 36.6 1.0
C3B N:HEM501 4.3 34.7 1.0
C2B N:HEM501 4.3 34.6 1.0
CA N:GLY131 4.8 40.9 1.0
NE2 N:GLN43 4.9 42.2 1.0

Iron binding site 7 out of 8 in 8ac4

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

b:32.5
occ:1.00
FE N:HEM502 0.0 32.5 1.0
ND N:HEM502 1.9 33.6 1.0
NA N:HEM502 2.0 32.7 1.0
NC N:HEM502 2.0 32.2 1.0
NE2 N:HIS96 2.0 35.0 1.0
NB N:HEM502 2.1 32.1 1.0
NE2 N:HIS197 2.1 33.9 1.0
C4C N:HEM502 2.9 33.8 1.0
C1D N:HEM502 2.9 32.2 1.0
C4D N:HEM502 2.9 33.6 1.0
C1A N:HEM502 2.9 33.3 1.0
CE1 N:HIS96 2.9 32.4 1.0
C4A N:HEM502 3.0 35.7 1.0
CE1 N:HIS197 3.0 33.0 1.0
C4B N:HEM502 3.0 32.4 1.0
C1B N:HEM502 3.0 32.1 1.0
C1C N:HEM502 3.0 33.5 1.0
CD2 N:HIS96 3.1 34.2 1.0
CD2 N:HIS197 3.2 34.6 1.0
CHD N:HEM502 3.4 32.1 1.0
CHA N:HEM502 3.4 33.3 1.0
CHB N:HEM502 3.4 32.8 1.0
CHC N:HEM502 3.5 33.6 1.0
ND1 N:HIS96 4.1 33.2 1.0
C3C N:HEM502 4.1 34.2 1.0
C2A N:HEM502 4.1 34.3 1.0
C2C N:HEM502 4.2 33.7 1.0
C3A N:HEM502 4.2 34.7 1.0
ND1 N:HIS197 4.2 34.5 1.0
C2D N:HEM502 4.2 33.2 1.0
C3D N:HEM502 4.2 35.0 1.0
CG N:HIS96 4.2 32.9 1.0
C3B N:HEM502 4.3 32.6 1.0
C2B N:HEM502 4.3 31.9 1.0
CG N:HIS197 4.3 35.7 1.0

Iron binding site 8 out of 8 in 8ac4

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

b:48.5
occ:1.00
FE O:HEC401 0.0 48.5 1.0
NE2 O:HIS128 2.0 47.7 1.0
NB O:HEC401 2.0 48.8 1.0
NC O:HEC401 2.0 50.0 1.0
ND O:HEC401 2.1 51.2 1.0
NA O:HEC401 2.1 49.3 1.0
SD O:MET248 2.3 55.2 1.0
CE1 O:HIS128 2.9 47.3 1.0
C4B O:HEC401 3.0 50.1 1.0
C4D O:HEC401 3.0 52.2 1.0
C4C O:HEC401 3.0 52.7 1.0
C1C O:HEC401 3.0 51.6 1.0
CD2 O:HIS128 3.0 47.5 1.0
C1B O:HEC401 3.0 48.7 1.0
C1A O:HEC401 3.1 50.8 1.0
C1D O:HEC401 3.1 52.7 1.0
C4A O:HEC401 3.1 47.6 1.0
CE O:MET248 3.3 53.3 1.0
CHA O:HEC401 3.4 50.9 1.0
CHC O:HEC401 3.4 49.0 1.0
CHD O:HEC401 3.4 51.1 1.0
CHB O:HEC401 3.4 47.6 1.0
CG O:MET248 3.5 57.8 1.0
ND1 O:HIS128 4.1 46.0 1.0
CB O:MET248 4.1 57.0 1.0
CG O:HIS128 4.1 47.2 1.0
C3B O:HEC401 4.3 51.4 1.0
C3C O:HEC401 4.3 54.6 1.0
C3D O:HEC401 4.3 55.9 1.0
C2C O:HEC401 4.3 52.4 1.0
C2D O:HEC401 4.3 55.0 1.0
C2B O:HEC401 4.4 49.8 1.0
C2A O:HEC401 4.4 50.3 1.0
C3A O:HEC401 4.4 49.1 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 17:14:59 2024

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