Iron in PDB 8abf: Complex III2 From Yarrowia Lipolytica, Oxidised with Ferricyanide, Int-Position

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, Oxidised with Ferricyanide, Int-Position

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

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 8abf

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

b:24.2
occ:1.00
FE C:HEM501 0.0 24.2 1.0
ND C:HEM501 1.9 25.2 1.0
NA C:HEM501 2.0 26.1 1.0
NE2 C:HIS82 2.0 24.1 1.0
NC C:HEM501 2.1 26.4 1.0
NE2 C:HIS183 2.1 23.6 1.0
NB C:HEM501 2.1 26.7 1.0
C1D C:HEM501 2.9 25.2 1.0
C4D C:HEM501 2.9 25.6 1.0
C1A C:HEM501 3.0 25.7 1.0
CE1 C:HIS82 3.0 23.7 1.0
C4A C:HEM501 3.0 26.3 1.0
CE1 C:HIS183 3.0 22.9 1.0
C4C C:HEM501 3.0 26.0 1.0
C4B C:HEM501 3.1 27.0 1.0
C1C C:HEM501 3.1 28.2 1.0
C1B C:HEM501 3.1 26.6 1.0
CD2 C:HIS82 3.1 23.3 1.0
CD2 C:HIS183 3.1 22.7 1.0
CHD C:HEM501 3.4 25.6 1.0
CHA C:HEM501 3.4 25.9 1.0
CHB C:HEM501 3.4 26.3 1.0
CHC C:HEM501 3.5 26.9 1.0
ND1 C:HIS82 4.1 23.1 1.0
ND1 C:HIS183 4.1 22.7 1.0
C2A C:HEM501 4.2 27.4 1.0
C2D C:HEM501 4.2 26.9 1.0
C3A C:HEM501 4.2 26.8 1.0
C3D C:HEM501 4.2 27.3 1.0
CG C:HIS82 4.2 24.6 1.0
CG C:HIS183 4.2 23.5 1.0
C3C C:HEM501 4.2 28.1 1.0
C2C C:HEM501 4.3 28.6 1.0
C3B C:HEM501 4.3 27.6 1.0
C2B C:HEM501 4.3 27.7 1.0
CA C:GLY131 4.8 30.8 1.0
NE2 C:GLN43 4.9 27.1 1.0

Iron binding site 2 out of 8 in 8abf

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

b:25.0
occ:1.00
FE C:HEM502 0.0 25.0 1.0
ND C:HEM502 1.9 25.7 1.0
NA C:HEM502 2.0 25.5 1.0
NC C:HEM502 2.1 24.9 1.0
NB C:HEM502 2.1 24.9 1.0
NE2 C:HIS197 2.1 23.2 1.0
NE2 C:HIS96 2.2 23.8 1.0
C4D C:HEM502 2.9 25.7 1.0
C1D C:HEM502 2.9 25.7 1.0
C4C C:HEM502 3.0 25.2 1.0
C1A C:HEM502 3.0 26.3 1.0
C4A C:HEM502 3.0 25.9 1.0
CE1 C:HIS197 3.0 23.6 1.0
C1B C:HEM502 3.1 25.5 1.0
C4B C:HEM502 3.1 25.0 1.0
C1C C:HEM502 3.1 25.1 1.0
CD2 C:HIS96 3.2 24.8 1.0
CD2 C:HIS197 3.2 23.9 1.0
CE1 C:HIS96 3.2 24.1 1.0
CHA C:HEM502 3.4 26.3 1.0
CHD C:HEM502 3.4 24.8 1.0
CHB C:HEM502 3.5 25.4 1.0
CHC C:HEM502 3.5 25.2 1.0
C3C C:HEM502 4.2 25.0 1.0
C3D C:HEM502 4.2 27.4 1.0
C2A C:HEM502 4.2 27.6 1.0
C2D C:HEM502 4.2 26.1 1.0
C3A C:HEM502 4.2 26.7 1.0
ND1 C:HIS197 4.2 23.1 1.0
C2C C:HEM502 4.2 24.9 1.0
CG C:HIS96 4.3 25.4 1.0
ND1 C:HIS96 4.3 25.7 1.0
C2B C:HEM502 4.3 26.0 1.0
CG C:HIS197 4.3 23.5 1.0
C3B C:HEM502 4.3 25.4 1.0

Iron binding site 3 out of 8 in 8abf

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

b:170.4
occ:1.00
FE1 P:FES301 0.0 170.4 1.0
SG P:CYS168 2.2 138.9 1.0
S2 P:FES301 2.2 172.4 1.0
S1 P:FES301 2.2 173.5 1.0
SG P:CYS187 2.3 153.1 1.0
CB P:CYS168 2.8 136.0 1.0
FE2 P:FES301 3.0 175.1 1.0
CB P:CYS187 3.1 158.7 1.0
OG P:SER192 3.6 167.4 1.0
CB P:HIS170 3.8 146.4 1.0
CA P:CYS168 4.3 131.1 1.0
N P:LEU171 4.4 161.2 1.0
ND1 P:HIS170 4.5 147.8 1.0
ND1 P:HIS190 4.5 180.4 1.0
N P:HIS170 4.6 145.5 1.0
CA P:CYS187 4.6 164.1 1.0
C P:CYS168 4.6 130.8 1.0
CG P:HIS170 4.6 147.3 1.0
CB P:CYS173 4.6 176.3 1.0
N P:CYS173 4.6 165.4 1.0
CA P:HIS170 4.7 149.3 1.0
CB P:CYS189 4.7 179.4 1.0
CB P:SER192 4.8 167.0 1.0
N P:GLY172 4.8 165.4 1.0
O P:CYS168 4.9 128.3 1.0
O P:CYS173 5.0 159.1 1.0
N P:HIS190 5.0 177.3 1.0

Iron binding site 4 out of 8 in 8abf

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

b:175.1
occ:1.00
FE2 P:FES301 0.0 175.1 1.0
ND1 P:HIS170 2.1 147.8 1.0
ND1 P:HIS190 2.1 180.4 1.0
S1 P:FES301 2.2 173.5 1.0
S2 P:FES301 2.2 172.4 1.0
CG P:HIS190 2.8 180.0 1.0
CB P:HIS190 3.0 180.2 1.0
CG P:HIS170 3.0 147.3 1.0
FE1 P:FES301 3.0 170.4 1.0
CE1 P:HIS170 3.1 145.4 1.0
CE1 P:HIS190 3.1 181.8 1.0
CB P:HIS170 3.3 146.4 1.0
N P:HIS190 3.7 177.3 1.0
CD2 P:HIS190 3.9 180.5 1.0
CA P:HIS190 3.9 178.5 1.0
NE2 P:HIS190 4.0 181.6 1.0
CD2 P:HIS170 4.1 148.9 1.0
NE2 P:HIS170 4.2 148.8 1.0
N P:LEU171 4.2 161.2 1.0
CB P:CYS189 4.3 179.4 1.0
SG P:CYS187 4.4 153.1 1.0
CB P:LEU171 4.5 174.8 1.0
CG P:LEU171 4.5 178.9 1.0
C P:CYS189 4.5 177.3 1.0
CA P:HIS170 4.6 149.3 1.0
SG P:CYS168 4.7 138.9 1.0
C P:HIS190 4.7 178.3 1.0
CG P:PRO204 4.7 162.7 1.0
C P:HIS170 4.8 154.2 1.0
CD1 P:LEU171 4.8 179.1 1.0
CB P:PRO204 5.0 164.8 1.0
CA P:CYS189 5.0 176.2 1.0

Iron binding site 5 out of 8 in 8abf

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

b:35.0
occ:1.00
FE D:HEC401 0.0 35.0 1.0
NE2 D:HIS128 2.0 30.4 1.0
NB D:HEC401 2.0 35.3 1.0
NC D:HEC401 2.0 36.9 1.0
ND D:HEC401 2.1 35.8 1.0
NA D:HEC401 2.1 35.5 1.0
SD D:MET248 2.3 35.5 1.0
CE1 D:HIS128 3.0 30.7 1.0
C4B D:HEC401 3.0 36.3 1.0
C4C D:HEC401 3.0 37.4 1.0
C4D D:HEC401 3.0 35.9 1.0
C1B D:HEC401 3.0 35.5 1.0
C1C D:HEC401 3.0 36.9 1.0
C1D D:HEC401 3.1 36.5 1.0
C4A D:HEC401 3.1 34.8 1.0
C1A D:HEC401 3.1 36.2 1.0
CD2 D:HIS128 3.1 29.8 1.0
CE D:MET248 3.3 34.5 1.0
CHA D:HEC401 3.4 35.2 1.0
CHB D:HEC401 3.4 34.4 1.0
CHC D:HEC401 3.4 36.1 1.0
CHD D:HEC401 3.4 37.4 1.0
CG D:MET248 3.4 36.1 1.0
CB D:MET248 4.1 37.4 1.0
ND1 D:HIS128 4.1 31.0 1.0
CG D:HIS128 4.2 31.9 1.0
C3C D:HEC401 4.3 39.0 1.0
C3B D:HEC401 4.3 37.9 1.0
C3D D:HEC401 4.3 37.3 1.0
C2D D:HEC401 4.3 37.1 1.0
C2C D:HEC401 4.3 37.6 1.0
C2B D:HEC401 4.4 36.6 1.0
C3A D:HEC401 4.4 35.6 1.0
C2A D:HEC401 4.4 35.9 1.0

Iron binding site 6 out of 8 in 8abf

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

b:25.2
occ:1.00
FE N:HEM501 0.0 25.2 1.0
ND N:HEM501 1.9 26.0 1.0
NA N:HEM501 2.0 26.3 1.0
NE2 N:HIS82 2.0 25.3 1.0
NC N:HEM501 2.1 26.0 1.0
NE2 N:HIS183 2.1 23.7 1.0
NB N:HEM501 2.1 26.6 1.0
C1D N:HEM501 2.9 25.5 1.0
C4D N:HEM501 2.9 26.2 1.0
C1A N:HEM501 2.9 26.4 1.0
CE1 N:HIS82 3.0 24.1 1.0
C4A N:HEM501 3.0 26.3 1.0
CE1 N:HIS183 3.0 24.1 1.0
C4B N:HEM501 3.0 26.7 1.0
C4C N:HEM501 3.1 26.1 1.0
C1C N:HEM501 3.1 27.1 1.0
CD2 N:HIS82 3.1 25.3 1.0
C1B N:HEM501 3.1 26.1 1.0
CD2 N:HIS183 3.1 23.0 1.0
CHA N:HEM501 3.4 25.7 1.0
CHD N:HEM501 3.4 26.1 1.0
CHC N:HEM501 3.5 26.8 1.0
CHB N:HEM501 3.5 26.1 1.0
ND1 N:HIS82 4.1 23.6 1.0
ND1 N:HIS183 4.1 23.3 1.0
C2A N:HEM501 4.2 27.4 1.0
CG N:HIS82 4.2 25.7 1.0
C2D N:HEM501 4.2 27.1 1.0
C3A N:HEM501 4.2 26.8 1.0
C3D N:HEM501 4.2 28.2 1.0
CG N:HIS183 4.2 24.1 1.0
C2C N:HEM501 4.3 28.1 1.0
C3C N:HEM501 4.3 28.2 1.0
C3B N:HEM501 4.3 27.5 1.0
C2B N:HEM501 4.3 26.9 1.0
CA N:GLY131 4.8 32.0 1.0
NE2 N:GLN43 4.8 26.6 1.0

Iron binding site 7 out of 8 in 8abf

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

b:24.6
occ:1.00
FE N:HEM502 0.0 24.6 1.0
ND N:HEM502 1.9 25.1 1.0
NA N:HEM502 2.0 25.3 1.0
NC N:HEM502 2.0 24.5 1.0
NE2 N:HIS96 2.1 23.3 1.0
NB N:HEM502 2.1 24.6 1.0
NE2 N:HIS197 2.1 22.6 1.0
C4D N:HEM502 2.9 25.1 1.0
C1D N:HEM502 2.9 25.2 1.0
C4C N:HEM502 3.0 25.4 1.0
CE1 N:HIS96 3.0 23.6 1.0
C1A N:HEM502 3.0 26.1 1.0
C4A N:HEM502 3.0 25.6 1.0
CE1 N:HIS197 3.0 23.1 1.0
C1B N:HEM502 3.1 24.7 1.0
C4B N:HEM502 3.1 24.9 1.0
C1C N:HEM502 3.1 24.8 1.0
CD2 N:HIS96 3.2 24.4 1.0
CD2 N:HIS197 3.2 22.9 1.0
CHA N:HEM502 3.4 25.8 1.0
CHD N:HEM502 3.4 25.4 1.0
CHB N:HEM502 3.4 25.3 1.0
CHC N:HEM502 3.5 24.9 1.0
ND1 N:HIS96 4.1 24.8 1.0
C3C N:HEM502 4.1 25.6 1.0
C3D N:HEM502 4.2 27.1 1.0
C2A N:HEM502 4.2 27.6 1.0
C2D N:HEM502 4.2 26.1 1.0
C3A N:HEM502 4.2 27.2 1.0
ND1 N:HIS197 4.2 23.9 1.0
C2C N:HEM502 4.2 25.2 1.0
CG N:HIS96 4.2 25.4 1.0
CG N:HIS197 4.3 24.6 1.0
C2B N:HEM502 4.3 25.5 1.0
C3B N:HEM502 4.3 25.4 1.0

Iron binding site 8 out of 8 in 8abf

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

b:35.0
occ:1.00
FE O:HEC401 0.0 35.0 1.0
NE2 O:HIS128 2.0 32.6 1.0
NB O:HEC401 2.0 36.0 1.0
NC O:HEC401 2.1 37.1 1.0
ND O:HEC401 2.1 36.0 1.0
NA O:HEC401 2.1 35.4 1.0
SD O:MET248 2.3 38.1 1.0
CE1 O:HIS128 3.0 32.2 1.0
C4B O:HEC401 3.0 36.4 1.0
C4C O:HEC401 3.0 37.2 1.0
CD2 O:HIS128 3.0 32.3 1.0
C1B O:HEC401 3.0 35.0 1.0
C4D O:HEC401 3.0 36.0 1.0
C1A O:HEC401 3.0 35.6 1.0
C1C O:HEC401 3.1 37.6 1.0
C4A O:HEC401 3.1 35.0 1.0
C1D O:HEC401 3.1 36.7 1.0
CE O:MET248 3.4 37.9 1.0
CHA O:HEC401 3.4 35.4 1.0
CHB O:HEC401 3.4 35.0 1.0
CHC O:HEC401 3.4 36.9 1.0
CHD O:HEC401 3.4 36.0 1.0
CG O:MET248 3.5 39.1 1.0
ND1 O:HIS128 4.1 32.6 1.0
CB O:MET248 4.1 41.8 1.0
CG O:HIS128 4.1 33.9 1.0
C3B O:HEC401 4.2 37.1 1.0
C3C O:HEC401 4.3 38.8 1.0
C2B O:HEC401 4.3 36.0 1.0
C3D O:HEC401 4.3 36.9 1.0
C2C O:HEC401 4.4 38.1 1.0
C2D O:HEC401 4.4 37.0 1.0
C2A O:HEC401 4.4 35.8 1.0
C3A O:HEC401 4.4 36.0 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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