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Iron in PDB 8ac5: Complex III2 From Yarrowia Lipolytica, with Decylubiquinol, Oxidised, B-Position

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, with Decylubiquinol, Oxidised, B-Position

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

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, with Decylubiquinol, Oxidised, B-Position (pdb code 8ac5). 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, with Decylubiquinol, Oxidised, B-Position, PDB code: 8ac5:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8ac5

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

b:35.1
occ:1.00
 FE C:HEC501 0.0 35.1 1.0
ND C:HEC501 1.9 39.5 1.0
NA C:HEC501 1.9 39.8 1.0
NE2 C:HIS82 2.0 36.4 1.0
NC C:HEC501 2.1 39.6 1.0
NE2 C:HIS183 2.1 40.5 1.0
NB C:HEC501 2.1 37.9 1.0
C4D C:HEC501 2.9 39.2 1.0
C1D C:HEC501 2.9 41.4 1.0
C1A C:HEC501 2.9 40.6 1.0
C4A C:HEC501 3.0 41.6 1.0
CE1 C:HIS183 3.0 40.8 1.0
CE1 C:HIS82 3.0 36.8 1.0
C4B C:HEC501 3.0 40.6 1.0
C4C C:HEC501 3.1 40.4 1.0
C1C C:HEC501 3.1 43.0 1.0
CD2 C:HIS82 3.1 36.4 1.0
C1B C:HEC501 3.1 40.7 1.0
CD2 C:HIS183 3.1 40.7 1.0
CHA C:HEC501 3.4 37.5 1.0
CHD C:HEC501 3.4 38.2 1.0
CHB C:HEC501 3.5 42.3 1.0
CHC C:HEC501 3.5 41.2 1.0
C3A C:HEC501 4.1 40.5 1.0
ND1 C:HIS82 4.1 36.2 1.0
ND1 C:HIS183 4.1 41.3 1.0
C2A C:HEC501 4.1 42.8 1.0
C3D C:HEC501 4.2 44.0 1.0
C2D C:HEC501 4.2 43.8 1.0
CG C:HIS82 4.2 37.2 1.0
CG C:HIS183 4.2 39.6 1.0
C2C C:HEC501 4.2 42.8 1.0
C3C C:HEC501 4.3 43.2 1.0
C3B C:HEC501 4.3 43.6 1.0
C2B C:HEC501 4.3 40.4 1.0
CA C:GLY131 4.8 44.6 1.0
NE2 C:GLN43 4.9 49.3 1.0

Iron binding site 2 out of 8 in 8ac5

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

b:36.4
occ:1.00
 FE C:HEC502 0.0 36.4 1.0
ND C:HEC502 1.9 38.1 1.0
NA C:HEC502 2.0 37.5 1.0
NC C:HEC502 2.0 37.7 1.0
NB C:HEC502 2.1 37.4 1.0
NE2 C:HIS197 2.2 37.7 1.0
NE2 C:HIS96 2.2 36.8 1.0
C4D C:HEC502 2.9 39.8 1.0
C1D C:HEC502 2.9 38.1 1.0
C4C C:HEC502 3.0 38.6 1.0
C1A C:HEC502 3.0 40.4 1.0
C4A C:HEC502 3.0 36.6 1.0
C4B C:HEC502 3.1 37.4 1.0
C1B C:HEC502 3.1 37.8 1.0
C1C C:HEC502 3.1 38.7 1.0
CE1 C:HIS197 3.1 38.9 1.0
CD2 C:HIS96 3.2 37.4 1.0
CE1 C:HIS96 3.2 40.9 1.0
CD2 C:HIS197 3.3 38.6 1.0
CHA C:HEC502 3.4 41.5 1.0
CHD C:HEC502 3.4 38.5 1.0
CHB C:HEC502 3.5 36.6 1.0
CHC C:HEC502 3.5 38.1 1.0
C3C C:HEC502 4.1 38.6 1.0
C3D C:HEC502 4.2 40.4 1.0
C2D C:HEC502 4.2 36.8 1.0
C2A C:HEC502 4.2 41.8 1.0
C3A C:HEC502 4.2 39.5 1.0
C2C C:HEC502 4.2 37.4 1.0
ND1 C:HIS197 4.3 39.6 1.0
C3B C:HEC502 4.3 37.7 1.0
CG C:HIS96 4.3 38.0 1.0
C2B C:HEC502 4.3 36.9 1.0
ND1 C:HIS96 4.3 41.0 1.0
CG C:HIS197 4.4 40.9 1.0

Iron binding site 3 out of 8 in 8ac5

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

b:147.4
occ:1.00
 FE1 P:FES301 0.0 147.4 1.0
SG P:CYS168 2.2 153.5 1.0
S2 P:FES301 2.2 136.7 1.0
S1 P:FES301 2.2 150.1 1.0
SG P:CYS187 2.3 159.2 1.0
CB P:CYS168 2.9 147.4 1.0
FE2 P:FES301 3.0 171.1 1.0
CB P:CYS187 3.1 163.5 1.0
OG P:SER192 3.6 163.5 1.0
CB P:HIS170 3.8 154.5 1.0
CA P:CYS168 4.3 151.4 1.0
ND1 P:HIS170 4.5 164.2 1.0
CB P:CYS189 4.5 164.0 1.0
N P:LEU171 4.5 153.4 1.0
ND1 P:HIS190 4.5 148.9 1.0
N P:HIS170 4.6 147.5 1.0
CA P:CYS187 4.6 177.1 1.0
CB P:CYS173 4.6 156.2 1.0
CG P:HIS170 4.6 166.8 1.0
C P:CYS168 4.7 157.2 1.0
CA P:HIS170 4.7 144.2 1.0
CB P:SER192 4.8 151.1 1.0
N P:CYS173 4.8 138.8 1.0
N P:HIS190 4.9 160.8 1.0
O P:CYS168 4.9 157.3 1.0
SG P:CYS173 5.0 170.9 1.0

Iron binding site 4 out of 8 in 8ac5

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

b:171.1
occ:1.00
 FE2 P:FES301 0.0 171.1 1.0
ND1 P:HIS170 2.1 164.2 1.0
ND1 P:HIS190 2.1 148.9 1.0
S2 P:FES301 2.2 136.7 1.0
S1 P:FES301 2.2 150.1 1.0
CG P:HIS190 2.8 146.0 1.0
FE1 P:FES301 3.0 147.4 1.0
CG P:HIS170 3.0 166.8 1.0
CB P:HIS190 3.0 156.3 1.0
CE1 P:HIS170 3.1 154.1 1.0
CE1 P:HIS190 3.1 153.8 1.0
CB P:HIS170 3.2 154.5 1.0
N P:HIS190 3.8 160.8 1.0
CD2 P:HIS190 3.9 148.5 1.0
CA P:HIS190 3.9 161.0 1.0
NE2 P:HIS190 4.0 157.2 1.0
CD2 P:HIS170 4.1 165.9 1.0
CB P:CYS189 4.2 164.0 1.0
NE2 P:HIS170 4.2 153.3 1.0
N P:LEU171 4.2 153.4 1.0
SG P:CYS187 4.4 159.2 1.0
CG P:LEU171 4.5 167.9 1.0
CB P:LEU171 4.5 161.1 1.0
C P:CYS189 4.5 163.7 1.0
CA P:HIS170 4.6 144.2 1.0
SG P:CYS168 4.6 153.5 1.0
CG P:PRO204 4.7 159.8 1.0
C P:HIS190 4.8 158.9 1.0
C P:HIS170 4.8 141.4 1.0
CD1 P:LEU171 4.8 171.8 1.0
CB P:PRO204 4.9 162.9 1.0
CA P:CYS189 5.0 168.3 1.0
CD P:PRO204 5.0 160.3 1.0

Iron binding site 5 out of 8 in 8ac5

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

b:47.6
occ:1.00
 FE D:HEC401 0.0 47.6 1.0
NE2 D:HIS128 2.0 47.9 1.0
NB D:HEC401 2.0 51.5 1.0
NC D:HEC401 2.0 53.4 1.0
ND D:HEC401 2.1 52.6 1.0
NA D:HEC401 2.1 52.0 1.0
SD D:MET248 2.3 60.9 1.0
CE1 D:HIS128 3.0 48.0 1.0
C4B D:HEC401 3.0 54.0 1.0
C4C D:HEC401 3.0 56.7 1.0
CD2 D:HIS128 3.0 49.0 1.0
C4D D:HEC401 3.1 55.6 1.0
C1C D:HEC401 3.1 55.9 1.0
C1A D:HEC401 3.1 52.1 1.0
C1B D:HEC401 3.1 53.8 1.0
C1D D:HEC401 3.1 51.8 1.0
C4A D:HEC401 3.1 51.4 1.0
CE D:MET248 3.3 56.3 1.0
CHA D:HEC401 3.4 53.7 1.0
CHD D:HEC401 3.4 54.5 1.0
CHC D:HEC401 3.4 51.2 1.0
CHB D:HEC401 3.4 49.5 1.0
CG D:MET248 3.5 53.8 1.0
CB D:MET248 4.1 57.4 1.0
ND1 D:HIS128 4.1 45.9 1.0
CG D:HIS128 4.1 46.5 1.0
C3B D:HEC401 4.3 54.9 1.0
C3C D:HEC401 4.3 55.5 1.0
C2C D:HEC401 4.4 56.1 1.0
C3D D:HEC401 4.4 57.1 1.0
C2A D:HEC401 4.4 55.1 1.0
C3A D:HEC401 4.4 51.7 1.0
C2B D:HEC401 4.4 54.9 1.0
C2D D:HEC401 4.4 54.5 1.0

Iron binding site 6 out of 8 in 8ac5

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

b:35.3
occ:1.00
 FE N:HEC501 0.0 35.3 1.0
ND N:HEC501 1.9 39.3 1.0
NA N:HEC501 1.9 35.0 1.0
NC N:HEC501 2.1 38.1 1.0
NE2 N:HIS82 2.1 34.2 1.0
NE2 N:HIS183 2.1 33.3 1.0
NB N:HEC501 2.1 38.0 1.0
C4D N:HEC501 2.9 39.0 1.0
C1D N:HEC501 2.9 37.1 1.0
C1A N:HEC501 2.9 35.9 1.0
C4A N:HEC501 3.0 36.9 1.0
CE1 N:HIS183 3.0 33.9 1.0
CE1 N:HIS82 3.0 34.0 1.0
C4C N:HEC501 3.0 41.1 1.0
C4B N:HEC501 3.0 41.0 1.0
C1C N:HEC501 3.1 39.3 1.0
C1B N:HEC501 3.1 37.4 1.0
CD2 N:HIS82 3.1 33.2 1.0
CD2 N:HIS183 3.1 34.4 1.0
CHA N:HEC501 3.4 34.1 1.0
CHD N:HEC501 3.4 36.8 1.0
CHB N:HEC501 3.4 37.2 1.0
CHC N:HEC501 3.5 40.3 1.0
ND1 N:HIS82 4.1 34.8 1.0
C3A N:HEC501 4.1 37.6 1.0
ND1 N:HIS183 4.1 34.8 1.0
C2A N:HEC501 4.2 38.5 1.0
C3D N:HEC501 4.2 42.4 1.0
C2D N:HEC501 4.2 41.3 1.0
CG N:HIS82 4.2 34.3 1.0
CG N:HIS183 4.2 34.5 1.0
C2C N:HEC501 4.3 43.1 1.0
C3C N:HEC501 4.3 45.4 1.0
C3B N:HEC501 4.3 42.0 1.0
C2B N:HEC501 4.3 39.5 1.0
CA N:GLY131 4.8 45.6 1.0
NE2 N:GLN43 4.9 51.6 1.0

Iron binding site 7 out of 8 in 8ac5

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

b:35.2
occ:1.00
 FE N:HEC502 0.0 35.2 1.0
ND N:HEC502 1.9 38.9 1.0
NA N:HEC502 2.0 38.1 1.0
NE2 N:HIS96 2.0 40.4 1.0
NC N:HEC502 2.0 36.1 1.0
NB N:HEC502 2.1 36.8 1.0
NE2 N:HIS197 2.2 39.5 1.0
CE1 N:HIS96 2.9 40.7 1.0
C4D N:HEC502 2.9 39.7 1.0
C1D N:HEC502 2.9 38.2 1.0
C4C N:HEC502 2.9 36.7 1.0
C1A N:HEC502 3.0 39.8 1.0
C4A N:HEC502 3.0 39.4 1.0
C1B N:HEC502 3.0 37.0 1.0
C4B N:HEC502 3.0 37.2 1.0
C1C N:HEC502 3.1 36.9 1.0
CD2 N:HIS96 3.1 41.6 1.0
CE1 N:HIS197 3.1 37.8 1.0
CD2 N:HIS197 3.3 40.0 1.0
CHD N:HEC502 3.4 35.0 1.0
CHA N:HEC502 3.4 38.4 1.0
CHB N:HEC502 3.4 37.1 1.0
CHC N:HEC502 3.5 35.6 1.0
ND1 N:HIS96 4.0 40.9 1.0
C3C N:HEC502 4.1 39.0 1.0
CG N:HIS96 4.2 39.7 1.0
C2D N:HEC502 4.2 38.5 1.0
C2A N:HEC502 4.2 44.0 1.0
C3D N:HEC502 4.2 40.7 1.0
C3A N:HEC502 4.2 42.4 1.0
C2C N:HEC502 4.2 36.5 1.0
ND1 N:HIS197 4.3 39.3 1.0
C3B N:HEC502 4.3 39.4 1.0
C2B N:HEC502 4.3 37.2 1.0
CG N:HIS197 4.4 40.0 1.0

Iron binding site 8 out of 8 in 8ac5

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

b:52.7
occ:1.00
 FE O:HEC401 0.0 52.7 1.0
NE2 O:HIS128 2.0 46.0 1.0
NB O:HEC401 2.1 52.5 1.0
NC O:HEC401 2.1 53.7 1.0
ND O:HEC401 2.1 53.0 1.0
NA O:HEC401 2.1 54.9 1.0
SD O:MET248 2.2 57.6 1.0
CE1 O:HIS128 3.0 46.6 1.0
C4B O:HEC401 3.0 54.6 1.0
C4C O:HEC401 3.0 53.9 1.0
CD2 O:HIS128 3.0 47.1 1.0
C1C O:HEC401 3.1 55.6 1.0
C4D O:HEC401 3.1 56.3 1.0
C1B O:HEC401 3.1 51.9 1.0
C1D O:HEC401 3.1 54.4 1.0
C1A O:HEC401 3.1 54.5 1.0
C4A O:HEC401 3.1 51.7 1.0
CE O:MET248 3.3 54.3 1.0
CHA O:HEC401 3.4 56.1 1.0
CHC O:HEC401 3.4 52.7 1.0
CHB O:HEC401 3.4 48.5 1.0
CHD O:HEC401 3.4 54.5 1.0
CG O:MET248 3.5 56.5 1.0
CB O:MET248 4.1 59.2 1.0
ND1 O:HIS128 4.1 48.9 1.0
CG O:HIS128 4.1 47.3 1.0
C3B O:HEC401 4.3 53.3 1.0
C3C O:HEC401 4.3 53.7 1.0
C2C O:HEC401 4.4 57.4 1.0
C2D O:HEC401 4.4 57.7 1.0
C3D O:HEC401 4.4 58.6 1.0
C2A O:HEC401 4.4 52.9 1.0
C3A O:HEC401 4.4 52.4 1.0
C2B O:HEC401 4.4 51.8 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 17:21:16 2024

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