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Iron in PDB 8abk: Complex III2 From Yarrowia Lipolytica, Decylubiquinol Bound, B- Position

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

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

Iron Binding Sites:

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

Iron binding site 1 out of 8 in 8abk

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

b:26.2
occ:1.00
 FE C:HEM501 0.0 26.2 1.0
ND C:HEM501 1.9 25.9 1.0
NA C:HEM501 2.0 26.7 1.0
NC C:HEM501 2.1 26.8 1.0
NE2 C:HIS183 2.1 27.4 1.0
NE2 C:HIS82 2.1 23.0 1.0
NB C:HEM501 2.1 26.7 1.0
C1D C:HEM501 2.9 25.9 1.0
C4D C:HEM501 2.9 25.8 1.0
C1A C:HEM501 3.0 26.6 1.0
CE1 C:HIS183 3.0 25.3 1.0
CE1 C:HIS82 3.0 23.4 1.0
C4A C:HEM501 3.0 26.5 1.0
C4C C:HEM501 3.1 27.8 1.0
C4B C:HEM501 3.1 27.0 1.0
C1C C:HEM501 3.1 28.1 1.0
C1B C:HEM501 3.1 27.1 1.0
CD2 C:HIS183 3.1 26.4 1.0
CD2 C:HIS82 3.1 22.4 1.0
CHA C:HEM501 3.4 25.2 1.0
CHD C:HEM501 3.4 26.2 1.0
CHC C:HEM501 3.5 27.3 1.0
CHB C:HEM501 3.5 26.7 1.0
ND1 C:HIS183 4.1 25.0 1.0
ND1 C:HIS82 4.1 25.1 1.0
C2A C:HEM501 4.2 27.4 1.0
C2D C:HEM501 4.2 26.0 1.0
C3D C:HEM501 4.2 26.0 1.0
C3A C:HEM501 4.2 26.9 1.0
CG C:HIS183 4.2 25.5 1.0
CG C:HIS82 4.2 25.3 1.0
C2C C:HEM501 4.3 28.9 1.0
C3C C:HEM501 4.3 29.5 1.0
C3B C:HEM501 4.3 27.3 1.0
C2B C:HEM501 4.3 26.7 1.0
CA C:GLY131 4.8 32.3 1.0
NE2 C:GLN43 4.9 30.4 1.0

Iron binding site 2 out of 8 in 8abk

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

b:23.6
occ:1.00
 FE C:HEM502 0.0 23.6 1.0
ND C:HEM502 1.9 23.8 1.0
NA C:HEM502 2.0 24.7 1.0
NC C:HEM502 2.1 24.4 1.0
NB C:HEM502 2.1 24.6 1.0
NE2 C:HIS197 2.2 28.1 1.0
NE2 C:HIS96 2.3 24.2 1.0
C4D C:HEM502 2.9 23.5 1.0
C1D C:HEM502 2.9 23.7 1.0
C4C C:HEM502 3.0 24.4 1.0
C1A C:HEM502 3.0 24.1 1.0
CE1 C:HIS197 3.0 27.0 1.0
C4B C:HEM502 3.0 24.9 1.0
C4A C:HEM502 3.1 26.0 1.0
C1B C:HEM502 3.1 25.4 1.0
C1C C:HEM502 3.1 24.4 1.0
CD2 C:HIS96 3.2 24.8 1.0
CE1 C:HIS96 3.3 24.9 1.0
CD2 C:HIS197 3.3 27.9 1.0
CHA C:HEM502 3.4 23.7 1.0
CHD C:HEM502 3.4 24.2 1.0
CHB C:HEM502 3.5 25.4 1.0
CHC C:HEM502 3.5 25.1 1.0
C3C C:HEM502 4.1 24.1 1.0
C3D C:HEM502 4.2 25.0 1.0
C2A C:HEM502 4.2 26.5 1.0
ND1 C:HIS197 4.2 28.0 1.0
C2D C:HEM502 4.2 24.9 1.0
C2C C:HEM502 4.2 24.0 1.0
C3A C:HEM502 4.3 26.5 1.0
C3B C:HEM502 4.3 26.3 1.0
C2B C:HEM502 4.3 26.6 1.0
CG C:HIS96 4.3 26.2 1.0
CG C:HIS197 4.3 28.3 1.0
ND1 C:HIS96 4.3 27.2 1.0

Iron binding site 3 out of 8 in 8abk

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

b:194.6
occ:1.00
 FE1 P:FES301 0.0 194.6 1.0
S2 P:FES301 2.2 199.0 1.0
S1 P:FES301 2.2 198.3 1.0
SG P:CYS168 2.2 185.1 1.0
SG P:CYS187 2.3 174.1 1.0
CB P:CYS168 2.9 176.2 1.0
FE2 P:FES301 3.0 208.9 1.0
CB P:CYS187 3.1 183.1 1.0
OG P:SER192 3.7 206.9 1.0
CB P:HIS170 3.8 229.2 1.0
CA P:CYS168 4.3 172.2 1.0
CB P:CYS173 4.5 164.5 1.0
ND1 P:HIS190 4.5 197.6 1.0
CA P:CYS187 4.5 192.6 1.0
N P:LEU171 4.5 208.4 1.0
ND1 P:HIS170 4.5 236.1 1.0
CB P:CYS189 4.6 193.2 1.0
N P:HIS170 4.6 216.8 1.0
C P:CYS168 4.6 176.1 1.0
CG P:HIS170 4.7 236.4 1.0
N P:CYS173 4.7 150.9 1.0
CA P:HIS170 4.7 220.9 1.0
CB P:SER192 4.8 206.6 1.0
O P:CYS168 4.9 169.2 1.0
N P:GLY172 4.9 189.2 1.0
N P:HIS190 4.9 201.6 1.0
SG P:CYS173 4.9 175.5 1.0

Iron binding site 4 out of 8 in 8abk

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

b:208.9
occ:1.00
 FE2 P:FES301 0.0 208.9 1.0
ND1 P:HIS170 2.1 236.1 1.0
ND1 P:HIS190 2.1 197.6 1.0
S2 P:FES301 2.2 199.0 1.0
S1 P:FES301 2.2 198.3 1.0
CG P:HIS190 2.8 199.3 1.0
CB P:HIS190 3.0 200.8 1.0
CG P:HIS170 3.0 236.4 1.0
FE1 P:FES301 3.0 194.6 1.0
CE1 P:HIS170 3.1 237.2 1.0
CE1 P:HIS190 3.1 195.9 1.0
CB P:HIS170 3.3 229.2 1.0
N P:HIS190 3.7 201.6 1.0
CD2 P:HIS190 3.9 199.9 1.0
CA P:HIS190 3.9 201.5 1.0
NE2 P:HIS190 4.0 197.9 1.0
CD2 P:HIS170 4.1 242.2 1.0
NE2 P:HIS170 4.2 242.3 1.0
N P:LEU171 4.2 208.4 1.0
CB P:CYS189 4.3 193.2 1.0
SG P:CYS187 4.4 174.1 1.0
CB P:LEU171 4.5 206.6 1.0
C P:CYS189 4.5 200.8 1.0
CG P:LEU171 4.5 209.0 1.0
CA P:HIS170 4.6 220.9 1.0
SG P:CYS168 4.7 185.1 1.0
C P:HIS190 4.7 202.7 1.0
CG P:PRO204 4.7 217.2 1.0
C P:HIS170 4.8 216.6 1.0
CD1 P:LEU171 4.9 206.8 1.0
CB P:PRO204 5.0 219.8 1.0
CA P:CYS189 5.0 198.1 1.0

Iron binding site 5 out of 8 in 8abk

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

b:37.3
occ:1.00
 FE D:HEC401 0.0 37.3 1.0
NE2 D:HIS128 2.1 37.7 1.0
NC D:HEC401 2.1 39.8 1.0
NB D:HEC401 2.1 38.6 1.0
ND D:HEC401 2.1 38.2 1.0
NA D:HEC401 2.1 37.7 1.0
SD D:MET248 2.2 42.4 1.0
CE1 D:HIS128 3.0 36.4 1.0
C4B D:HEC401 3.0 40.4 1.0
C4D D:HEC401 3.0 38.4 1.0
C4C D:HEC401 3.0 41.4 1.0
C1C D:HEC401 3.1 41.0 1.0
C1B D:HEC401 3.1 38.8 1.0
C4A D:HEC401 3.1 38.1 1.0
C1A D:HEC401 3.1 37.7 1.0
C1D D:HEC401 3.1 40.3 1.0
CD2 D:HIS128 3.1 37.2 1.0
CE D:MET248 3.3 37.8 1.0
CHA D:HEC401 3.4 38.4 1.0
CHC D:HEC401 3.4 41.2 1.0
CHB D:HEC401 3.4 38.1 1.0
CHD D:HEC401 3.4 39.2 1.0
CG D:MET248 3.5 40.9 1.0
CB D:MET248 4.1 41.8 1.0
ND1 D:HIS128 4.1 35.2 1.0
CG D:HIS128 4.2 36.4 1.0
C3B D:HEC401 4.3 41.1 1.0
C3C D:HEC401 4.3 43.5 1.0
C3D D:HEC401 4.3 41.1 1.0
C2D D:HEC401 4.4 41.0 1.0
C3A D:HEC401 4.4 38.9 1.0
C2B D:HEC401 4.4 40.6 1.0
C2A D:HEC401 4.4 38.3 1.0
C2C D:HEC401 4.4 40.5 1.0

Iron binding site 6 out of 8 in 8abk

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

b:25.7
occ:1.00
 FE N:HEM501 0.0 25.7 1.0
ND N:HEM501 1.9 26.0 1.0
NA N:HEM501 2.0 26.6 1.0
NE2 N:HIS183 2.0 25.9 1.0
NC N:HEM501 2.1 26.9 1.0
NE2 N:HIS82 2.1 22.7 1.0
NB N:HEM501 2.1 26.1 1.0
C4D N:HEM501 2.9 24.9 1.0
C1D N:HEM501 2.9 27.1 1.0
CE1 N:HIS183 3.0 24.8 1.0
C1A N:HEM501 3.0 25.6 1.0
C4A N:HEM501 3.0 26.6 1.0
C4B N:HEM501 3.1 27.3 1.0
CD2 N:HIS183 3.1 25.8 1.0
C4C N:HEM501 3.1 28.3 1.0
CE1 N:HIS82 3.1 23.1 1.0
C1C N:HEM501 3.1 28.6 1.0
C1B N:HEM501 3.1 26.9 1.0
CD2 N:HIS82 3.1 22.4 1.0
CHA N:HEM501 3.4 24.7 1.0
CHD N:HEM501 3.4 26.7 1.0
CHB N:HEM501 3.5 27.3 1.0
CHC N:HEM501 3.5 28.3 1.0
ND1 N:HIS183 4.1 25.9 1.0
CG N:HIS183 4.2 25.2 1.0
C3A N:HEM501 4.2 26.5 1.0
ND1 N:HIS82 4.2 22.9 1.0
C2A N:HEM501 4.2 27.2 1.0
C3D N:HEM501 4.2 26.7 1.0
C2D N:HEM501 4.2 26.5 1.0
CG N:HIS82 4.2 24.3 1.0
C2C N:HEM501 4.3 31.7 1.0
C3C N:HEM501 4.3 31.4 1.0
C3B N:HEM501 4.3 26.2 1.0
C2B N:HEM501 4.3 27.9 1.0
CA N:GLY131 4.7 31.8 1.0
NE2 N:GLN43 4.9 31.5 1.0

Iron binding site 7 out of 8 in 8abk

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

b:23.4
occ:1.00
 FE N:HEM502 0.0 23.4 1.0
ND N:HEM502 1.9 23.9 1.0
NA N:HEM502 2.0 24.0 1.0
NC N:HEM502 2.0 24.2 1.0
NE2 N:HIS96 2.0 23.8 1.0
NB N:HEM502 2.1 24.7 1.0
NE2 N:HIS197 2.2 24.9 1.0
C4D N:HEM502 2.9 23.9 1.0
C1D N:HEM502 2.9 25.4 1.0
CE1 N:HIS96 2.9 22.1 1.0
C1A N:HEM502 3.0 23.9 1.0
C4C N:HEM502 3.0 24.4 1.0
C1B N:HEM502 3.0 24.9 1.0
C4A N:HEM502 3.0 23.5 1.0
C4B N:HEM502 3.0 24.6 1.0
CE1 N:HIS197 3.0 23.6 1.0
C1C N:HEM502 3.1 24.7 1.0
CD2 N:HIS96 3.1 24.6 1.0
CD2 N:HIS197 3.3 24.9 1.0
CHA N:HEM502 3.4 23.8 1.0
CHB N:HEM502 3.4 23.7 1.0
CHD N:HEM502 3.4 24.7 1.0
CHC N:HEM502 3.5 24.4 1.0
ND1 N:HIS96 4.1 24.3 1.0
C3D N:HEM502 4.1 25.8 1.0
C3C N:HEM502 4.2 23.4 1.0
C2D N:HEM502 4.2 25.7 1.0
C2A N:HEM502 4.2 25.2 1.0
CG N:HIS96 4.2 25.1 1.0
C2C N:HEM502 4.2 23.2 1.0
ND1 N:HIS197 4.2 24.4 1.0
C3A N:HEM502 4.2 25.2 1.0
C2B N:HEM502 4.3 25.2 1.0
C3B N:HEM502 4.3 25.9 1.0
CG N:HIS197 4.3 25.2 1.0

Iron binding site 8 out of 8 in 8abk

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

b:35.5
occ:1.00
 FE O:HEC401 0.0 35.5 1.0
NE2 O:HIS128 2.0 37.4 1.0
NB O:HEC401 2.1 36.6 1.0
NA O:HEC401 2.1 35.5 1.0
NC O:HEC401 2.1 38.0 1.0
ND O:HEC401 2.1 37.0 1.0
SD O:MET248 2.3 40.1 1.0
CE1 O:HIS128 2.9 37.2 1.0
CD2 O:HIS128 3.0 35.5 1.0
C4B O:HEC401 3.0 38.3 1.0
C1B O:HEC401 3.0 36.8 1.0
C4D O:HEC401 3.1 35.8 1.0
C4A O:HEC401 3.1 35.3 1.0
C1A O:HEC401 3.1 36.6 1.0
C4C O:HEC401 3.1 39.0 1.0
C1C O:HEC401 3.1 38.6 1.0
C1D O:HEC401 3.1 39.1 1.0
CE O:MET248 3.3 38.2 1.0
CHB O:HEC401 3.4 35.9 1.0
CHA O:HEC401 3.4 34.9 1.0
CHC O:HEC401 3.4 38.3 1.0
CHD O:HEC401 3.5 38.0 1.0
CG O:MET248 3.5 39.7 1.0
ND1 O:HIS128 4.1 34.7 1.0
CB O:MET248 4.1 42.9 1.0
CG O:HIS128 4.1 35.1 1.0
C3B O:HEC401 4.3 38.8 1.0
C3C O:HEC401 4.3 40.4 1.0
C3D O:HEC401 4.4 37.4 1.0
C3A O:HEC401 4.4 36.0 1.0
C2B O:HEC401 4.4 39.4 1.0
C2A O:HEC401 4.4 37.4 1.0
C2D O:HEC401 4.4 38.2 1.0
C2C O:HEC401 4.4 38.7 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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