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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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

Go back to Iron Binding Sites List in 8abk
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: Wed Apr 5 07:54:44 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy