Atomistry » Iron » PDB 7zx5-8abf » 8ab9
Atomistry »
  Iron »
    PDB 7zx5-8abf »
      8ab9 »

Iron in PDB 8ab9: Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, B-Position

Enzymatic activity of Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, B-Position

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

Iron Binding Sites:

The binding sites of Iron atom in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, B-Position (pdb code 8ab9). 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, Ascorbate-Reduced, B-Position, PDB code: 8ab9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 1 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:34.4
occ:1.00
 FE C:HEM501 0.0 34.4 1.0
ND C:HEM501 1.9 37.0 1.0
NA C:HEM501 1.9 36.3 1.0
NE2 C:HIS183 2.0 29.6 1.0
NC C:HEM501 2.0 37.4 1.0
NE2 C:HIS82 2.0 37.4 1.0
NB C:HEM501 2.1 37.3 1.0
C1D C:HEM501 2.9 38.1 1.0
C4D C:HEM501 2.9 36.9 1.0
C1A C:HEM501 2.9 36.9 1.0
C4A C:HEM501 3.0 36.4 1.0
CE1 C:HIS183 3.0 32.0 1.0
CE1 C:HIS82 3.0 41.6 1.0
C4B C:HEM501 3.0 38.1 1.0
C4C C:HEM501 3.0 38.1 1.0
C1C C:HEM501 3.0 40.5 1.0
C1B C:HEM501 3.1 39.7 1.0
CD2 C:HIS183 3.1 31.6 1.0
CD2 C:HIS82 3.1 36.9 1.0
CHA C:HEM501 3.4 35.1 1.0
CHD C:HEM501 3.4 36.6 1.0
CHC C:HEM501 3.4 38.3 1.0
CHB C:HEM501 3.4 37.1 1.0
C3A C:HEM501 4.1 38.0 1.0
ND1 C:HIS183 4.1 32.3 1.0
ND1 C:HIS82 4.1 39.9 1.0
C2A C:HEM501 4.1 40.8 1.0
C2D C:HEM501 4.1 37.9 1.0
C3D C:HEM501 4.2 37.8 1.0
CG C:HIS82 4.2 36.7 1.0
CG C:HIS183 4.2 33.1 1.0
C2C C:HEM501 4.3 43.7 1.0
C3C C:HEM501 4.3 42.5 1.0
C3B C:HEM501 4.3 42.5 1.0
C2B C:HEM501 4.3 42.1 1.0
CA C:GLY131 4.8 42.1 1.0
NE2 C:GLN43 4.9 54.4 1.0

Iron binding site 2 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 2 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:30.2
occ:1.00
 FE C:HEM502 0.0 30.2 1.0
ND C:HEM502 1.9 34.2 1.0
NA C:HEM502 2.0 38.1 1.0
NC C:HEM502 2.0 34.8 1.0
NB C:HEM502 2.1 32.8 1.0
NE2 C:HIS197 2.2 31.6 1.0
NE2 C:HIS96 2.2 37.9 1.0
C4D C:HEM502 2.9 36.5 1.0
C1D C:HEM502 2.9 37.0 1.0
C4C C:HEM502 3.0 34.7 1.0
C1A C:HEM502 3.0 41.1 1.0
C4A C:HEM502 3.0 40.2 1.0
CE1 C:HIS197 3.0 33.8 1.0
C4B C:HEM502 3.0 34.3 1.0
C1B C:HEM502 3.0 34.5 1.0
C1C C:HEM502 3.1 36.8 1.0
CD2 C:HIS96 3.1 35.4 1.0
CE1 C:HIS96 3.2 46.7 1.0
CD2 C:HIS197 3.3 32.5 1.0
CHA C:HEM502 3.4 37.9 1.0
CHD C:HEM502 3.4 35.8 1.0
CHB C:HEM502 3.4 38.8 1.0
CHC C:HEM502 3.5 35.5 1.0
C3C C:HEM502 4.1 35.9 1.0
C3D C:HEM502 4.1 40.2 1.0
C2D C:HEM502 4.1 38.2 1.0
C2A C:HEM502 4.2 44.7 1.0
C3A C:HEM502 4.2 41.8 1.0
C2C C:HEM502 4.2 36.3 1.0
ND1 C:HIS197 4.2 35.1 1.0
CG C:HIS96 4.3 36.5 1.0
C3B C:HEM502 4.3 35.4 1.0
ND1 C:HIS96 4.3 44.0 1.0
C2B C:HEM502 4.3 34.7 1.0
CG C:HIS197 4.3 33.8 1.0

Iron binding site 3 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 3 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:103.6
occ:1.00
 FE1 P:FES301 0.0 103.6 1.0
SG P:CYS168 2.1 138.4 1.0
S2 P:FES301 2.2 93.6 1.0
S1 P:FES301 2.2 104.4 1.0
SG P:CYS187 2.3 126.6 1.0
CB P:CYS168 2.8 137.2 1.0
FE2 P:FES301 3.0 107.2 1.0
CB P:CYS187 3.1 134.9 1.0
OG P:SER192 3.6 141.8 1.0
CB P:HIS170 3.7 130.1 1.0
CA P:CYS168 4.3 136.4 1.0
N P:LEU171 4.3 107.6 1.0
ND1 P:HIS170 4.5 139.0 1.0
N P:HIS170 4.5 115.3 1.0
CB P:CYS173 4.5 120.0 1.0
ND1 P:HIS190 4.6 136.1 1.0
CA P:CYS187 4.6 142.6 1.0
CG P:HIS170 4.6 142.0 1.0
CA P:HIS170 4.6 116.0 1.0
C P:CYS168 4.6 135.2 1.0
CB P:CYS189 4.7 145.9 1.0
CB P:SER192 4.7 135.0 1.0
N P:GLY172 4.7 120.8 1.0
N P:CYS173 4.7 108.5 1.0
SG P:CYS173 4.9 153.6 1.0
N P:HIS190 4.9 138.0 1.0
O P:CYS168 5.0 129.1 1.0
OH P:TYR194 5.0 144.2 1.0

Iron binding site 4 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 4 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe301

b:107.2
occ:1.00
 FE2 P:FES301 0.0 107.2 1.0
ND1 P:HIS170 2.0 139.0 1.0
ND1 P:HIS190 2.1 136.1 1.0
S2 P:FES301 2.2 93.6 1.0
S1 P:FES301 2.2 104.4 1.0
CG P:HIS190 2.8 133.4 1.0
CG P:HIS170 3.0 142.0 1.0
CB P:HIS190 3.0 137.4 1.0
FE1 P:FES301 3.0 103.6 1.0
CE1 P:HIS170 3.0 139.7 1.0
CE1 P:HIS190 3.2 136.8 1.0
CB P:HIS170 3.2 130.1 1.0
N P:HIS190 3.7 138.0 1.0
CA P:HIS190 3.9 135.2 1.0
CD2 P:HIS190 3.9 137.7 1.0
NE2 P:HIS190 4.1 139.8 1.0
CD2 P:HIS170 4.1 149.0 1.0
N P:LEU171 4.1 107.6 1.0
NE2 P:HIS170 4.1 146.6 1.0
SG P:CYS187 4.3 126.6 1.0
CB P:LEU171 4.3 106.4 1.0
CB P:CYS189 4.3 145.9 1.0
CG P:LEU171 4.4 114.9 1.0
CA P:HIS170 4.5 116.0 1.0
C P:CYS189 4.6 152.1 1.0
SG P:CYS168 4.6 138.4 1.0
C P:HIS190 4.7 129.5 1.0
C P:HIS170 4.7 110.2 1.0
CD1 P:LEU171 4.7 112.9 1.0
CG P:PRO204 4.8 145.1 1.0
CA P:LEU171 4.8 107.1 1.0
CB P:PRO204 4.9 146.0 1.0
CD P:PRO204 5.0 150.0 1.0
OG P:SER192 5.0 141.8 1.0

Iron binding site 5 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 5 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:43.2
occ:1.00
 FE D:HEC401 0.0 43.2 1.0
NE2 D:HIS128 2.0 53.4 1.0
NB D:HEC401 2.0 45.3 1.0
ND D:HEC401 2.0 45.3 1.0
NA D:HEC401 2.1 42.4 1.0
NC D:HEC401 2.1 45.6 1.0
SD D:MET248 2.2 46.3 1.0
CE1 D:HIS128 3.0 51.5 1.0
C4B D:HEC401 3.0 47.9 1.0
C4D D:HEC401 3.0 47.9 1.0
C4C D:HEC401 3.0 45.9 1.0
C4A D:HEC401 3.0 42.9 1.0
C1B D:HEC401 3.0 46.4 1.0
C1D D:HEC401 3.0 45.7 1.0
C1A D:HEC401 3.0 43.3 1.0
CD2 D:HIS128 3.1 53.1 1.0
C1C D:HEC401 3.1 48.5 1.0
CE D:MET248 3.3 47.8 1.0
CHA D:HEC401 3.4 44.6 1.0
CHB D:HEC401 3.4 43.6 1.0
CHD D:HEC401 3.4 45.0 1.0
CHC D:HEC401 3.4 49.3 1.0
CG D:MET248 3.4 53.6 1.0
CB D:MET248 4.0 51.8 1.0
ND1 D:HIS128 4.1 51.6 1.0
CG D:HIS128 4.2 49.9 1.0
C3B D:HEC401 4.2 46.9 1.0
C3C D:HEC401 4.3 48.7 1.0
C3A D:HEC401 4.3 46.2 1.0
C3D D:HEC401 4.3 51.7 1.0
C2B D:HEC401 4.3 46.7 1.0
C2D D:HEC401 4.3 50.6 1.0
C2A D:HEC401 4.3 45.9 1.0
C2C D:HEC401 4.4 50.4 1.0

Iron binding site 6 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 6 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe501

b:30.4
occ:1.00
 FE N:HEM501 0.0 30.4 1.0
ND N:HEM501 1.9 35.0 1.0
NA N:HEM501 2.0 33.6 1.0
NE2 N:HIS183 2.0 34.9 1.0
NC N:HEM501 2.0 35.0 1.0
NE2 N:HIS82 2.0 34.7 1.0
NB N:HEM501 2.1 34.7 1.0
C4D N:HEM501 2.9 35.8 1.0
C1D N:HEM501 2.9 35.0 1.0
C1A N:HEM501 2.9 35.2 1.0
CE1 N:HIS183 3.0 37.7 1.0
C4B N:HEM501 3.0 36.6 1.0
C4A N:HEM501 3.0 34.6 1.0
CE1 N:HIS82 3.0 35.4 1.0
C1C N:HEM501 3.0 38.0 1.0
C4C N:HEM501 3.0 36.0 1.0
C1B N:HEM501 3.0 38.2 1.0
CD2 N:HIS183 3.1 36.5 1.0
CD2 N:HIS82 3.1 35.6 1.0
CHA N:HEM501 3.4 34.4 1.0
CHD N:HEM501 3.4 34.2 1.0
CHC N:HEM501 3.4 38.3 1.0
CHB N:HEM501 3.4 36.5 1.0
ND1 N:HIS183 4.1 36.2 1.0
ND1 N:HIS82 4.1 36.1 1.0
C3D N:HEM501 4.1 37.8 1.0
C2A N:HEM501 4.2 39.1 1.0
C3A N:HEM501 4.2 36.8 1.0
C2D N:HEM501 4.2 35.6 1.0
CG N:HIS183 4.2 35.8 1.0
CG N:HIS82 4.2 33.7 1.0
C3B N:HEM501 4.2 38.8 1.0
C2C N:HEM501 4.2 38.7 1.0
C3C N:HEM501 4.3 39.3 1.0
C2B N:HEM501 4.3 38.6 1.0
CA N:GLY131 4.8 45.5 1.0
NE2 N:GLN43 4.9 50.3 1.0

Iron binding site 7 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 7 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe502

b:33.4
occ:1.00
 FE N:HEM502 0.0 33.4 1.0
ND N:HEM502 1.9 37.8 1.0
NA N:HEM502 2.0 38.7 1.0
NC N:HEM502 2.0 33.4 1.0
NE2 N:HIS96 2.0 38.7 1.0
NB N:HEM502 2.1 35.4 1.0
NE2 N:HIS197 2.1 36.8 1.0
C1D N:HEM502 2.9 38.3 1.0
C4D N:HEM502 2.9 39.4 1.0
C4C N:HEM502 2.9 35.0 1.0
CE1 N:HIS96 2.9 40.8 1.0
C1A N:HEM502 3.0 42.0 1.0
C4B N:HEM502 3.0 35.3 1.0
C4A N:HEM502 3.0 40.0 1.0
CE1 N:HIS197 3.0 36.2 1.0
C1C N:HEM502 3.0 33.6 1.0
C1B N:HEM502 3.0 37.4 1.0
CD2 N:HIS96 3.1 38.8 1.0
CD2 N:HIS197 3.2 37.5 1.0
CHD N:HEM502 3.4 36.6 1.0
CHA N:HEM502 3.4 39.4 1.0
CHB N:HEM502 3.4 38.4 1.0
CHC N:HEM502 3.5 34.0 1.0
ND1 N:HIS96 4.1 39.7 1.0
C3C N:HEM502 4.1 36.2 1.0
C2D N:HEM502 4.1 39.0 1.0
C2A N:HEM502 4.2 46.5 1.0
C3D N:HEM502 4.2 41.1 1.0
C2C N:HEM502 4.2 34.2 1.0
C3A N:HEM502 4.2 43.0 1.0
ND1 N:HIS197 4.2 37.7 1.0
CG N:HIS96 4.2 37.7 1.0
C3B N:HEM502 4.3 37.2 1.0
C2B N:HEM502 4.3 36.6 1.0
CG N:HIS197 4.3 37.0 1.0

Iron binding site 8 out of 8 in 8ab9

Go back to Iron Binding Sites List in 8ab9
Iron binding site 8 out of 8 in the Complex III2 From Yarrowia Lipolytica, Ascorbate-Reduced, 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, Ascorbate-Reduced, B-Position within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Fe401

b:43.8
occ:1.00
 FE O:HEC401 0.0 43.8 1.0
NE2 O:HIS128 2.0 51.7 1.0
NA O:HEC401 2.0 41.4 1.0
ND O:HEC401 2.0 46.0 1.0
NC O:HEC401 2.1 45.2 1.0
NB O:HEC401 2.1 44.9 1.0
SD O:MET248 2.2 50.3 1.0
CE1 O:HIS128 2.9 49.4 1.0
C4A O:HEC401 3.0 42.0 1.0
C4C O:HEC401 3.0 45.7 1.0
CD2 O:HIS128 3.0 52.2 1.0
C4B O:HEC401 3.0 47.3 1.0
C1D O:HEC401 3.0 46.8 1.0
C1A O:HEC401 3.0 42.0 1.0
C4D O:HEC401 3.0 49.0 1.0
C1B O:HEC401 3.1 44.4 1.0
C1C O:HEC401 3.1 47.7 1.0
CE O:MET248 3.3 52.4 1.0
CHD O:HEC401 3.4 47.4 1.0
CHA O:HEC401 3.4 44.6 1.0
CHB O:HEC401 3.4 41.7 1.0
CHC O:HEC401 3.4 48.6 1.0
CG O:MET248 3.5 48.8 1.0
CB O:MET248 4.0 51.4 1.0
ND1 O:HIS128 4.0 50.8 1.0
CG O:HIS128 4.1 49.0 1.0
C3C O:HEC401 4.3 47.3 1.0
C3B O:HEC401 4.3 44.9 1.0
C3A O:HEC401 4.3 45.5 1.0
C2D O:HEC401 4.3 49.8 1.0
C2A O:HEC401 4.3 45.1 1.0
C3D O:HEC401 4.4 51.1 1.0
C2B O:HEC401 4.4 44.8 1.0
C2C O:HEC401 4.4 50.0 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 16:15:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy