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Iron in PDB 1nu1: Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)

Enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)

All present enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno):
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno), PDB code: 1nu1 was solved by X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.-A.Yu, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 3.20
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 153.842, 153.842, 590.374, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 29.6

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) (pdb code 1nu1). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno), PDB code: 1nu1:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1nu1

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Iron binding site 1 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe381

b:31.4
occ:1.00
 FE C:HEM381 0.0 31.4 1.0
ND C:HEM381 2.0 41.6 1.0
NB C:HEM381 2.0 41.5 1.0
NC C:HEM381 2.0 43.9 1.0
NE2 C:HIS182 2.0 15.9 1.0
NE2 C:HIS83 2.1 4.5 1.0
NA C:HEM381 2.1 40.0 1.0
CE1 C:HIS83 2.8 15.6 1.0
CE1 C:HIS182 2.9 15.9 1.0
C4C C:HEM381 3.0 48.8 1.0
C4D C:HEM381 3.0 49.4 1.0
C1D C:HEM381 3.1 44.9 1.0
CD2 C:HIS182 3.1 17.6 1.0
C4B C:HEM381 3.1 49.1 1.0
C1A C:HEM381 3.1 43.4 1.0
C1C C:HEM381 3.1 41.5 1.0
C1B C:HEM381 3.1 41.3 1.0
C4A C:HEM381 3.1 40.6 1.0
CD2 C:HIS83 3.3 10.1 1.0
CHA C:HEM381 3.6 48.8 1.0
CHD C:HEM381 3.6 48.6 1.0
CHB C:HEM381 3.6 36.2 1.0
CHC C:HEM381 3.6 45.8 1.0
ND1 C:HIS83 4.0 23.0 1.0
ND1 C:HIS182 4.1 22.3 1.0
C3C C:HEM381 4.1 48.1 1.0
C3D C:HEM381 4.2 49.0 1.0
CG C:HIS182 4.2 18.5 1.0
C2D C:HEM381 4.2 45.2 1.0
C2C C:HEM381 4.2 36.4 1.0
C3B C:HEM381 4.2 47.9 1.0
C2B C:HEM381 4.2 47.3 1.0
CG C:HIS83 4.3 15.7 1.0
C2A C:HEM381 4.4 38.9 1.0
C3A C:HEM381 4.4 39.1 1.0
CA C:GLY48 4.9 25.3 1.0
CA C:GLY130 5.0 29.6 1.0

Iron binding site 2 out of 5 in 1nu1

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Iron binding site 2 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe382

b:24.9
occ:1.00
 FE C:HEM382 0.0 24.9 1.0
ND C:HEM382 1.9 29.4 1.0
NB C:HEM382 2.0 35.9 1.0
NC C:HEM382 2.0 33.9 1.0
NA C:HEM382 2.1 24.1 1.0
NE2 C:HIS196 2.2 12.3 1.0
NE2 C:HIS97 2.4 21.8 1.0
C4D C:HEM382 3.0 33.9 1.0
C4C C:HEM382 3.0 38.3 1.0
C4B C:HEM382 3.0 35.7 1.0
C1A C:HEM382 3.0 31.2 1.0
C1C C:HEM382 3.0 31.8 1.0
C1B C:HEM382 3.0 23.2 1.0
C1D C:HEM382 3.0 32.5 1.0
C4A C:HEM382 3.0 30.4 1.0
CE1 C:HIS196 3.1 17.5 1.0
CD2 C:HIS97 3.1 20.4 1.0
CD2 C:HIS196 3.3 15.9 1.0
CHA C:HEM382 3.5 38.9 1.0
CE1 C:HIS97 3.5 23.0 1.0
CHC C:HEM382 3.6 37.3 1.0
CHD C:HEM382 3.6 42.6 1.0
CHB C:HEM382 3.6 23.5 1.0
C3D C:HEM382 4.1 30.1 1.0
C3C C:HEM382 4.1 29.2 1.0
C2B C:HEM382 4.1 26.7 1.0
C2C C:HEM382 4.1 29.4 1.0
C3B C:HEM382 4.1 31.0 1.0
C2D C:HEM382 4.1 35.3 1.0
ND1 C:HIS196 4.2 11.6 1.0
C2A C:HEM382 4.3 28.7 1.0
C3A C:HEM382 4.3 29.6 1.0
CG C:HIS97 4.3 30.9 1.0
CG C:HIS196 4.4 21.9 1.0
ND1 C:HIS97 4.5 36.7 1.0

Iron binding site 3 out of 5 in 1nu1

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Iron binding site 3 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe242

b:28.5
occ:1.00
 FE D:HEM242 0.0 28.5 1.0
ND D:HEM242 2.0 29.1 1.0
NC D:HEM242 2.0 32.6 1.0
NB D:HEM242 2.0 31.3 1.0
NA D:HEM242 2.1 34.2 1.0
NE2 D:HIS41 2.3 23.9 1.0
C4D D:HEM242 3.0 30.2 1.0
C1D D:HEM242 3.0 29.8 1.0
C4C D:HEM242 3.0 32.3 1.0
C1B D:HEM242 3.0 30.5 1.0
C1C D:HEM242 3.0 37.0 1.0
CE1 D:HIS41 3.1 29.6 1.0
C4B D:HEM242 3.1 33.0 1.0
C1A D:HEM242 3.1 34.9 1.0
C4A D:HEM242 3.1 35.0 1.0
SD D:MET160 3.1 28.4 1.0
CD2 D:HIS41 3.4 28.4 1.0
CE D:MET160 3.5 26.7 1.0
CG D:MET160 3.5 30.3 1.0
CHA D:HEM242 3.6 37.1 1.0
CHD D:HEM242 3.6 30.2 1.0
CHB D:HEM242 3.6 34.4 1.0
CHC D:HEM242 3.6 39.0 1.0
C2D D:HEM242 4.1 30.1 1.0
C3D D:HEM242 4.1 30.6 1.0
C3C D:HEM242 4.1 36.7 1.0
C2C D:HEM242 4.1 35.8 1.0
C2B D:HEM242 4.1 29.4 1.0
C3B D:HEM242 4.2 29.7 1.0
ND1 D:HIS41 4.3 33.3 1.0
C2A D:HEM242 4.4 35.1 1.0
C3A D:HEM242 4.4 32.5 1.0
CB D:PRO110 4.4 34.1 1.0
CG D:HIS41 4.5 33.3 1.0
CB D:MET160 4.5 33.9 1.0
CA D:PRO110 4.7 34.5 1.0

Iron binding site 4 out of 5 in 1nu1

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Iron binding site 4 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:43.1
occ:1.00
 FE1 E:FES200 0.0 43.1 1.0
S1 E:FES200 2.2 36.5 1.0
S2 E:FES200 2.2 23.4 1.0
SG E:CYS158 2.4 8.4 1.0
FE2 E:FES200 2.7 40.3 1.0
SG E:CYS139 2.7 2.8 1.0
CB E:CYS160 3.4 29.0 1.0
CB E:CYS158 3.4 28.3 1.0
CB E:CYS139 3.5 24.7 1.0
CB E:CYS144 3.6 31.6 1.0
CB E:HIS141 3.8 27.6 1.0
ND1 E:HIS161 4.0 23.8 1.0
OG E:SER163 4.2 34.9 1.0
N E:LEU142 4.3 29.4 1.0
ND1 E:HIS141 4.3 16.8 1.0
N E:HIS161 4.4 28.3 1.0
SG E:CYS160 4.5 28.3 1.0
N E:CYS144 4.5 31.9 1.0
CA E:CYS160 4.5 29.2 1.0
CG E:HIS141 4.6 22.6 1.0
CA E:CYS144 4.6 31.8 1.0
CE1 E:HIS161 4.7 28.1 1.0
CA E:HIS141 4.7 27.7 1.0
N E:CYS160 4.8 29.8 1.0
CA E:CYS158 4.8 28.4 1.0
N E:HIS141 4.8 27.3 1.0
CB E:SER163 4.8 27.8 1.0
SG E:CYS144 4.8 24.7 1.0
C E:CYS160 4.9 28.6 1.0
OH E:TYR165 4.9 37.2 1.0
CA E:CYS139 5.0 25.6 1.0

Iron binding site 5 out of 5 in 1nu1

Go back to Iron Binding Sites List in 1nu1
Iron binding site 5 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Mitochondrial Cytochrome BC1 Complexed with 2- Nonyl-4-Hydroxyquinoline N-Oxide (Nqno) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:40.3
occ:1.00
 FE2 E:FES200 0.0 40.3 1.0
ND1 E:HIS161 2.1 23.8 1.0
S2 E:FES200 2.2 23.4 1.0
ND1 E:HIS141 2.2 16.8 1.0
S1 E:FES200 2.2 36.5 1.0
FE1 E:FES200 2.7 43.1 1.0
CG E:HIS161 2.9 27.9 1.0
CB E:HIS161 3.0 28.3 1.0
CG E:HIS141 3.1 22.6 1.0
CE1 E:HIS161 3.1 28.1 1.0
CE1 E:HIS141 3.2 16.0 1.0
CB E:HIS141 3.3 27.6 1.0
N E:HIS161 3.4 28.3 1.0
CA E:HIS161 3.7 28.2 1.0
CB E:CYS160 3.9 29.0 1.0
CG E:PRO175 4.0 26.0 1.0
CD2 E:HIS161 4.0 29.3 1.0
C E:CYS160 4.1 28.6 1.0
NE2 E:HIS161 4.1 31.4 1.0
OG E:SER163 4.1 34.9 1.0
CD2 E:HIS141 4.2 19.3 1.0
NE2 E:HIS141 4.2 14.6 1.0
N E:LEU142 4.3 29.4 1.0
C E:HIS161 4.4 27.8 1.0
CA E:CYS160 4.6 29.2 1.0
SG E:CYS139 4.7 2.8 1.0
CA E:HIS141 4.7 27.7 1.0
CG E:LEU142 4.8 26.9 1.0
SG E:CYS158 4.8 8.4 1.0
O E:HIS161 4.8 28.0 1.0
CB E:LEU142 4.8 30.3 1.0
CB E:PRO175 4.8 27.0 1.0
O E:CYS160 4.9 28.4 1.0
C E:HIS141 4.9 28.4 1.0
CD1 E:LEU142 5.0 25.0 1.0

Reference:

X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.-A.Yu, D.Xia. Structural Basis For the Quinone Reduction in the Bc(1) Complex: A Comparative Analysis of Crystal Structures of Mitochondrial Cytochrome Bc(1) with Bound Substrate and Inhibitors at the Q(I) Site Biochemistry V. 42 9067 2003.
ISSN: ISSN 0006-2960
PubMed: 12885240
DOI: 10.1021/BI0341814
Page generated: Wed Jul 16 18:54:25 2025

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