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Iron in PDB 1ntz: Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone

Enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone

All present enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone:
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone, PDB code: 1ntz 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) 28.99 / 2.60
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 153.828, 153.828, 596.671, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 28.3

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone (pdb code 1ntz). 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 Complex Bound with Ubiquinone, PDB code: 1ntz:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1ntz

Go back to Iron Binding Sites List in 1ntz
Iron binding site 1 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone


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 Complex Bound with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe381

b:34.8
occ:1.00
FE C:HEM381 0.0 34.8 1.0
NB C:HEM381 2.0 47.6 1.0
ND C:HEM381 2.0 43.4 1.0
NC C:HEM381 2.0 48.8 1.0
NE2 C:HIS182 2.1 17.5 1.0
NE2 C:HIS83 2.1 21.4 1.0
NA C:HEM381 2.2 37.6 1.0
CE1 C:HIS83 3.0 22.8 1.0
CE1 C:HIS182 3.0 19.9 1.0
C4C C:HEM381 3.0 51.5 1.0
C1C C:HEM381 3.1 43.7 1.0
C1D C:HEM381 3.1 48.0 1.0
C4B C:HEM381 3.1 53.1 1.0
C4D C:HEM381 3.1 50.1 1.0
C1B C:HEM381 3.1 45.8 1.0
C1A C:HEM381 3.1 39.1 1.0
C4A C:HEM381 3.1 42.5 1.0
CD2 C:HIS182 3.2 20.6 1.0
CD2 C:HIS83 3.2 20.5 1.0
CHD C:HEM381 3.6 49.1 1.0
CHA C:HEM381 3.6 44.1 1.0
CHB C:HEM381 3.6 44.3 1.0
CHC C:HEM381 3.6 50.0 1.0
C3C C:HEM381 4.1 47.0 1.0
C2C C:HEM381 4.1 44.0 1.0
ND1 C:HIS182 4.2 28.8 1.0
ND1 C:HIS83 4.2 26.7 1.0
C3B C:HEM381 4.2 55.1 1.0
C2D C:HEM381 4.2 55.4 1.0
C2B C:HEM381 4.2 52.9 1.0
C3D C:HEM381 4.2 52.3 1.0
CG C:HIS182 4.3 25.2 1.0
CG C:HIS83 4.3 21.2 1.0
C3A C:HEM381 4.4 41.1 1.0
C2A C:HEM381 4.4 39.1 1.0
NE2 C:GLN44 4.8 32.8 1.0
CA C:GLY130 5.0 35.7 1.0

Iron binding site 2 out of 5 in 1ntz

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Iron binding site 2 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone


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 Complex Bound with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe382

b:35.2
occ:1.00
FE C:HEM382 0.0 35.2 1.0
NB C:HEM382 2.0 45.3 1.0
NC C:HEM382 2.0 38.2 1.0
ND C:HEM382 2.0 39.8 1.0
NA C:HEM382 2.1 35.5 1.0
NE2 C:HIS196 2.2 20.0 1.0
NE2 C:HIS97 2.2 31.3 1.0
CD2 C:HIS97 3.0 35.2 1.0
C1C C:HEM382 3.0 40.0 1.0
C4C C:HEM382 3.0 33.1 1.0
C4B C:HEM382 3.1 42.9 1.0
C1B C:HEM382 3.1 38.6 1.0
C4A C:HEM382 3.1 40.7 1.0
C1A C:HEM382 3.1 35.3 1.0
C4D C:HEM382 3.1 38.5 1.0
C1D C:HEM382 3.1 40.3 1.0
CD2 C:HIS196 3.1 30.9 1.0
CE1 C:HIS196 3.2 17.1 1.0
CE1 C:HIS97 3.4 32.0 1.0
CHC C:HEM382 3.6 40.4 1.0
CHA C:HEM382 3.6 36.7 1.0
CHB C:HEM382 3.6 38.4 1.0
CHD C:HEM382 3.6 40.3 1.0
C2C C:HEM382 4.1 44.8 1.0
C3C C:HEM382 4.1 38.7 1.0
C2B C:HEM382 4.2 39.5 1.0
C3B C:HEM382 4.2 44.4 1.0
CG C:HIS97 4.2 32.0 1.0
C3D C:HEM382 4.2 32.5 1.0
C2D C:HEM382 4.2 37.9 1.0
ND1 C:HIS196 4.3 33.1 1.0
CG C:HIS196 4.3 29.3 1.0
C3A C:HEM382 4.3 39.8 1.0
C2A C:HEM382 4.3 34.6 1.0
ND1 C:HIS97 4.4 39.6 1.0

Iron binding site 3 out of 5 in 1ntz

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Iron binding site 3 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone


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 Complex Bound with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe242

b:23.6
occ:1.00
FE D:HEM242 0.0 23.6 1.0
NC D:HEM242 2.0 20.5 1.0
ND D:HEM242 2.0 14.9 1.0
NB D:HEM242 2.0 22.0 1.0
NA D:HEM242 2.2 14.1 1.0
NE2 D:HIS41 2.4 41.6 1.0
SD D:MET160 2.8 42.8 1.0
C4C D:HEM242 3.0 20.6 1.0
C1D D:HEM242 3.0 16.7 1.0
C1C D:HEM242 3.1 23.6 1.0
C4D D:HEM242 3.1 17.7 1.0
C4B D:HEM242 3.1 21.6 1.0
C1B D:HEM242 3.1 20.6 1.0
C1A D:HEM242 3.1 17.5 1.0
C4A D:HEM242 3.1 8.6 1.0
CE1 D:HIS41 3.4 43.5 1.0
CD2 D:HIS41 3.4 41.7 1.0
CE D:MET160 3.4 43.8 1.0
CG D:MET160 3.5 44.5 1.0
CHD D:HEM242 3.6 17.7 1.0
CHA D:HEM242 3.6 19.7 1.0
CHC D:HEM242 3.6 26.9 1.0
CHB D:HEM242 3.6 10.6 1.0
C2D D:HEM242 4.1 18.5 1.0
C3D D:HEM242 4.2 19.5 1.0
C2C D:HEM242 4.2 20.2 1.0
C3C D:HEM242 4.2 22.5 1.0
C2B D:HEM242 4.2 20.8 1.0
C3B D:HEM242 4.2 19.8 1.0
CB D:MET160 4.2 48.2 1.0
C2A D:HEM242 4.4 20.7 1.0
C3A D:HEM242 4.4 19.5 1.0
ND1 D:HIS41 4.5 46.3 1.0
CB D:PRO110 4.6 44.7 1.0
CG D:HIS41 4.6 43.7 1.0
CA D:PRO110 5.0 44.8 1.0

Iron binding site 4 out of 5 in 1ntz

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Iron binding site 4 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone


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 Complex Bound with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:99.1
occ:1.00
FE1 E:FES200 0.0 99.1 1.0
S2 E:FES200 2.2 98.2 1.0
S1 E:FES200 2.2 97.7 1.0
SG E:CYS139 2.7 47.7 1.0
FE2 E:FES200 2.7 94.1 1.0
SG E:CYS158 2.9 55.2 1.0
CB E:CYS158 3.2 53.6 1.0
CB E:CYS139 3.3 48.3 1.0
CB E:CYS144 4.0 50.4 1.0
OG E:SER163 4.2 49.2 1.0
CB E:CYS160 4.3 53.6 1.0
CB E:HIS141 4.3 46.9 1.0
CB E:SER163 4.4 50.4 1.0
CA E:CYS158 4.5 53.6 1.0
N E:CYS144 4.5 49.7 1.0
SG E:CYS144 4.6 58.4 1.0
N E:LEU142 4.6 46.9 1.0
O E:CYS158 4.6 53.7 1.0
C E:CYS158 4.7 53.7 1.0
SG E:CYS160 4.7 58.6 1.0
N E:HIS161 4.8 53.0 1.0
CA E:CYS139 4.8 48.3 1.0
CA E:CYS144 4.8 50.4 1.0
N E:CYS160 4.9 53.7 1.0
ND1 E:HIS161 4.9 52.2 1.0
ND1 E:HIS141 5.0 45.1 1.0

Iron binding site 5 out of 5 in 1ntz

Go back to Iron Binding Sites List in 1ntz
Iron binding site 5 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex Bound with Ubiquinone


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 Complex Bound with Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:94.1
occ:1.00
FE2 E:FES200 0.0 94.1 1.0
S2 E:FES200 2.2 98.2 1.0
S1 E:FES200 2.2 97.7 1.0
ND1 E:HIS161 2.5 52.2 1.0
FE1 E:FES200 2.7 99.1 1.0
ND1 E:HIS141 2.8 45.1 1.0
CG E:HIS161 3.4 52.9 1.0
CE1 E:HIS161 3.4 53.0 1.0
CB E:HIS161 3.6 52.6 1.0
CG E:HIS141 3.6 46.1 1.0
CB E:HIS141 3.6 46.9 1.0
N E:HIS161 3.8 53.0 1.0
CB E:CYS160 3.9 53.6 1.0
CE1 E:HIS141 3.9 43.9 1.0
N E:LEU142 3.9 46.9 1.0
CG E:LEU142 4.0 40.1 1.0
CB E:LEU142 4.1 46.7 1.0
CA E:HIS161 4.2 52.6 1.0
C E:CYS160 4.3 53.3 1.0
CD1 E:LEU142 4.5 39.1 1.0
CD2 E:HIS161 4.5 52.7 1.0
NE2 E:HIS161 4.5 53.8 1.0
CA E:LEU142 4.5 47.0 1.0
CA E:CYS160 4.6 53.5 1.0
SG E:CYS139 4.7 47.7 1.0
C E:HIS141 4.7 46.9 1.0
CA E:HIS141 4.8 46.9 1.0
CD2 E:HIS141 4.8 45.2 1.0
OG E:SER163 4.9 49.2 1.0
NE2 E:HIS141 4.9 44.3 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: Sat Aug 3 12:01:40 2024

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