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Iron in PDB 1ntm: Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom

Enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom

All present enzymatic activity of Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom:
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom, PDB code: 1ntm was solved by X.Gao, X.Wen, L.Esser, B.Quinn, L.Yu, C.Yu, D.Xia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 154.325, 154.325, 593.161, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.5

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom (pdb code 1ntm). 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 at 2.4 Angstrom, PDB code: 1ntm:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 1ntm

Go back to Iron Binding Sites List in 1ntm
Iron binding site 1 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom


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 at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe381

b:21.8
occ:1.00
FE C:HEM381 0.0 21.8 1.0
ND C:HEM381 2.0 27.8 1.0
NB C:HEM381 2.0 32.1 1.0
NC C:HEM381 2.0 36.8 1.0
NE2 C:HIS182 2.1 2.0 1.0
NE2 C:HIS83 2.1 7.0 1.0
NA C:HEM381 2.1 32.6 1.0
CE1 C:HIS83 2.9 15.4 1.0
C4D C:HEM381 3.0 31.6 1.0
C1D C:HEM381 3.0 32.6 1.0
CE1 C:HIS182 3.0 2.0 1.0
C4C C:HEM381 3.0 36.4 1.0
C4B C:HEM381 3.1 39.6 1.0
C1B C:HEM381 3.1 35.2 1.0
C1C C:HEM381 3.1 27.3 1.0
C4A C:HEM381 3.1 30.6 1.0
C1A C:HEM381 3.1 26.1 1.0
CD2 C:HIS182 3.1 9.0 1.0
CD2 C:HIS83 3.3 9.0 1.0
CHA C:HEM381 3.6 29.6 1.0
CHD C:HEM381 3.6 36.0 1.0
CHB C:HEM381 3.6 35.4 1.0
CHC C:HEM381 3.7 34.0 1.0
C3D C:HEM381 4.1 35.7 1.0
C2D C:HEM381 4.1 36.3 1.0
ND1 C:HIS83 4.1 19.2 1.0
C3C C:HEM381 4.1 33.7 1.0
ND1 C:HIS182 4.1 11.3 1.0
C3B C:HEM381 4.1 41.8 1.0
C2C C:HEM381 4.2 25.6 1.0
C2B C:HEM381 4.2 39.9 1.0
CG C:HIS182 4.2 14.6 1.0
CG C:HIS83 4.3 16.6 1.0
C3A C:HEM381 4.4 29.6 1.0
C2A C:HEM381 4.4 27.1 1.0
NE2 C:GLN44 4.8 21.2 1.0
CA C:GLY48 4.9 22.6 1.0

Iron binding site 2 out of 5 in 1ntm

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Iron binding site 2 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom


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 at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe382

b:23.1
occ:1.00
FE C:HEM382 0.0 23.1 1.0
ND C:HEM382 2.0 25.3 1.0
NB C:HEM382 2.0 24.1 1.0
NC C:HEM382 2.0 27.8 1.0
NA C:HEM382 2.1 25.0 1.0
NE2 C:HIS196 2.1 6.9 1.0
NE2 C:HIS97 2.3 9.7 1.0
CD2 C:HIS97 3.0 17.1 1.0
C1C C:HEM382 3.0 27.1 1.0
C4C C:HEM382 3.0 23.5 1.0
CD2 C:HIS196 3.0 17.6 1.0
C1D C:HEM382 3.0 31.3 1.0
C4D C:HEM382 3.1 25.6 1.0
C4B C:HEM382 3.1 25.0 1.0
C1B C:HEM382 3.1 24.8 1.0
C4A C:HEM382 3.1 24.5 1.0
C1A C:HEM382 3.1 19.5 1.0
CE1 C:HIS196 3.2 17.3 1.0
CE1 C:HIS97 3.5 17.9 1.0
CHA C:HEM382 3.6 23.1 1.0
CHD C:HEM382 3.6 33.2 1.0
CHC C:HEM382 3.6 28.2 1.0
CHB C:HEM382 3.6 26.3 1.0
C2C C:HEM382 4.1 28.0 1.0
C3C C:HEM382 4.1 26.6 1.0
C2D C:HEM382 4.1 29.4 1.0
C3B C:HEM382 4.2 30.4 1.0
C3D C:HEM382 4.2 22.6 1.0
C2B C:HEM382 4.2 25.4 1.0
CG C:HIS196 4.2 18.1 1.0
ND1 C:HIS196 4.2 23.6 1.0
CG C:HIS97 4.2 18.1 1.0
C3A C:HEM382 4.4 23.9 1.0
C2A C:HEM382 4.4 16.2 1.0
ND1 C:HIS97 4.4 26.8 1.0
CD1 C:LEU37 5.0 16.0 1.0

Iron binding site 3 out of 5 in 1ntm

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Iron binding site 3 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom


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 at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe242

b:16.4
occ:1.00
FE D:HEM242 0.0 16.4 1.0
NC D:HEM242 2.0 23.1 1.0
ND D:HEM242 2.0 14.1 1.0
NB D:HEM242 2.0 14.8 1.0
NA D:HEM242 2.1 10.4 1.0
NE2 D:HIS41 2.2 22.6 1.0
SD D:MET160 2.9 23.2 1.0
C4C D:HEM242 3.0 24.9 1.0
C1C D:HEM242 3.0 26.9 1.0
C1D D:HEM242 3.0 17.5 1.0
C4D D:HEM242 3.0 13.9 1.0
C1B D:HEM242 3.1 11.8 1.0
C4B D:HEM242 3.1 16.0 1.0
C1A D:HEM242 3.1 11.4 1.0
C4A D:HEM242 3.1 5.7 1.0
CE1 D:HIS41 3.1 22.3 1.0
CD2 D:HIS41 3.3 24.3 1.0
CG D:MET160 3.5 24.6 1.0
CHD D:HEM242 3.6 22.3 1.0
CHA D:HEM242 3.6 15.6 1.0
CE D:MET160 3.6 28.3 1.0
CHC D:HEM242 3.6 25.7 1.0
CHB D:HEM242 3.6 2.0 1.0
C2C D:HEM242 4.1 25.6 1.0
C3C D:HEM242 4.1 29.2 1.0
C2D D:HEM242 4.1 17.8 1.0
C3D D:HEM242 4.1 14.1 1.0
C2B D:HEM242 4.2 14.2 1.0
C3B D:HEM242 4.2 13.8 1.0
ND1 D:HIS41 4.3 27.9 1.0
CB D:MET160 4.3 26.5 1.0
CG D:HIS41 4.4 27.3 1.0
C2A D:HEM242 4.4 13.1 1.0
C3A D:HEM242 4.4 8.3 1.0
CB D:PRO110 4.8 28.7 1.0

Iron binding site 4 out of 5 in 1ntm

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Iron binding site 4 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom


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 at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe197

b:44.1
occ:1.00
FE1 E:FES197 0.0 44.1 1.0
S2 E:FES197 2.2 43.6 1.0
S1 E:FES197 2.2 41.4 1.0
SG E:CYS158 2.3 28.5 1.0
SG E:CYS139 2.6 25.9 1.0
FE2 E:FES197 2.7 38.7 1.0
CB E:CYS158 3.2 26.2 1.0
CB E:CYS139 3.4 23.6 1.0
CB E:CYS144 4.1 22.2 1.0
OG E:SER163 4.1 19.5 1.0
CB E:CYS160 4.2 25.6 1.0
CB E:HIS141 4.2 21.6 1.0
CB E:SER163 4.4 21.1 1.0
CA E:CYS158 4.5 26.1 1.0
ND1 E:HIS161 4.6 20.7 1.0
N E:LEU142 4.6 21.2 1.0
N E:HIS161 4.6 24.4 1.0
O E:CYS158 4.6 26.3 1.0
N E:CYS144 4.7 21.9 1.0
C E:CYS158 4.7 26.2 1.0
N E:CYS160 4.8 25.8 1.0
ND1 E:HIS141 4.8 20.4 1.0
SG E:CYS160 4.8 32.8 1.0
CA E:CYS139 4.8 23.6 1.0
SG E:CYS144 4.9 29.4 1.0
CA E:CYS160 4.9 25.5 1.0
CA E:CYS144 4.9 22.2 1.0
CG E:HIS141 5.0 20.6 1.0

Iron binding site 5 out of 5 in 1ntm

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Iron binding site 5 out of 5 in the Crystal Structure of Mitochondrial Cytochrome BC1 Complex at 2.4 Angstrom


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 at 2.4 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe197

b:38.7
occ:1.00
FE2 E:FES197 0.0 38.7 1.0
ND1 E:HIS161 2.0 20.7 1.0
S2 E:FES197 2.2 43.6 1.0
S1 E:FES197 2.2 41.4 1.0
FE1 E:FES197 2.7 44.1 1.0
ND1 E:HIS141 2.7 20.4 1.0
CG E:HIS161 3.0 21.0 1.0
CE1 E:HIS161 3.0 20.7 1.0
CB E:HIS161 3.3 23.6 1.0
N E:HIS161 3.5 24.4 1.0
CG E:HIS141 3.6 20.6 1.0
CB E:HIS141 3.7 21.6 1.0
CE1 E:HIS141 3.7 20.4 1.0
CB E:CYS160 3.8 25.6 1.0
CA E:HIS161 4.0 23.7 1.0
C E:CYS160 4.0 25.0 1.0
NE2 E:HIS161 4.1 20.7 1.0
CD2 E:HIS161 4.1 20.2 1.0
N E:LEU142 4.2 21.2 1.0
CA E:CYS160 4.4 25.5 1.0
CB E:LEU142 4.4 20.9 1.0
CG E:LEU142 4.4 15.2 1.0
CD1 E:LEU142 4.6 8.0 1.0
SG E:CYS139 4.7 25.9 1.0
SG E:CYS158 4.7 28.5 1.0
O E:CYS160 4.8 25.1 1.0
C E:HIS161 4.8 23.1 1.0
CD2 E:HIS141 4.8 19.9 1.0
NE2 E:HIS141 4.8 20.6 1.0
CA E:LEU142 4.8 21.1 1.0
CA E:HIS141 4.9 21.7 1.0
OG E:SER163 4.9 19.5 1.0
C E:HIS141 4.9 21.4 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 12:01:06 2024

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