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Iron in PDB 4pd4: Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action

Enzymatic activity of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action

All present enzymatic activity of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action:
1.10.2.2;

Protein crystallography data

The structure of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action, PDB code: 4pd4 was solved by D.Birth, W.-C.Kao, C.Hunte, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.99 / 3.04
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 212.260, 150.880, 143.090, 90.00, 115.18, 90.00
R / Rfree (%) 26.8 / 29.7

Other elements in 4pd4:

The structure of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action (pdb code 4pd4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action, PDB code: 4pd4:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 4pd4

Go back to Iron Binding Sites List in 4pd4
Iron binding site 1 out of 5 in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe4001

b:0.0
occ:1.00
 FE C:HEM4001 0.0 0.0 1.0
NE2 C:HIS82 1.9 1.8 1.0
NC C:HEM4001 2.0 3.0 1.0
NE2 C:HIS183 2.0 2.3 1.0
NB C:HEM4001 2.0 2.5 1.0
ND C:HEM4001 2.1 2.0 1.0
NA C:HEM4001 2.1 3.0 1.0
CE1 C:HIS183 2.8 2.6 1.0
CE1 C:HIS82 2.9 1.8 1.0
CD2 C:HIS82 3.0 2.4 1.0
C1C C:HEM4001 3.0 2.7 1.0
C4C C:HEM4001 3.0 2.5 1.0
C4B C:HEM4001 3.0 2.2 1.0
C1D C:HEM4001 3.0 2.6 1.0
C4D C:HEM4001 3.1 2.9 1.0
C1A C:HEM4001 3.1 3.3 1.0
CD2 C:HIS183 3.1 1.9 1.0
C1B C:HEM4001 3.2 2.5 1.0
C4A C:HEM4001 3.2 3.3 1.0
CHC C:HEM4001 3.4 2.3 1.0
CHD C:HEM4001 3.4 2.6 1.0
CHA C:HEM4001 3.4 4.5 1.0
CHB C:HEM4001 3.6 3.0 1.0
ND1 C:HIS183 4.0 2.1 1.0
ND1 C:HIS82 4.0 1.6 1.0
CG C:HIS82 4.1 2.6 1.0
CG C:HIS183 4.2 1.9 1.0
C3C C:HEM4001 4.2 2.0 1.0
C2C C:HEM4001 4.2 2.3 1.0
C3B C:HEM4001 4.3 3.4 1.0
C2D C:HEM4001 4.3 3.3 1.0
C3D C:HEM4001 4.3 2.4 1.0
C2B C:HEM4001 4.4 2.2 1.0
C2A C:HEM4001 4.4 4.0 1.0
C3A C:HEM4001 4.4 3.7 1.0
CA C:GLY131 4.5 3.6 1.0
NE2 C:GLN43 4.8 2.3 1.0

Iron binding site 2 out of 5 in 4pd4

Go back to Iron Binding Sites List in 4pd4
Iron binding site 2 out of 5 in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe4002

b:3.3
occ:1.00
 FE C:HEM4002 0.0 3.3 1.0
NA C:HEM4002 1.9 6.1 1.0
NE2 C:HIS96 2.0 4.8 1.0
NB C:HEM4002 2.0 4.6 1.0
ND C:HEM4002 2.0 5.2 1.0
NC C:HEM4002 2.1 4.5 1.0
NE2 C:HIS197 2.2 5.0 1.0
CE1 C:HIS96 2.7 5.4 1.0
CE1 C:HIS197 2.9 3.9 1.0
C4A C:HEM4002 3.0 6.4 1.0
C1A C:HEM4002 3.0 6.3 1.0
C4D C:HEM4002 3.0 6.5 1.0
C1B C:HEM4002 3.0 5.0 1.0
C1C C:HEM4002 3.1 4.6 1.0
C1D C:HEM4002 3.1 4.7 1.0
C4B C:HEM4002 3.1 4.1 1.0
C4C C:HEM4002 3.1 4.3 1.0
CD2 C:HIS96 3.2 3.7 1.0
CHA C:HEM4002 3.3 7.5 1.0
CD2 C:HIS197 3.3 3.1 1.0
CHB C:HEM4002 3.4 4.8 1.0
CHD C:HEM4002 3.4 4.7 1.0
CHC C:HEM4002 3.5 4.3 1.0
ND1 C:HIS96 3.9 5.9 1.0
ND1 C:HIS197 4.1 2.8 1.0
C3A C:HEM4002 4.2 6.8 1.0
CG C:HIS96 4.2 4.7 1.0
C2A C:HEM4002 4.2 6.2 1.0
C3D C:HEM4002 4.2 4.7 1.0
C2D C:HEM4002 4.3 4.3 1.0
C2B C:HEM4002 4.3 6.1 1.0
C3B C:HEM4002 4.3 5.4 1.0
C2C C:HEM4002 4.3 3.1 1.0
C3C C:HEM4002 4.3 3.2 1.0
CG C:HIS197 4.3 3.0 1.0

Iron binding site 3 out of 5 in 4pd4

Go back to Iron Binding Sites List in 4pd4
Iron binding site 3 out of 5 in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe401

b:32.7
occ:1.00
 FE D:HEM401 0.0 32.7 1.0
ND D:HEM401 2.0 27.0 1.0
NC D:HEM401 2.0 35.7 1.0
NB D:HEM401 2.1 29.8 1.0
NA D:HEM401 2.1 32.4 1.0
SD D:MET225 2.1 42.6 1.0
NE2 D:HIS105 2.2 34.8 1.0
C1D D:HEM401 3.0 30.9 1.0
C4D D:HEM401 3.0 28.4 1.0
C4C D:HEM401 3.0 34.6 1.0
C1C D:HEM401 3.1 36.8 1.0
C1B D:HEM401 3.1 31.8 1.0
CE1 D:HIS105 3.1 32.7 1.0
C4A D:HEM401 3.1 28.2 1.0
C4B D:HEM401 3.1 31.3 1.0
C1A D:HEM401 3.2 32.1 1.0
CD2 D:HIS105 3.2 35.7 1.0
CHD D:HEM401 3.4 31.2 1.0
CHA D:HEM401 3.4 32.0 1.0
CE D:MET225 3.4 32.6 1.0
CHC D:HEM401 3.5 34.2 1.0
CHB D:HEM401 3.5 31.3 1.0
CG D:MET225 3.6 37.0 1.0
CB D:MET225 4.2 37.4 1.0
C3C D:HEM401 4.2 34.4 1.0
C2D D:HEM401 4.3 34.2 1.0
ND1 D:HIS105 4.3 32.6 1.0
C3D D:HEM401 4.3 32.5 1.0
C2C D:HEM401 4.3 35.0 1.0
CG D:HIS105 4.3 35.2 1.0
C2B D:HEM401 4.3 33.6 1.0
C3A D:HEM401 4.4 24.9 1.0
C3B D:HEM401 4.4 32.0 1.0
C2A D:HEM401 4.4 25.0 1.0

Iron binding site 4 out of 5 in 4pd4

Go back to Iron Binding Sites List in 4pd4
Iron binding site 4 out of 5 in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:7.5
occ:1.00
 FE1 E:FES301 0.0 7.5 1.0
SG E:CYS178 2.1 9.6 1.0
S1 E:FES301 2.1 6.4 1.0
SG E:CYS159 2.2 5.2 1.0
S2 E:FES301 2.3 7.9 1.0
CB E:CYS178 3.0 12.2 1.0
FE2 E:FES301 3.1 13.7 1.0
CB E:CYS159 3.2 4.0 1.0
CB E:HIS161 4.0 4.3 1.0
CB E:CYS180 4.1 12.0 1.0
O E:CYS178 4.3 12.6 1.0
N E:HIS181 4.3 12.5 1.0
CA E:CYS178 4.4 12.7 1.0
C E:CYS178 4.5 13.4 1.0
CB E:SER183 4.5 9.3 1.0
ND1 E:HIS161 4.6 3.0 1.0
CA E:CYS159 4.6 4.8 1.0
O E:CYS159 4.6 6.3 1.0
ND1 E:HIS181 4.6 8.4 1.0
CB E:CYS164 4.7 5.5 1.0
OG E:SER183 4.7 6.7 1.0
CG E:HIS161 4.8 3.0 1.0
N E:SER183 4.8 9.5 1.0
N E:CYS164 4.8 5.2 1.0
N E:CYS180 4.8 14.3 1.0
CA E:CYS180 4.8 12.2 1.0
N E:LEU162 4.8 3.9 1.0
C E:CYS159 4.9 4.3 1.0
SG E:CYS164 5.0 6.0 1.0
N E:HIS161 5.0 4.4 1.0

Iron binding site 5 out of 5 in 4pd4

Go back to Iron Binding Sites List in 4pd4
Iron binding site 5 out of 5 in the Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe301

b:13.7
occ:1.00
 FE2 E:FES301 0.0 13.7 1.0
ND1 E:HIS181 1.8 8.4 1.0
ND1 E:HIS161 2.0 3.0 1.0
S1 E:FES301 2.2 6.4 1.0
S2 E:FES301 2.2 7.9 1.0
CE1 E:HIS181 2.8 9.4 1.0
CG E:HIS181 2.9 10.0 1.0
CG E:HIS161 3.0 3.0 1.0
CE1 E:HIS161 3.0 2.8 1.0
FE1 E:FES301 3.1 7.5 1.0
CB E:HIS181 3.3 8.8 1.0
CB E:HIS161 3.3 4.3 1.0
N E:HIS181 3.4 12.5 1.0
CA E:HIS181 3.8 10.5 1.0
NE2 E:HIS181 3.9 11.4 1.0
CD2 E:HIS181 4.0 9.2 1.0
CB E:CYS180 4.0 12.0 1.0
NE2 E:HIS161 4.1 3.1 1.0
CD2 E:HIS161 4.1 3.2 1.0
N E:LEU162 4.1 3.9 1.0
C E:CYS180 4.2 11.5 1.0
CB E:LEU162 4.5 4.8 1.0
C E:HIS181 4.5 12.4 1.0
CG E:PRO195 4.5 4.3 1.0
SG E:CYS159 4.6 5.2 1.0
CA E:CYS180 4.7 12.2 1.0
CA E:HIS161 4.7 5.0 1.0
O E:HIS181 4.7 12.6 1.0
CG E:LEU162 4.7 3.0 1.0
CD1 E:LEU162 4.7 3.0 1.0
SG E:CYS178 4.7 9.6 1.0
C E:HIS161 4.8 4.5 1.0
CA E:LEU162 4.8 6.7 1.0
O E:CYS180 4.9 12.2 1.0

Reference:

D.Birth, W.C.Kao, C.Hunte. Structural Analysis of Atovaquone-Inhibited Cytochrome BC1 Complex Reveals the Molecular Basis of Antimalarial Drug Action. Nat Commun V. 5 4029 2014.
ISSN: ESSN 2041-1723
PubMed: 24893593
DOI: 10.1038/NCOMMS5029
Page generated: Tue Aug 5 13:38:19 2025

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