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Iron in PDB 2wqy: Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II

Enzymatic activity of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II

All present enzymatic activity of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II:
1.3.5.1;

Protein crystallography data

The structure of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II, PDB code: 2wqy was solved by J.Ruprecht, S.Iwata, G.Cecchini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.09 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.700, 200.753, 67.631, 90.00, 90.06, 90.00
R / Rfree (%) 18.4 / 22.3

Other elements in 2wqy:

The structure of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II also contains other interesting chemical elements:

Potassium (K) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II (pdb code 2wqy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II, PDB code: 2wqy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 2wqy

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Iron binding site 1 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:17.8
occ:1.00
FE1 B:FES1002 0.0 17.8 1.0
S2 B:FES1002 2.2 16.4 1.0
S1 B:FES1002 2.2 16.4 1.0
SG B:CYS73 2.2 18.4 1.0
SG B:CYS85 2.2 19.3 1.0
FE2 B:FES1002 2.8 14.8 1.0
CB B:CYS85 3.2 17.6 1.0
CB B:CYS73 3.5 17.9 1.0
N B:CYS73 3.9 13.6 1.0
N B:CYS85 4.1 19.3 1.0
SG B:CYS65 4.2 15.3 1.0
CA B:CYS73 4.3 15.5 1.0
CA B:CYS85 4.3 19.9 1.0
N B:GLY68 4.5 19.3 1.0
CB B:LEU83 4.5 12.2 1.0
CA B:GLY68 4.5 14.2 1.0
CD2 B:LEU45 4.6 17.8 1.0
SG B:CYS70 4.7 16.0 1.0
N B:ARG66 4.8 20.6 1.0
N B:SER72 4.8 10.4 1.0
CD2 B:LEU83 5.0 19.3 1.0

Iron binding site 2 out of 20 in 2wqy

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Iron binding site 2 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:14.8
occ:1.00
FE2 B:FES1002 0.0 14.8 1.0
S1 B:FES1002 2.2 16.4 1.0
S2 B:FES1002 2.2 16.4 1.0
SG B:CYS70 2.2 16.0 1.0
SG B:CYS65 2.3 15.3 1.0
FE1 B:FES1002 2.8 17.8 1.0
CB B:CYS70 3.3 13.9 1.0
N B:CYS65 3.4 16.2 1.0
CB B:CYS65 3.5 5.8 1.0
N B:CYS70 3.6 16.0 1.0
N B:GLY71 3.7 13.2 1.0
CA B:CYS70 3.8 18.0 1.0
CA B:CYS65 3.9 16.3 1.0
N B:SER72 4.0 10.4 1.0
N B:ARG66 4.1 20.6 1.0
C B:CYS70 4.2 17.6 1.0
SG B:CYS85 4.2 19.3 1.0
CB B:SER72 4.3 15.4 1.0
C B:CYS65 4.3 17.1 1.0
N B:SER64 4.4 14.5 1.0
N B:ILE69 4.5 16.6 1.0
C B:SER64 4.5 14.4 1.0
N B:GLY68 4.6 19.3 1.0
OG B:SER72 4.6 20.8 1.0
CA B:SER72 4.7 13.8 1.0
N B:CYS73 4.7 13.6 1.0
SG B:CYS73 4.7 18.4 1.0
CA B:GLY71 4.7 15.6 1.0
CA B:GLY68 4.8 14.2 1.0
C B:GLY71 4.8 17.0 1.0
C B:ILE69 4.8 18.1 1.0
CA B:SER64 4.9 15.6 1.0
C B:GLY68 5.0 15.4 1.0

Iron binding site 3 out of 20 in 2wqy

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Iron binding site 3 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:18.4
occ:1.00
FE1 B:SF41003 0.0 18.4 1.0
S2 B:SF41003 2.2 17.6 1.0
S4 B:SF41003 2.2 17.0 1.0
SG B:CYS164 2.2 24.2 1.0
S3 B:SF41003 2.3 17.0 1.0
FE2 B:SF41003 2.7 17.7 1.0
FE3 B:SF41003 2.7 19.7 1.0
FE4 B:SF41003 2.8 21.4 1.0
CB B:CYS164 3.3 17.7 1.0
S1 B:SF41003 3.8 19.0 1.0
N B:CYS164 4.0 20.0 1.0
CB B:ALA182 4.1 13.3 1.0
CA B:CYS164 4.2 18.7 1.0
CA B:ALA182 4.5 16.2 1.0
SG B:CYS158 4.5 19.0 1.0
SG B:CYS161 4.6 20.4 1.0
SG B:CYS225 4.8 22.1 1.0
N B:CYS163 4.8 19.3 1.0
N B:ALA182 4.9 17.7 1.0
N B:ALA162 4.9 18.5 1.0

Iron binding site 4 out of 20 in 2wqy

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Iron binding site 4 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:17.7
occ:1.00
FE2 B:SF41003 0.0 17.7 1.0
S3 B:SF41003 2.2 17.0 1.0
S4 B:SF41003 2.3 17.0 1.0
S1 B:SF41003 2.3 19.0 1.0
SG B:CYS158 2.3 19.0 1.0
FE1 B:SF41003 2.7 18.4 1.0
FE4 B:SF41003 2.7 21.4 1.0
FE3 B:SF41003 2.8 19.7 1.0
CB B:CYS158 3.3 13.2 1.0
CA B:CYS158 3.7 16.6 1.0
S2 B:SF41003 3.8 17.6 1.0
N B:ILE159 3.9 15.8 1.0
N B:LEU160 4.0 19.6 1.0
C B:CYS158 4.2 17.9 1.0
O B:HOH2234 4.5 25.1 1.0
CA B:LEU160 4.6 20.1 1.0
SG B:CYS164 4.7 24.2 1.0
CD2 B:LEU229 4.8 18.1 1.0
N B:CYS161 4.8 16.8 1.0
CB B:ALA182 4.8 13.3 1.0
SG B:CYS225 4.9 22.1 1.0
SG B:CYS161 4.9 20.4 1.0
CE B:MET185 4.9 20.9 1.0
C B:ILE159 4.9 19.6 1.0

Iron binding site 5 out of 20 in 2wqy

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Iron binding site 5 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:19.7
occ:1.00
FE3 B:SF41003 0.0 19.7 1.0
S2 B:SF41003 2.2 17.6 1.0
S4 B:SF41003 2.2 17.0 1.0
SG B:CYS225 2.2 22.1 1.0
S1 B:SF41003 2.3 19.0 1.0
FE1 B:SF41003 2.7 18.4 1.0
FE2 B:SF41003 2.8 17.7 1.0
FE4 B:SF41003 2.8 21.4 1.0
CB B:CYS225 3.3 17.6 1.0
S3 B:SF41003 3.9 17.0 1.0
CA B:CYS225 3.9 20.2 1.0
CD B:PRO226 4.2 26.9 1.0
CD2 B:LEU229 4.3 18.1 1.0
CB B:LEU229 4.6 20.4 1.0
C B:CYS225 4.6 22.7 1.0
SG B:CYS164 4.7 24.2 1.0
CB B:LYS227 4.7 29.6 1.0
N B:PRO226 4.7 23.0 1.0
SG B:CYS161 4.7 20.4 1.0
N B:LYS227 4.8 24.2 1.0
CB B:CYS164 4.9 17.7 1.0
CG B:PRO226 5.0 26.6 1.0
CG B:LYS227 5.0 32.0 1.0

Iron binding site 6 out of 20 in 2wqy

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Iron binding site 6 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:21.4
occ:1.00
FE4 B:SF41003 0.0 21.4 1.0
S3 B:SF41003 2.2 17.0 1.0
S1 B:SF41003 2.2 19.0 1.0
SG B:CYS161 2.3 20.4 1.0
S2 B:SF41003 2.3 17.6 1.0
FE2 B:SF41003 2.7 17.7 1.0
FE1 B:SF41003 2.8 18.4 1.0
FE3 B:SF41003 2.8 19.7 1.0
CB B:CYS161 3.6 13.6 1.0
N B:CYS161 3.6 16.8 1.0
S4 B:SF41003 3.8 17.0 1.0
N B:ALA162 4.0 18.5 1.0
CA B:CYS161 4.1 16.6 1.0
CD B:PRO226 4.3 26.9 1.0
N B:CYS163 4.3 19.3 1.0
CG1 B:ILE159 4.4 14.9 1.0
C B:CYS161 4.5 17.1 1.0
N B:LEU160 4.6 19.6 1.0
SG B:CYS158 4.6 19.0 1.0
CG B:PRO226 4.6 26.6 1.0
CB B:CYS163 4.7 20.7 1.0
SG B:CYS225 4.7 22.1 1.0
C B:LEU160 4.7 18.9 1.0
SG B:CYS164 4.7 24.2 1.0
CA B:LEU160 4.8 20.1 1.0
N B:ILE159 4.9 15.8 1.0
N B:CYS164 4.9 20.0 1.0
CA B:ALA162 4.9 19.3 1.0

Iron binding site 7 out of 20 in 2wqy

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Iron binding site 7 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:19.9
occ:1.00
FE1 B:F3S1004 0.0 19.9 1.0
SG B:CYS215 2.2 20.2 1.0
S1 B:F3S1004 2.2 25.5 1.0
S2 B:F3S1004 2.2 18.5 1.0
S3 B:F3S1004 2.3 20.1 1.0
FE4 B:F3S1004 2.7 19.2 1.0
FE3 B:F3S1004 2.8 19.3 1.0
CB B:CYS215 3.4 18.4 1.0
CA B:CYS215 3.8 22.1 1.0
N B:THR217 3.8 26.3 1.0
OH B:TYR178 3.9 22.6 1.0
S4 B:F3S1004 4.0 17.8 1.0
N B:HIS216 4.1 19.0 1.0
CA B:THR217 4.1 22.8 1.0
CD1 B:ILE235 4.2 17.1 1.0
C B:CYS215 4.2 22.0 1.0
N B:ILE218 4.3 21.3 1.0
O B:HOH2277 4.6 22.5 1.0
C B:THR217 4.7 24.5 1.0
SG B:CYS168 4.7 20.4 1.0
SG B:CYS221 4.8 22.9 1.0
C B:HIS216 4.8 23.9 1.0
N B:MET219 4.9 22.6 1.0

Iron binding site 8 out of 20 in 2wqy

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Iron binding site 8 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:19.3
occ:1.00
FE3 B:F3S1004 0.0 19.3 1.0
S4 B:F3S1004 2.2 17.8 1.0
S1 B:F3S1004 2.3 25.5 1.0
S3 B:F3S1004 2.3 20.1 1.0
SG B:CYS221 2.3 22.9 1.0
FE4 B:F3S1004 2.6 19.2 1.0
FE1 B:F3S1004 2.8 19.9 1.0
CB B:CYS221 3.3 18.6 1.0
S2 B:F3S1004 3.9 18.5 1.0
N B:CYS221 3.9 21.3 1.0
N B:MET219 3.9 22.6 1.0
CA B:MET219 4.1 22.8 1.0
CA B:CYS221 4.2 23.1 1.0
N B:ASN220 4.3 25.0 1.0
C B:MET219 4.5 24.2 1.0
SG B:CYS168 4.6 20.4 1.0
CB B:PRO181 4.7 14.6 1.0
CD1 B:ILE235 4.8 17.1 1.0
CA B:GLY232 4.8 18.4 1.0
SG B:CYS215 4.8 20.2 1.0
CG B:PRO181 4.9 14.2 1.0
CB B:CYS168 5.0 17.3 1.0
N B:ILE218 5.0 21.3 1.0

Iron binding site 9 out of 20 in 2wqy

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Iron binding site 9 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:19.2
occ:1.00
FE4 B:F3S1004 0.0 19.2 1.0
S4 B:F3S1004 2.2 17.8 1.0
S3 B:F3S1004 2.2 20.1 1.0
SG B:CYS168 2.2 20.4 1.0
S2 B:F3S1004 2.2 18.5 1.0
FE3 B:F3S1004 2.6 19.3 1.0
FE1 B:F3S1004 2.7 19.9 1.0
CB B:CYS168 3.2 17.3 1.0
S1 B:F3S1004 3.8 25.5 1.0
CA B:CYS168 4.1 17.4 1.0
OH B:TYR178 4.1 22.6 1.0
CB B:ILE218 4.6 22.3 1.0
CE2 B:TYR178 4.7 20.2 1.0
SG B:CYS221 4.7 22.9 1.0
SG B:CYS215 4.8 20.2 1.0
C B:CYS168 4.8 20.6 1.0
CB B:SER170 4.9 23.3 1.0
CZ B:TYR178 4.9 16.4 1.0
CD B:PRO169 4.9 19.8 1.0
CD B:PRO181 4.9 15.8 1.0

Iron binding site 10 out of 20 in 2wqy

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Iron binding site 10 out of 20 in the Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe143

b:29.8
occ:1.00
FE C:HEM143 0.0 29.8 1.0
NA C:HEM143 1.9 28.2 1.0
NC C:HEM143 2.0 31.5 1.0
NE2 C:HIS98 2.0 28.6 1.0
NE2 D:HIS46 2.0 28.7 1.0
NB C:HEM143 2.0 27.8 1.0
ND C:HEM143 2.0 31.9 1.0
CD2 C:HIS98 2.9 26.7 1.0
C1A C:HEM143 3.0 28.7 1.0
CD2 D:HIS46 3.0 25.5 1.0
C4A C:HEM143 3.0 32.2 1.0
CE1 D:HIS46 3.0 31.5 1.0
CE1 C:HIS98 3.0 29.3 1.0
C1C C:HEM143 3.0 30.2 1.0
C4C C:HEM143 3.0 33.0 1.0
C4B C:HEM143 3.0 29.2 1.0
C4D C:HEM143 3.1 24.3 1.0
C1B C:HEM143 3.1 31.0 1.0
C1D C:HEM143 3.1 31.3 1.0
CHA C:HEM143 3.4 23.2 1.0
CHC C:HEM143 3.4 29.1 1.0
CHB C:HEM143 3.4 30.4 1.0
CHD C:HEM143 3.4 32.6 1.0
CG C:HIS98 4.1 29.5 1.0
ND1 C:HIS98 4.1 26.4 1.0
ND1 D:HIS46 4.1 33.5 1.0
CG D:HIS46 4.1 29.9 1.0
C2A C:HEM143 4.2 33.1 1.0
C3A C:HEM143 4.2 32.6 1.0
C2C C:HEM143 4.3 32.6 1.0
C3C C:HEM143 4.3 32.8 1.0
C3B C:HEM143 4.3 33.5 1.0
C3D C:HEM143 4.3 32.0 1.0
C2B C:HEM143 4.3 30.9 1.0
C2D C:HEM143 4.3 31.7 1.0
CE1 C:HIS42 5.0 30.3 1.0

Reference:

J.Ruprecht, S.Iwata, G.Cecchini. Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II To Be Published.
Page generated: Sun Dec 13 14:55:49 2020

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