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Iron in PDB 3aef: Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket, PDB code: 3aef was solved by S.Harada, T.Sasaki, M.Shindo, Y.Kido, D.K.Inaoka, J.Omori, A.Osanai, K.Sakamoto, J.Mao, S.Matsuoka, M.Inoue, T.Honma, A.Tanaka, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.88 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.222, 84.209, 293.319, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket (pdb code 3aef). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket, PDB code: 3aef:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3aef

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Iron binding site 1 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


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 Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:44.3
occ:1.00
 FE1 B:FES302 0.0 44.3 1.0
SG B:CYS65 2.1 43.2 1.0
S1 B:FES302 2.2 43.5 1.0
S2 B:FES302 2.2 39.6 1.0
SG B:CYS70 2.4 38.8 1.0
FE2 B:FES302 2.9 44.5 1.0
CB B:CYS65 3.2 43.4 1.0
CB B:CYS70 3.4 39.2 1.0
N B:CYS70 3.5 39.1 1.0
N B:GLY71 3.5 38.6 1.0
N B:CYS65 3.6 43.5 1.0
CA B:CYS70 3.8 38.7 1.0
CA B:CYS65 3.8 44.2 1.0
N B:ARG66 3.9 45.8 1.0
N B:GLY68 4.0 44.2 1.0
N B:ILE69 4.0 40.6 1.0
CA B:GLY68 4.1 42.6 1.0
C B:CYS70 4.1 38.2 1.0
N B:SER72 4.2 38.9 1.0
SG B:CYS85 4.2 44.2 1.0
C B:CYS65 4.3 45.2 1.0
CA B:GLY71 4.5 38.3 1.0
C B:GLY68 4.5 41.7 1.0
C B:ILE69 4.6 38.7 1.0
N B:GLU67 4.8 46.8 1.0
C B:SER64 4.8 43.7 1.0
C B:GLY71 4.8 38.3 1.0
N B:SER64 4.9 42.2 1.0
CB B:SER72 4.9 40.1 1.0
CA B:ILE69 4.9 39.4 1.0
SG B:CYS73 5.0 44.5 1.0
N B:CYS73 5.0 40.9 1.0

Iron binding site 2 out of 10 in 3aef

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Iron binding site 2 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


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 Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:44.5
occ:1.00
 FE2 B:FES302 0.0 44.5 1.0
S1 B:FES302 2.2 43.5 1.0
S2 B:FES302 2.2 39.6 1.0
SG B:CYS73 2.3 44.5 1.0
SG B:CYS85 2.4 44.2 1.0
FE1 B:FES302 2.9 44.3 1.0
CB B:CYS85 3.4 46.6 1.0
CB B:CYS73 3.5 43.0 1.0
N B:CYS73 4.0 40.9 1.0
CB B:LEU83 4.2 42.9 1.0
CA B:CYS73 4.2 42.2 1.0
N B:CYS85 4.2 47.1 1.0
CA B:GLY68 4.4 42.6 1.0
SG B:CYS65 4.4 43.2 1.0
CA B:CYS85 4.4 47.9 1.0
N B:GLY68 4.4 44.2 1.0
CD2 B:LEU83 4.6 39.0 1.0
N B:ARG66 4.8 45.8 1.0
SG B:CYS70 4.8 38.8 1.0
CG B:LEU83 4.8 40.8 1.0
N B:SER72 4.8 38.9 1.0
C B:CYS73 4.9 42.2 1.0
N B:ALA84 4.9 45.2 1.0
CA B:LEU83 4.9 43.6 1.0
CD1 B:LEU83 5.0 39.5 1.0
CD2 B:LEU45 5.0 44.1 1.0

Iron binding site 3 out of 10 in 3aef

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Iron binding site 3 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


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 Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:34.6
occ:1.00
 FE1 B:SF4303 0.0 34.6 1.0
S3 B:SF4303 2.3 33.4 1.0
S4 B:SF4303 2.3 35.9 1.0
S2 B:SF4303 2.3 33.9 1.0
SG B:CYS158 2.3 33.1 1.0
FE4 B:SF4303 2.6 32.1 1.0
FE2 B:SF4303 2.7 34.6 1.0
FE3 B:SF4303 2.7 36.1 1.0
CB B:CYS158 3.3 34.0 1.0
CA B:CYS158 3.5 34.5 1.0
N B:ILE159 3.6 34.9 1.0
S1 B:SF4303 3.9 34.6 1.0
C B:CYS158 4.1 34.7 1.0
CD1 B:LEU229 4.2 39.1 1.0
N B:LEU160 4.2 34.4 1.0
CA B:ILE159 4.7 35.1 1.0
N B:CYS158 4.8 35.0 1.0
SG B:CYS164 4.8 37.1 1.0
CA B:LEU160 4.9 34.5 1.0
C B:ILE159 5.0 34.7 1.0

Iron binding site 4 out of 10 in 3aef

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Iron binding site 4 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


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 Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:34.6
occ:1.00
 FE2 B:SF4303 0.0 34.6 1.0
S1 B:SF4303 2.3 34.6 1.0
S4 B:SF4303 2.3 35.9 1.0
S3 B:SF4303 2.3 33.4 1.0
SG B:CYS161 2.6 37.8 1.0
FE3 B:SF4303 2.7 36.1 1.0
FE1 B:SF4303 2.7 34.6 1.0
FE4 B:SF4303 2.7 32.1 1.0
CB B:CYS161 3.8 36.8 1.0
S2 B:SF4303 3.9 33.9 1.0
N B:CYS161 3.9 35.6 1.0
N B:ALA162 4.0 35.8 1.0
CD B:PRO226 4.2 42.8 1.0
CG B:PRO226 4.3 42.6 1.0
CA B:CYS161 4.3 36.2 1.0
N B:CYS163 4.4 37.1 1.0
C B:CYS161 4.5 36.2 1.0
SG B:CYS164 4.7 37.1 1.0
SG B:CYS158 4.7 33.1 1.0
N B:ILE159 4.7 34.9 1.0
CB B:CYS163 4.7 38.5 1.0
SG B:CYS225 4.7 43.3 1.0
N B:LEU160 4.8 34.4 1.0
CB B:ILE159 4.9 35.7 1.0
N B:CYS164 4.9 37.1 1.0
CA B:ALA162 4.9 36.0 1.0

Iron binding site 5 out of 10 in 3aef

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Iron binding site 5 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


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 Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:36.1
occ:1.00
 FE3 B:SF4303 0.0 36.1 1.0
S4 B:SF4303 2.3 35.9 1.0
S1 B:SF4303 2.3 34.6 1.0
S2 B:SF4303 2.3 33.9 1.0
SG B:CYS225 2.4 43.3 1.0
FE2 B:SF4303 2.7 34.6 1.0
FE1 B:SF4303 2.7 34.6 1.0
FE4 B:SF4303 2.8 32.1 1.0
CB B:CYS225 3.3 42.9 1.0
CD1 B:LEU229 3.9 39.1 1.0
S3 B:SF4303 4.0 33.4 1.0
CA B:CYS225 4.1 43.2 1.0
CD B:PRO226 4.2 42.8 1.0
CB B:LEU229 4.4 39.9 1.0
CG B:LEU229 4.4 39.8 1.0
C B:CYS225 4.6 43.9 1.0
N B:PRO226 4.6 43.6 1.0
CB B:LYS227 4.6 42.4 1.0
SG B:CYS164 4.7 37.1 1.0
CG B:PRO226 4.7 42.6 1.0
N B:LYS227 4.8 43.2 1.0
CG B:LYS227 4.9 42.6 1.0

Iron binding site 6 out of 10 in 3aef

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Iron binding site 6 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:32.1
occ:1.00
 FE4 B:SF4303 0.0 32.1 1.0
S3 B:SF4303 2.3 33.4 1.0
S2 B:SF4303 2.3 33.9 1.0
S1 B:SF4303 2.3 34.6 1.0
SG B:CYS164 2.3 37.1 1.0
FE1 B:SF4303 2.6 34.6 1.0
FE2 B:SF4303 2.7 34.6 1.0
FE3 B:SF4303 2.8 36.1 1.0
CB B:CYS164 3.4 36.5 1.0
S4 B:SF4303 3.9 35.9 1.0
CB B:ALA182 4.1 34.5 1.0
N B:CYS164 4.1 37.1 1.0
CA B:CYS164 4.4 36.8 1.0
SG B:CYS158 4.4 33.1 1.0
CA B:ALA182 4.4 34.8 1.0
CG B:PRO231 4.6 37.1 1.0
N B:ALA162 4.9 35.8 1.0
SG B:CYS161 4.9 37.8 1.0
SG B:CYS225 4.9 43.3 1.0
N B:ALA182 4.9 34.9 1.0
N B:CYS163 5.0 37.1 1.0

Iron binding site 7 out of 10 in 3aef

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Iron binding site 7 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:36.0
occ:1.00
 FE1 B:F3S304 0.0 36.0 1.0
FE4 B:F3S304 2.2 41.0 1.0
S3 B:F3S304 2.2 35.8 1.0
S2 B:F3S304 2.2 37.2 1.0
S1 B:F3S304 2.3 35.2 1.0
SG B:CYS215 2.4 35.3 1.0
FE3 B:F3S304 2.9 37.1 1.0
CB B:CYS215 3.3 34.4 1.0
CA B:CYS215 3.7 34.6 1.0
SG B:CYS168 3.9 31.8 1.0
OH B:TYR178 4.0 32.0 1.0
S4 B:F3S304 4.0 38.0 1.0
N B:THR217 4.1 37.1 1.0
CD1 B:ILE235 4.2 33.4 1.0
N B:ILE218 4.2 38.0 1.0
N B:HIS216 4.3 35.5 1.0
C B:CYS215 4.3 35.1 1.0
CA B:THR217 4.4 37.8 1.0
C B:THR217 4.8 38.2 1.0
SG B:CYS221 4.8 36.9 1.0
N B:MET219 4.9 38.2 1.0
N B:CYS215 4.9 34.3 1.0

Iron binding site 8 out of 10 in 3aef

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Iron binding site 8 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:37.1
occ:1.00
 FE3 B:F3S304 0.0 37.1 1.0
SG B:CYS221 2.2 36.9 1.0
S1 B:F3S304 2.2 35.2 1.0
S4 B:F3S304 2.2 38.0 1.0
S3 B:F3S304 2.2 35.8 1.0
FE4 B:F3S304 2.3 41.0 1.0
FE1 B:F3S304 2.9 36.0 1.0
CB B:CYS221 3.2 36.5 1.0
N B:MET219 3.8 38.2 1.0
N B:CYS221 3.9 37.3 1.0
CA B:MET219 4.0 38.3 1.0
SG B:CYS168 4.1 31.8 1.0
S2 B:F3S304 4.1 37.2 1.0
CA B:CYS221 4.2 37.0 1.0
N B:ASN220 4.4 38.4 1.0
C B:MET219 4.5 38.8 1.0
CB B:PRO181 4.7 35.7 1.0
CD1 B:ILE235 4.8 33.4 1.0
CA B:GLY232 4.8 37.1 1.0
CG B:PRO181 4.8 35.5 1.0
CB B:CYS168 4.8 34.9 1.0
N B:ILE218 4.8 38.0 1.0
SG B:CYS215 4.9 35.3 1.0
C B:ILE218 4.9 38.4 1.0
C B:ASN220 5.0 38.3 1.0

Iron binding site 9 out of 10 in 3aef

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Iron binding site 9 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:41.0
occ:1.00
 FE4 B:F3S304 0.0 41.0 1.0
S2 B:F3S304 2.1 37.2 1.0
FE1 B:F3S304 2.2 36.0 1.0
S3 B:F3S304 2.2 35.8 1.0
S4 B:F3S304 2.2 38.0 1.0
SG B:CYS168 2.2 31.8 1.0
FE3 B:F3S304 2.3 37.1 1.0
S1 B:F3S304 3.1 35.2 1.0
CB B:CYS168 3.6 34.9 1.0
CB B:ILE218 4.2 37.5 1.0
N B:MET219 4.3 38.2 1.0
N B:ILE218 4.3 38.0 1.0
CA B:CYS168 4.4 35.4 1.0
SG B:CYS221 4.4 36.9 1.0
SG B:CYS215 4.5 35.3 1.0
CG1 B:ILE218 4.6 36.2 1.0
OH B:TYR178 4.7 32.0 1.0
CA B:ILE218 4.7 37.9 1.0
CD1 B:ILE218 4.9 34.7 1.0
CB B:CYS221 5.0 36.5 1.0

Iron binding site 10 out of 10 in 3aef

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Iron binding site 10 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1305

b:42.2
occ:1.00
 FE C:HEM1305 0.0 42.2 1.0
NC C:HEM1305 1.9 42.4 1.0
NB C:HEM1305 2.0 42.9 1.0
NA C:HEM1305 2.0 43.2 1.0
ND C:HEM1305 2.1 42.2 1.0
NE2 D:HIS79 2.1 41.0 1.0
NE2 C:HIS101 2.2 40.9 1.0
C4C C:HEM1305 2.9 43.3 1.0
CD2 C:HIS101 3.0 39.7 1.0
C1C C:HEM1305 3.0 43.1 1.0
C1B C:HEM1305 3.0 43.2 1.0
C4A C:HEM1305 3.0 44.1 1.0
C1D C:HEM1305 3.0 42.0 1.0
CE1 D:HIS79 3.0 40.6 1.0
C4B C:HEM1305 3.1 43.2 1.0
C1A C:HEM1305 3.1 44.3 1.0
CD2 D:HIS79 3.1 39.5 1.0
C4D C:HEM1305 3.1 42.0 1.0
CE1 C:HIS101 3.3 40.7 1.0
CHD C:HEM1305 3.3 43.0 1.0
CHB C:HEM1305 3.4 43.9 1.0
CHC C:HEM1305 3.4 42.6 1.0
CHA C:HEM1305 3.5 43.1 1.0
C3C C:HEM1305 4.1 44.4 1.0
ND1 D:HIS79 4.2 40.1 1.0
CG C:HIS101 4.2 39.1 1.0
C2C C:HEM1305 4.2 43.6 1.0
CG D:HIS79 4.2 38.6 1.0
C2B C:HEM1305 4.3 42.9 1.0
C3A C:HEM1305 4.3 44.5 1.0
C3B C:HEM1305 4.3 43.6 1.0
ND1 C:HIS101 4.3 40.5 1.0
C2A C:HEM1305 4.3 46.0 1.0
C2D C:HEM1305 4.3 41.8 1.0
C3D C:HEM1305 4.4 41.6 1.0
NE2 C:HIS45 4.7 42.3 1.0

Reference:

S.Harada, T.Sasaki, M.Shindo, Y.Kido, D.K.Inaoka, J.Omori, A.Osanai, K.Sakamoto, J.Mao, S.Matsuoka, M.Inoue, T.Honma, A.Tanaka, K.Kita. Crystal Structure of Porcine Heart Mitochondrial Complex II with An Empty Quinone-Binding Pocket To Be Published.
Page generated: Sun Aug 4 06:55:49 2024

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