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Iron in PDB 3aee: Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5, PDB code: 3aee 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) 48.96 / 3.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.751, 83.841, 293.735, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 28.2

Other elements in 3aee:

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5 (pdb code 3aee). 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 Bound with Atpenin A5, PDB code: 3aee:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3aee

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Iron binding site 1 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:82.9
occ:1.00
 FE1 B:FES302 0.0 82.9 1.0
SG B:CYS73 2.0 90.9 1.0
S2 B:FES302 2.2 81.2 1.0
S1 B:FES302 2.2 82.9 1.0
SG B:CYS85 2.5 96.4 1.0
FE2 B:FES302 3.0 82.7 1.0
CB B:CYS73 3.2 90.0 1.0
CB B:CYS85 3.6 98.0 1.0
N B:CYS73 3.8 88.1 1.0
CA B:CYS73 4.1 88.8 1.0
N B:CYS85 4.2 95.5 1.0
N B:GLY68 4.4 97.0 1.0
CA B:GLY68 4.5 95.2 1.0
CB B:LEU83 4.5 92.0 1.0
CA B:CYS85 4.5 98.7 1.0
SG B:CYS70 4.6 92.5 1.0
N B:SER72 4.7 87.5 1.0
SG B:CYS65 4.7 96.2 1.0
N B:ARG66 4.7 98.6 1.0
CD2 B:LEU45 4.7 98.1 1.0
CA B:ARG66 4.7 99.5 1.0
C B:CYS73 4.7 88.6 1.0
N B:ALA84 4.9 90.7 1.0
C B:SER72 4.9 87.3 1.0
N B:GLU67 5.0 99.9 1.0

Iron binding site 2 out of 10 in 3aee

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Iron binding site 2 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:82.7
occ:1.00
 FE2 B:FES302 0.0 82.7 1.0
SG B:CYS70 2.0 92.5 1.0
S2 B:FES302 2.2 81.2 1.0
S1 B:FES302 2.2 82.9 1.0
SG B:CYS65 2.3 96.2 1.0
FE1 B:FES302 3.0 82.9 1.0
CB B:CYS70 3.2 92.0 1.0
N B:CYS70 3.4 92.5 1.0
N B:CYS65 3.5 96.8 1.0
CB B:CYS65 3.5 98.3 1.0
N B:GLY71 3.6 88.9 1.0
CA B:CYS70 3.7 91.4 1.0
N B:ARG66 3.8 98.6 1.0
CA B:CYS65 3.9 98.9 1.0
C B:CYS70 4.1 89.4 1.0
N B:SER72 4.1 87.5 1.0
N B:ILE69 4.1 95.1 1.0
N B:GLY68 4.2 97.0 1.0
C B:CYS65 4.2 99.9 1.0
SG B:CYS85 4.3 96.4 1.0
N B:GLU67 4.5 99.9 1.0
CB B:SER72 4.5 88.2 1.0
C B:SER64 4.5 96.9 1.0
CA B:GLY68 4.5 95.2 1.0
C B:ILE69 4.6 93.6 1.0
N B:SER64 4.6 93.5 1.0
CA B:GLY71 4.7 87.5 1.0
CA B:ARG66 4.7 99.5 1.0
C B:GLY68 4.8 95.1 1.0
SG B:CYS73 4.8 90.9 1.0
CB B:SER64 4.9 94.3 1.0
CA B:SER64 4.9 95.1 1.0
CA B:SER72 4.9 87.3 1.0
C B:GLY71 4.9 86.8 1.0
OG B:SER72 4.9 88.0 1.0
N B:CYS73 4.9 88.1 1.0
CA B:ILE69 5.0 95.2 1.0

Iron binding site 3 out of 10 in 3aee

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Iron binding site 3 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:84.0
occ:1.00
 FE1 B:F3S304 0.0 84.0 1.0
S3 B:F3S304 2.2 85.1 1.0
S1 B:F3S304 2.2 84.1 1.0
S2 B:F3S304 2.2 86.7 1.0
SG B:CYS215 2.4 75.1 1.0
FE4 B:F3S304 2.4 86.1 1.0
FE3 B:F3S304 2.8 85.9 1.0
CB B:CYS215 3.4 76.0 1.0
CA B:CYS215 3.8 76.3 1.0
OH B:TYR178 3.8 76.1 1.0
N B:THR217 4.0 77.7 1.0
N B:HIS216 4.1 77.2 1.0
SG B:CYS168 4.2 73.7 1.0
S4 B:F3S304 4.3 83.2 1.0
CA B:THR217 4.3 77.9 1.0
CD1 B:ILE235 4.3 75.1 1.0
C B:CYS215 4.4 77.0 1.0
N B:ILE218 4.5 78.1 1.0
SG B:CYS221 4.9 78.7 1.0
C B:HIS216 5.0 78.3 1.0
C B:THR217 5.0 78.5 1.0
CZ B:TYR178 5.0 76.5 1.0

Iron binding site 4 out of 10 in 3aee

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Iron binding site 4 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:85.9
occ:1.00
 FE3 B:F3S304 0.0 85.9 1.0
S1 B:F3S304 2.2 84.1 1.0
S3 B:F3S304 2.2 85.1 1.0
S4 B:F3S304 2.2 83.2 1.0
FE4 B:F3S304 2.2 86.1 1.0
SG B:CYS221 2.4 78.7 1.0
FE1 B:F3S304 2.8 84.0 1.0
CB B:CYS221 3.4 77.8 1.0
N B:CYS221 3.9 79.6 1.0
S2 B:F3S304 4.0 86.7 1.0
N B:MET219 4.0 79.1 1.0
CA B:MET219 4.2 80.1 1.0
CA B:CYS221 4.3 79.2 1.0
N B:ASN220 4.3 80.8 1.0
SG B:CYS168 4.3 73.7 1.0
CB B:PRO181 4.6 73.1 1.0
CG B:PRO181 4.6 73.2 1.0
C B:MET219 4.6 81.1 1.0
CB B:CYS168 4.7 75.4 1.0
CA B:GLY232 4.8 75.4 1.0
CE B:MET219 4.8 79.5 1.0
C B:ASN220 5.0 81.0 1.0
N B:ILE218 5.0 78.1 1.0

Iron binding site 5 out of 10 in 3aee

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Iron binding site 5 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:86.1
occ:1.00
 FE4 B:F3S304 0.0 86.1 1.0
S2 B:F3S304 2.2 86.7 1.0
S4 B:F3S304 2.2 83.2 1.0
S3 B:F3S304 2.2 85.1 1.0
FE3 B:F3S304 2.2 85.9 1.0
SG B:CYS168 2.4 73.7 1.0
FE1 B:F3S304 2.4 84.0 1.0
S1 B:F3S304 3.2 84.1 1.0
CB B:CYS168 3.4 75.4 1.0
CA B:CYS168 4.1 76.6 1.0
CB B:ILE218 4.3 78.1 1.0
CD1 B:ILE218 4.5 76.0 1.0
SG B:CYS221 4.6 78.7 1.0
OH B:TYR178 4.6 76.1 1.0
N B:MET219 4.6 79.1 1.0
N B:ILE218 4.6 78.1 1.0
CD B:PRO169 4.7 78.0 1.0
CG1 B:ILE218 4.7 77.1 1.0
SG B:CYS215 4.8 75.1 1.0
CA B:ILE218 4.9 78.7 1.0
C B:CYS168 5.0 77.2 1.0
N B:ASN220 5.0 80.8 1.0

Iron binding site 6 out of 10 in 3aee

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Iron binding site 6 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:76.8
occ:1.00
 FE1 B:SF4303 0.0 76.8 1.0
S2 B:SF4303 2.3 77.3 1.0
S3 B:SF4303 2.3 77.8 1.0
S4 B:SF4303 2.3 78.0 1.0
SG B:CYS158 2.4 81.5 1.0
FE3 B:SF4303 2.7 77.9 1.0
FE4 B:SF4303 2.7 77.0 1.0
FE2 B:SF4303 2.8 79.7 1.0
CB B:CYS158 3.5 81.2 1.0
N B:ILE159 3.7 81.6 1.0
N B:LEU160 3.8 80.2 1.0
CA B:CYS158 3.8 81.7 1.0
S1 B:SF4303 3.9 79.3 1.0
N B:CYS161 4.2 81.5 1.0
C B:CYS158 4.2 81.4 1.0
CA B:LEU160 4.3 80.1 1.0
CD1 B:LEU229 4.5 78.0 1.0
CA B:ILE159 4.7 81.3 1.0
C B:ILE159 4.7 80.6 1.0
C B:LEU160 4.8 80.8 1.0
CB B:CYS161 4.9 83.3 1.0
SG B:CYS161 5.0 85.0 1.0

Iron binding site 7 out of 10 in 3aee

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Iron binding site 7 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:79.7
occ:1.00
 FE2 B:SF4303 0.0 79.7 1.0
S4 B:SF4303 2.3 78.0 1.0
S1 B:SF4303 2.3 79.3 1.0
S3 B:SF4303 2.3 77.8 1.0
SG B:CYS225 2.7 79.9 1.0
FE3 B:SF4303 2.7 77.9 1.0
FE1 B:SF4303 2.8 76.8 1.0
FE4 B:SF4303 2.8 77.0 1.0
CB B:CYS225 3.6 81.5 1.0
S2 B:SF4303 3.9 77.3 1.0
CD1 B:LEU229 4.0 78.0 1.0
CD B:PRO226 4.1 83.7 1.0
CB B:LEU229 4.1 78.7 1.0
CA B:CYS225 4.3 82.6 1.0
CG B:LEU229 4.3 79.1 1.0
N B:PRO226 4.8 85.4 1.0
CB B:LYS227 4.8 85.0 1.0
C B:CYS225 4.9 85.2 1.0
SG B:CYS158 4.9 81.5 1.0
N B:LYS227 4.9 86.4 1.0
CG B:PRO231 4.9 74.8 1.0
CB B:CYS164 5.0 82.1 1.0

Iron binding site 8 out of 10 in 3aee

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Iron binding site 8 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:77.9
occ:1.00
 FE3 B:SF4303 0.0 77.9 1.0
S2 B:SF4303 2.3 77.3 1.0
S4 B:SF4303 2.3 78.0 1.0
S1 B:SF4303 2.3 79.3 1.0
CB B:CYS164 2.6 82.1 1.0
FE1 B:SF4303 2.7 76.8 1.0
FE2 B:SF4303 2.7 79.7 1.0
FE4 B:SF4303 2.8 77.0 1.0
SG B:CYS164 2.8 83.0 1.0
CA B:CYS164 3.8 83.0 1.0
S3 B:SF4303 3.9 77.8 1.0
CB B:ALA182 4.1 73.1 1.0
N B:CYS164 4.1 83.9 1.0
CA B:ALA182 4.3 73.0 1.0
CG B:PRO231 4.4 74.8 1.0
SG B:CYS158 4.5 81.5 1.0
N B:ALA182 4.8 73.0 1.0

Iron binding site 9 out of 10 in 3aee

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Iron binding site 9 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:77.0
occ:1.00
 FE4 B:SF4303 0.0 77.0 1.0
S1 B:SF4303 2.3 79.3 1.0
S3 B:SF4303 2.3 77.8 1.0
S2 B:SF4303 2.3 77.3 1.0
CB B:CYS161 2.7 83.3 1.0
FE1 B:SF4303 2.7 76.8 1.0
FE2 B:SF4303 2.8 79.7 1.0
FE3 B:SF4303 2.8 77.9 1.0
SG B:CYS161 2.9 85.0 1.0
N B:CYS161 3.5 81.5 1.0
CA B:CYS161 3.7 82.5 1.0
CD B:PRO226 3.9 83.7 1.0
S4 B:SF4303 4.0 78.0 1.0
N B:ALA162 4.2 82.6 1.0
CB B:CYS164 4.3 82.1 1.0
N B:CYS164 4.3 83.9 1.0
CB B:CYS163 4.4 86.0 1.0
CG B:PRO226 4.5 85.4 1.0
N B:CYS163 4.5 84.7 1.0
C B:CYS161 4.5 82.8 1.0
C B:LEU160 4.7 80.8 1.0
SG B:CYS225 4.8 79.9 1.0
CA B:CYS164 4.9 83.0 1.0
N B:LEU160 5.0 80.2 1.0
CA B:CYS163 5.0 85.7 1.0
SG B:CYS158 5.0 81.5 1.0
SG B:CYS163 5.0 87.0 1.0

Iron binding site 10 out of 10 in 3aee

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Iron binding site 10 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with Atpenin A5


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 Bound with Atpenin A5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1305

b:92.7
occ:1.00
 FE C:HEM1305 0.0 92.7 1.0
NB C:HEM1305 2.0 92.7 1.0
NC C:HEM1305 2.0 93.1 1.0
ND C:HEM1305 2.1 92.3 1.0
NA C:HEM1305 2.1 93.0 1.0
NE2 C:HIS101 2.1 88.5 1.0
NE2 D:HIS79 2.2 87.1 1.0
CD2 C:HIS101 3.0 89.1 1.0
C1C C:HEM1305 3.0 93.3 1.0
C4B C:HEM1305 3.0 93.0 1.0
C4C C:HEM1305 3.1 93.5 1.0
CE1 D:HIS79 3.1 87.5 1.0
C1B C:HEM1305 3.1 92.9 1.0
C1D C:HEM1305 3.1 92.2 1.0
C4D C:HEM1305 3.1 92.1 1.0
C4A C:HEM1305 3.1 93.3 1.0
C1A C:HEM1305 3.1 93.1 1.0
CE1 C:HIS101 3.2 88.2 1.0
CD2 D:HIS79 3.2 86.9 1.0
CHC C:HEM1305 3.4 93.1 1.0
CHD C:HEM1305 3.4 92.9 1.0
CHA C:HEM1305 3.4 92.8 1.0
CHB C:HEM1305 3.4 93.4 1.0
ND1 D:HIS79 4.2 87.5 1.0
CG C:HIS101 4.2 89.4 1.0
ND1 C:HIS101 4.3 88.8 1.0
C2C C:HEM1305 4.3 93.8 1.0
C3C C:HEM1305 4.3 94.1 1.0
C3B C:HEM1305 4.3 92.9 1.0
C2B C:HEM1305 4.3 92.8 1.0
C3A C:HEM1305 4.3 93.2 1.0
C2A C:HEM1305 4.3 93.3 1.0
CG D:HIS79 4.3 86.7 1.0
C3D C:HEM1305 4.3 91.6 1.0
C2D C:HEM1305 4.3 91.9 1.0
NE2 C:HIS45 4.7 90.2 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 Bound with Atpenin A5 To Be Published.
Page generated: Sun Aug 4 06:55:49 2024

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