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Iron in PDB 1zp0: Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone

Enzymatic activity of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone

All present enzymatic activity of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone, PDB code: 1zp0 was solved by F.Sun, X.Huo, Y.Zhai, A.Wang, J.Xu, D.Su, M.Bartlam, Z.Rao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.330, 83.531, 294.180, 90.00, 90.00, 90.00
R / Rfree (%) 26.8 / 29.3

Other elements in 1zp0:

The structure of Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone (pdb code 1zp0). 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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone, PDB code: 1zp0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 1zp0

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Iron binding site 1 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:54.8
occ:1.00
FE1 B:FES302 0.0 54.8 1.0
S2 B:FES302 2.0 70.1 1.0
S1 B:FES302 2.3 71.2 1.0
SG B:CYS73 2.6 70.8 1.0
SG B:CYS85 2.7 58.4 1.0
FE2 B:FES302 2.7 56.7 1.0
CB B:CYS73 3.2 66.1 1.0
CB B:CYS85 3.5 49.1 1.0
N B:CYS73 3.8 64.6 1.0
CA B:CYS73 4.2 68.3 1.0
N B:CYS85 4.3 60.8 1.0
N B:GLY68 4.3 54.0 1.0
N B:ARG66 4.4 68.2 1.0
CA B:GLY68 4.4 53.5 1.0
CB B:LEU83 4.4 64.3 1.0
CA B:ARG66 4.5 69.6 1.0
SG B:CYS65 4.5 60.9 1.0
CA B:CYS85 4.5 59.6 1.0
N B:SER72 4.6 52.3 1.0
N B:GLU67 4.9 62.6 1.0
C B:SER72 4.9 62.0 1.0
SG B:CYS70 4.9 71.1 1.0
CD2 B:LEU83 4.9 36.2 1.0
CD2 B:LEU45 5.0 57.2 1.0

Iron binding site 2 out of 10 in 1zp0

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Iron binding site 2 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:56.7
occ:1.00
FE2 B:FES302 0.0 56.7 1.0
S1 B:FES302 2.0 71.2 1.0
S2 B:FES302 2.0 70.1 1.0
SG B:CYS70 2.5 71.1 1.0
SG B:CYS65 2.6 60.9 1.0
FE1 B:FES302 2.7 54.8 1.0
N B:CYS65 3.5 62.7 1.0
CB B:CYS70 3.6 65.4 1.0
CB B:CYS65 3.7 67.0 1.0
N B:ARG66 3.7 68.2 1.0
N B:GLY71 3.8 58.5 1.0
N B:CYS70 3.9 52.1 1.0
N B:SER72 3.9 52.3 1.0
CA B:CYS65 3.9 64.8 1.0
CA B:CYS70 4.1 59.4 1.0
C B:CYS65 4.2 68.6 1.0
CB B:SER72 4.3 67.2 1.0
C B:CYS70 4.3 60.0 1.0
N B:SER64 4.4 54.3 1.0
N B:GLY68 4.4 54.0 1.0
C B:SER64 4.5 62.5 1.0
OG B:SER72 4.5 69.5 1.0
N B:ILE69 4.6 59.2 1.0
SG B:CYS85 4.6 58.4 1.0
CA B:ARG66 4.6 69.6 1.0
N B:GLU67 4.6 62.6 1.0
CA B:SER72 4.7 59.5 1.0
N B:CYS73 4.7 64.6 1.0
CA B:GLY71 4.7 59.6 1.0
SG B:CYS73 4.7 70.8 1.0
CA B:SER64 4.8 55.8 1.0
CB B:SER64 4.8 44.2 1.0
C B:GLY71 4.8 57.7 1.0
CA B:GLY68 4.8 53.5 1.0

Iron binding site 3 out of 10 in 1zp0

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Iron binding site 3 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:37.9
occ:1.00
FE1 B:SF4303 0.0 37.9 1.0
S2 B:SF4303 2.1 48.2 1.0
S4 B:SF4303 2.4 45.7 1.0
SG B:CYS164 2.6 77.2 1.0
S3 B:SF4303 2.6 41.7 1.0
FE3 B:SF4303 2.8 49.1 1.0
FE4 B:SF4303 2.9 47.8 1.0
CB B:CYS164 2.9 43.4 1.0
FE2 B:SF4303 3.1 33.3 1.0
N B:CYS164 3.7 48.7 1.0
CA B:CYS164 3.9 43.2 1.0
S1 B:SF4303 3.9 44.6 1.0
CB B:ALA182 4.2 56.4 1.0
CA B:ALA182 4.4 55.5 1.0
CG B:PRO231 4.5 44.5 1.0
N B:ALA182 4.7 64.0 1.0
N B:SER165 4.7 32.6 1.0
N B:CYS163 4.8 70.9 1.0
C B:CYS163 4.9 57.4 1.0
C B:CYS164 4.9 39.1 1.0

Iron binding site 4 out of 10 in 1zp0

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Iron binding site 4 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:33.3
occ:1.00
FE2 B:SF4303 0.0 33.3 1.0
S3 B:SF4303 2.3 41.7 1.0
S4 B:SF4303 2.3 45.7 1.0
S1 B:SF4303 2.3 44.6 1.0
SG B:CYS158 2.8 85.1 1.0
FE4 B:SF4303 2.8 47.8 1.0
FE3 B:SF4303 2.9 49.1 1.0
FE1 B:SF4303 3.1 37.9 1.0
CB B:CYS158 3.5 74.0 1.0
CA B:CYS158 3.7 70.0 1.0
S2 B:SF4303 3.8 48.2 1.0
N B:ILE159 3.9 74.4 1.0
N B:LEU160 3.9 60.2 1.0
C B:CYS158 4.2 72.7 1.0
CA B:LEU160 4.5 54.5 1.0
CD1 B:LEU229 4.6 81.1 1.0
N B:CYS161 4.8 55.6 1.0
C B:ILE159 4.9 69.2 1.0
CA B:ILE159 4.9 74.7 1.0
CB B:ALA182 5.0 56.4 1.0

Iron binding site 5 out of 10 in 1zp0

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Iron binding site 5 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:49.1
occ:1.00
FE3 B:SF4303 0.0 49.1 1.0
S4 B:SF4303 2.0 45.7 1.0
S2 B:SF4303 2.3 48.2 1.0
S1 B:SF4303 2.3 44.6 1.0
FE4 B:SF4303 2.7 47.8 1.0
SG B:CYS225 2.8 66.1 1.0
FE1 B:SF4303 2.8 37.9 1.0
FE2 B:SF4303 2.9 33.3 1.0
CB B:CYS225 3.4 73.3 1.0
S3 B:SF4303 3.8 41.7 1.0
CA B:CYS225 4.0 75.6 1.0
CD B:PRO226 4.3 75.9 1.0
CD1 B:LEU229 4.3 81.1 1.0
CB B:LEU229 4.4 68.2 1.0
CG B:LEU229 4.5 71.2 1.0
N B:PRO226 4.7 76.1 1.0
C B:CYS225 4.7 79.7 1.0
CB B:CYS164 4.9 43.4 1.0
CG B:PRO231 4.9 44.5 1.0
CB B:LYS227 4.9 73.5 1.0
N B:LYS227 5.0 79.1 1.0

Iron binding site 6 out of 10 in 1zp0

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Iron binding site 6 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:47.8
occ:1.00
FE4 B:SF4303 0.0 47.8 1.0
S1 B:SF4303 1.9 44.6 1.0
S2 B:SF4303 2.0 48.2 1.0
S3 B:SF4303 2.0 41.7 1.0
FE3 B:SF4303 2.7 49.1 1.0
SG B:CYS161 2.8 74.7 1.0
FE2 B:SF4303 2.8 33.3 1.0
FE1 B:SF4303 2.9 37.9 1.0
N B:CYS161 3.7 55.6 1.0
S4 B:SF4303 3.7 45.7 1.0
CB B:CYS161 3.9 57.2 1.0
N B:ALA162 4.1 64.5 1.0
CD B:PRO226 4.2 75.9 1.0
CA B:CYS161 4.3 55.6 1.0
SG B:CYS163 4.4 82.1 1.0
N B:CYS163 4.4 70.9 1.0
N B:LEU160 4.5 60.2 1.0
CB B:CYS163 4.5 58.0 1.0
C B:CYS161 4.7 59.0 1.0
C B:LEU160 4.7 56.3 1.0
N B:CYS164 4.7 48.7 1.0
CA B:LEU160 4.8 54.5 1.0
SG B:CYS225 4.9 66.1 1.0
N B:ILE159 4.9 74.4 1.0
CA B:CYS163 5.0 61.4 1.0
CG B:PRO226 5.0 81.9 1.0

Iron binding site 7 out of 10 in 1zp0

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Iron binding site 7 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:48.7
occ:1.00
FE1 B:F3S304 0.0 48.7 1.0
S3 B:F3S304 2.1 53.1 1.0
S2 B:F3S304 2.1 59.6 1.0
S1 B:F3S304 2.2 54.4 1.0
FE3 B:F3S304 2.3 51.1 1.0
SG B:CYS215 2.7 51.7 1.0
FE4 B:F3S304 2.9 53.0 1.0
CB B:CYS215 3.3 42.1 1.0
S4 B:F3S304 3.8 39.7 1.0
CA B:CYS215 3.8 42.3 1.0
N B:THR217 3.8 80.8 1.0
OH B:TYR178 4.0 58.2 1.0
CA B:THR217 4.1 79.2 1.0
N B:ILE218 4.1 65.8 1.0
N B:HIS216 4.2 55.6 1.0
C B:CYS215 4.3 46.5 1.0
SG B:CYS168 4.6 25.6 1.0
C B:THR217 4.6 71.5 1.0
N B:MET219 4.8 65.5 1.0
C B:HIS216 4.9 68.1 1.0

Iron binding site 8 out of 10 in 1zp0

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Iron binding site 8 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:51.1
occ:1.00
FE3 B:F3S304 0.0 51.1 1.0
S1 B:F3S304 1.9 54.4 1.0
S3 B:F3S304 2.0 53.1 1.0
S4 B:F3S304 2.1 39.7 1.0
FE1 B:F3S304 2.3 48.7 1.0
FE4 B:F3S304 2.5 53.0 1.0
SG B:CYS168 2.6 25.6 1.0
S2 B:F3S304 3.1 59.6 1.0
CB B:CYS168 3.6 38.3 1.0
OH B:TYR178 4.1 58.2 1.0
CG B:PRO181 4.3 57.8 1.0
CA B:CYS168 4.5 50.6 1.0
CB B:ILE218 4.7 58.0 1.0
N B:ILE218 4.7 65.8 1.0
SG B:CYS215 4.8 51.7 1.0
N B:MET219 4.8 65.5 1.0
CB B:CYS215 4.9 42.1 1.0
CD1 B:ILE218 4.9 52.2 1.0
CA B:CYS215 4.9 42.3 1.0

Iron binding site 9 out of 10 in 1zp0

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Iron binding site 9 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:53.0
occ:1.00
FE4 B:F3S304 0.0 53.0 1.0
S2 B:F3S304 1.9 59.6 1.0
S4 B:F3S304 2.3 39.7 1.0
S3 B:F3S304 2.4 53.1 1.0
FE3 B:F3S304 2.5 51.1 1.0
SG B:CYS221 2.6 66.2 1.0
FE1 B:F3S304 2.9 48.7 1.0
CB B:CYS221 3.3 62.0 1.0
N B:CYS221 3.9 68.6 1.0
S1 B:F3S304 4.0 54.4 1.0
N B:MET219 4.0 65.5 1.0
CG B:PRO181 4.1 57.8 1.0
CA B:MET219 4.1 68.3 1.0
CA B:CYS221 4.2 59.7 1.0
N B:ASN220 4.3 66.5 1.0
C B:MET219 4.4 69.5 1.0
CA B:GLY232 4.6 44.7 1.0
CB B:PRO181 4.6 48.5 1.0
N B:GLY232 4.7 46.6 1.0
CE B:MET219 4.8 77.4 1.0
SG B:CYS168 4.8 25.6 1.0
N B:THR222 4.9 47.6 1.0
C B:ASN220 5.0 72.9 1.0

Iron binding site 10 out of 10 in 1zp0

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Iron binding site 10 out of 10 in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone


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 Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe305

b:71.4
occ:1.00
FE C:HEM305 0.0 71.4 1.0
ND C:HEM305 2.0 63.9 1.0
NB C:HEM305 2.1 74.5 1.0
NA C:HEM305 2.1 74.1 1.0
NC C:HEM305 2.1 66.9 1.0
NE2 D:HIS79 2.2 53.5 1.0
NE2 C:HIS101 2.4 46.2 1.0
CD2 C:HIS101 3.0 55.7 1.0
C1D C:HEM305 3.0 61.5 1.0
C4D C:HEM305 3.1 67.8 1.0
C4C C:HEM305 3.1 70.8 1.0
C4B C:HEM305 3.1 76.8 1.0
C1A C:HEM305 3.1 76.0 1.0
C1C C:HEM305 3.1 72.8 1.0
C4A C:HEM305 3.1 74.9 1.0
C1B C:HEM305 3.1 77.5 1.0
CE1 D:HIS79 3.2 60.8 1.0
CD2 D:HIS79 3.2 54.6 1.0
CHD C:HEM305 3.4 63.7 1.0
CHA C:HEM305 3.4 74.4 1.0
CHC C:HEM305 3.4 77.2 1.0
CHB C:HEM305 3.5 76.9 1.0
CE1 C:HIS101 3.5 58.6 1.0
C3D C:HEM305 4.3 69.2 1.0
ND1 D:HIS79 4.3 63.1 1.0
C2D C:HEM305 4.3 66.3 1.0
CG C:HIS101 4.3 59.9 1.0
C3B C:HEM305 4.3 81.0 1.0
C3C C:HEM305 4.3 74.5 1.0
C2C C:HEM305 4.3 74.2 1.0
C2A C:HEM305 4.3 78.6 1.0
C3A C:HEM305 4.3 77.0 1.0
C2B C:HEM305 4.3 81.9 1.0
CG D:HIS79 4.3 58.4 1.0
ND1 C:HIS101 4.5 62.5 1.0
NE2 C:HIS45 5.0 56.5 1.0

Reference:

F.Sun, X.Huo, Y.Zhai, A.Wang, J.Xu, D.Su, M.Bartlam, Z.Rao. Crystal Structure of Mitochondrial Respiratory Membrane Protein Complex II Cell(Cambridge,Mass.) V. 121 1043 2005.
ISSN: ISSN 0092-8674
PubMed: 15989954
DOI: 10.1016/J.CELL.2005.05.025
Page generated: Sun Dec 13 14:39:02 2020

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