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Iron in PDB 3sfd: Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol

Enzymatic activity of Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol

All present enzymatic activity of Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol, PDB code: 3sfd was solved by Q.J.Zhou, Y.J.Zhai, M.Liu, F.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.310, 83.360, 293.100, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 28.6

Other elements in 3sfd:

The structure of Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 10 in 3sfd

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Iron binding site 1 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:42.4
occ:1.00
 FE1 B:FES302 0.0 42.4 1.0
SG B:CYS73 2.0 51.5 1.0
S1 B:FES302 2.2 39.4 1.0
S2 B:FES302 2.2 38.9 1.0
SG B:CYS85 2.6 56.1 1.0
FE2 B:FES302 3.0 41.9 1.0
CB B:CYS85 3.3 59.0 1.0
CB B:CYS73 3.5 52.2 1.0
N B:CYS73 3.5 51.6 1.0
CA B:CYS73 4.1 52.3 1.0
CB B:LEU83 4.1 56.9 1.0
N B:SER72 4.1 50.9 1.0
N B:CYS85 4.2 59.0 1.0
CA B:CYS85 4.3 59.4 1.0
SG B:CYS65 4.4 52.2 1.0
N B:GLY68 4.5 53.1 1.0
CA B:GLY68 4.6 52.5 1.0
C B:SER72 4.6 51.3 1.0
SG B:CYS70 4.6 50.4 1.0
N B:ARG66 4.7 54.1 1.0
CA B:SER72 4.7 51.2 1.0
CB B:SER72 4.8 51.0 1.0
CA B:ARG66 4.8 54.5 1.0
CD2 B:LEU83 4.9 56.4 1.0
CG B:LEU83 4.9 56.6 1.0
CA B:LEU83 5.0 57.1 1.0

Iron binding site 2 out of 10 in 3sfd

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Iron binding site 2 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:41.9
occ:1.00
 FE2 B:FES302 0.0 41.9 1.0
SG B:CYS70 2.0 50.4 1.0
S2 B:FES302 2.2 38.9 1.0
S1 B:FES302 2.2 39.4 1.0
SG B:CYS65 2.3 52.2 1.0
FE1 B:FES302 3.0 42.4 1.0
CB B:CYS65 3.2 53.4 1.0
N B:CYS65 3.3 53.3 1.0
CB B:CYS70 3.3 50.7 1.0
N B:CYS70 3.5 50.7 1.0
N B:GLY71 3.6 50.6 1.0
CA B:CYS65 3.7 53.4 1.0
N B:SER72 3.7 50.9 1.0
CA B:CYS70 3.8 50.6 1.0
N B:ARG66 3.8 54.1 1.0
CB B:SER72 4.0 51.0 1.0
OG B:SER72 4.1 51.4 1.0
C B:CYS70 4.1 50.6 1.0
N B:ILE69 4.2 51.8 1.0
C B:CYS65 4.2 53.7 1.0
N B:GLY68 4.3 53.1 1.0
SG B:CYS85 4.4 56.1 1.0
C B:SER64 4.4 53.2 1.0
N B:SER64 4.5 53.5 1.0
CA B:SER72 4.5 51.2 1.0
CA B:GLY68 4.5 52.5 1.0
CA B:GLY71 4.5 50.7 1.0
C B:ILE69 4.6 51.0 1.0
C B:GLY71 4.6 50.8 1.0
N B:GLU67 4.6 54.2 1.0
C B:GLY68 4.8 52.3 1.0
CA B:SER64 4.8 53.3 1.0
CA B:ARG66 4.8 54.5 1.0
SG B:CYS73 4.8 51.5 1.0
CB B:SER64 4.8 53.2 1.0
N B:CYS73 4.9 51.6 1.0

Iron binding site 3 out of 10 in 3sfd

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Iron binding site 3 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:35.4
occ:1.00
 FE1 B:SF4303 0.0 35.4 1.0
S3 B:SF4303 2.3 35.9 1.0
S2 B:SF4303 2.3 35.1 1.0
S4 B:SF4303 2.3 36.2 1.0
SG B:CYS158 2.5 46.4 1.0
FE4 B:SF4303 2.6 34.5 1.0
FE2 B:SF4303 2.7 36.9 1.0
FE3 B:SF4303 2.7 36.2 1.0
CB B:CYS158 3.5 47.0 1.0
S1 B:SF4303 3.8 36.8 1.0
N B:ILE159 3.9 46.7 1.0
CA B:CYS158 3.9 46.8 1.0
O B:HOH269 4.1 38.6 1.0
N B:LEU160 4.1 45.8 1.0
C B:CYS158 4.3 46.8 1.0
CD1 B:LEU229 4.4 46.3 1.0
SG B:CYS164 4.7 47.1 1.0
CA B:LEU160 4.7 45.8 1.0
N B:CYS161 4.7 45.9 1.0
CB B:ALA182 4.7 36.6 1.0
CA B:ILE159 4.9 46.3 1.0
C B:ILE159 4.9 46.0 1.0
SG B:CYS225 5.0 46.6 1.0
SG B:CYS161 5.0 44.1 1.0

Iron binding site 4 out of 10 in 3sfd

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Iron binding site 4 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:36.9
occ:1.00
 FE2 B:SF4303 0.0 36.9 1.0
S1 B:SF4303 2.3 36.8 1.0
S4 B:SF4303 2.3 36.2 1.0
S3 B:SF4303 2.3 35.9 1.0
SG B:CYS161 2.4 44.1 1.0
FE1 B:SF4303 2.7 35.4 1.0
FE3 B:SF4303 2.7 36.2 1.0
FE4 B:SF4303 2.8 34.5 1.0
CB B:CYS161 3.6 45.7 1.0
N B:CYS161 3.7 45.9 1.0
N B:ALA162 3.9 45.8 1.0
S2 B:SF4303 3.9 35.1 1.0
CA B:CYS161 4.0 45.7 1.0
CD B:PRO226 4.1 47.2 1.0
N B:CYS163 4.3 46.4 1.0
C B:CYS161 4.3 45.8 1.0
CG B:PRO226 4.5 47.2 1.0
CB B:CYS163 4.5 46.3 1.0
SG B:CYS164 4.7 47.1 1.0
SG B:CYS225 4.7 46.6 1.0
N B:LEU160 4.7 45.8 1.0
C B:LEU160 4.8 45.9 1.0
N B:CYS164 4.8 46.5 1.0
CA B:ALA162 4.8 46.1 1.0
SG B:CYS158 4.9 46.4 1.0
N B:ILE159 4.9 46.7 1.0
CA B:CYS163 5.0 46.3 1.0
CB B:ILE159 5.0 46.4 1.0

Iron binding site 5 out of 10 in 3sfd

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Iron binding site 5 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:36.2
occ:1.00
 FE3 B:SF4303 0.0 36.2 1.0
S4 B:SF4303 2.3 36.2 1.0
S1 B:SF4303 2.3 36.8 1.0
S2 B:SF4303 2.3 35.1 1.0
SG B:CYS225 2.4 46.6 1.0
FE1 B:SF4303 2.7 35.4 1.0
FE2 B:SF4303 2.7 36.9 1.0
FE4 B:SF4303 2.8 34.5 1.0
CB B:CYS225 3.2 46.5 1.0
CA B:CYS225 3.9 46.6 1.0
S3 B:SF4303 4.0 35.9 1.0
CD B:PRO226 4.1 47.2 1.0
CD1 B:LEU229 4.2 46.3 1.0
CB B:LEU229 4.5 45.0 1.0
CG B:LEU229 4.5 45.2 1.0
C B:CYS225 4.6 46.9 1.0
N B:PRO226 4.6 47.1 1.0
CB B:LYS227 4.7 47.2 1.0
N B:LYS227 4.8 47.2 1.0
SG B:CYS161 4.8 44.1 1.0
SG B:CYS164 4.9 47.1 1.0
CG B:PRO226 5.0 47.2 1.0

Iron binding site 6 out of 10 in 3sfd

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Iron binding site 6 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:34.5
occ:1.00
 FE4 B:SF4303 0.0 34.5 1.0
SG B:CYS164 2.3 47.1 1.0
S2 B:SF4303 2.3 35.1 1.0
S3 B:SF4303 2.3 35.9 1.0
S1 B:SF4303 2.3 36.8 1.0
FE1 B:SF4303 2.6 35.4 1.0
FE2 B:SF4303 2.8 36.9 1.0
FE3 B:SF4303 2.8 36.2 1.0
CB B:CYS164 3.1 46.4 1.0
N B:CYS164 3.9 46.5 1.0
CB B:ALA182 3.9 36.6 1.0
S4 B:SF4303 3.9 36.2 1.0
CA B:CYS164 4.1 46.4 1.0
CA B:ALA182 4.3 36.9 1.0
SG B:CYS158 4.7 46.4 1.0
N B:ALA162 4.8 45.8 1.0
N B:ALA182 4.8 37.0 1.0
SG B:CYS161 4.8 44.1 1.0
N B:CYS163 4.8 46.4 1.0
CG B:PRO231 5.0 42.1 1.0
SG B:CYS225 5.0 46.6 1.0

Iron binding site 7 out of 10 in 3sfd

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Iron binding site 7 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:40.4
occ:1.00
 FE1 B:F3S304 0.0 40.4 1.0
S1 B:F3S304 2.2 35.4 1.0
S3 B:F3S304 2.2 38.8 1.0
S2 B:F3S304 2.2 40.8 1.0
SG B:CYS221 2.2 43.2 1.0
FE4 B:F3S304 2.3 41.8 1.0
FE3 B:F3S304 2.8 40.1 1.0
CB B:CYS221 3.2 43.8 1.0
N B:CYS221 3.8 44.0 1.0
N B:MET219 3.8 42.0 1.0
CA B:MET219 4.1 42.4 1.0
S4 B:F3S304 4.1 44.0 1.0
CA B:CYS221 4.1 43.9 1.0
N B:ASN220 4.2 43.2 1.0
SG B:CYS168 4.4 40.5 1.0
C B:MET219 4.5 42.8 1.0
CE B:MET219 4.5 43.8 1.0
CD1 B:ILE235 4.6 43.6 1.0
CB B:PRO181 4.7 36.6 1.0
CG B:PRO181 4.7 36.5 1.0
CA B:GLY232 4.7 42.2 1.0
SG B:CYS215 4.8 38.9 1.0
C B:ASN220 4.9 44.0 1.0
CB B:CYS168 4.9 42.8 1.0
N B:ILE218 4.9 40.8 1.0
C B:ILE218 4.9 41.3 1.0

Iron binding site 8 out of 10 in 3sfd

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Iron binding site 8 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:40.1
occ:1.00
 FE3 B:F3S304 0.0 40.1 1.0
SG B:CYS215 2.2 38.9 1.0
S3 B:F3S304 2.2 38.8 1.0
S4 B:F3S304 2.2 44.0 1.0
S1 B:F3S304 2.2 35.4 1.0
FE4 B:F3S304 2.4 41.8 1.0
FE1 B:F3S304 2.8 40.4 1.0
CB B:CYS215 3.3 40.8 1.0
CA B:CYS215 3.7 41.0 1.0
OH B:TYR178 3.9 37.2 1.0
N B:THR217 3.9 40.9 1.0
N B:HIS216 4.2 41.2 1.0
S2 B:F3S304 4.2 40.8 1.0
CA B:THR217 4.2 40.9 1.0
CD1 B:ILE235 4.2 43.6 1.0
C B:CYS215 4.3 41.2 1.0
N B:ILE218 4.3 40.8 1.0
SG B:CYS168 4.3 40.5 1.0
C B:THR217 4.7 40.8 1.0
SG B:CYS221 4.8 43.2 1.0
C B:HIS216 4.9 41.0 1.0
N B:MET219 4.9 42.0 1.0

Iron binding site 9 out of 10 in 3sfd

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Iron binding site 9 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:41.8
occ:1.00
 FE4 B:F3S304 0.0 41.8 1.0
S4 B:F3S304 2.2 44.0 1.0
S3 B:F3S304 2.2 38.8 1.0
S2 B:F3S304 2.2 40.8 1.0
FE1 B:F3S304 2.3 40.4 1.0
SG B:CYS168 2.4 40.5 1.0
FE3 B:F3S304 2.4 40.1 1.0
S1 B:F3S304 3.3 35.4 1.0
CB B:CYS168 3.5 42.8 1.0
CB B:ILE218 4.2 40.5 1.0
CA B:CYS168 4.4 43.0 1.0
N B:MET219 4.4 42.0 1.0
N B:ILE218 4.4 40.8 1.0
OH B:TYR178 4.5 37.2 1.0
SG B:CYS221 4.5 43.2 1.0
SG B:CYS215 4.5 38.9 1.0
CG1 B:ILE218 4.7 39.6 1.0
CD1 B:ILE218 4.7 37.8 1.0
CA B:ILE218 4.8 40.7 1.0
CB B:CYS221 5.0 43.8 1.0

Iron binding site 10 out of 10 in 3sfd

Go back to Iron Binding Sites List in 3sfd
Iron binding site 10 out of 10 in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol


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 Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1305

b:72.7
occ:1.00
 FE C:HEM1305 0.0 72.7 1.0
NE2 C:HIS101 2.0 57.9 1.0
NB C:HEM1305 2.1 73.4 1.0
ND C:HEM1305 2.1 73.1 1.0
NC C:HEM1305 2.1 73.6 1.0
NA C:HEM1305 2.1 73.5 1.0
NE2 D:HIS79 2.3 46.7 1.0
CD2 C:HIS101 2.9 58.6 1.0
CE1 D:HIS79 2.9 47.5 1.0
CE1 C:HIS101 3.0 58.3 1.0
C4B C:HEM1305 3.1 73.8 1.0
C4C C:HEM1305 3.1 73.5 1.0
C4D C:HEM1305 3.1 72.9 1.0
C1A C:HEM1305 3.1 72.9 1.0
C1C C:HEM1305 3.1 73.6 1.0
C1B C:HEM1305 3.1 74.0 1.0
C1D C:HEM1305 3.1 73.1 1.0
C4A C:HEM1305 3.1 73.2 1.0
CHC C:HEM1305 3.4 73.5 1.0
CHA C:HEM1305 3.4 72.6 1.0
CHD C:HEM1305 3.5 73.4 1.0
CD2 D:HIS79 3.5 47.5 1.0
CHB C:HEM1305 3.5 73.7 1.0
CG C:HIS101 4.1 58.9 1.0
ND1 C:HIS101 4.1 58.6 1.0
ND1 D:HIS79 4.2 48.3 1.0
C3B C:HEM1305 4.3 74.2 1.0
C2D C:HEM1305 4.3 73.0 1.0
C3D C:HEM1305 4.3 72.7 1.0
C2B C:HEM1305 4.4 74.3 1.0
C3A C:HEM1305 4.4 72.9 1.0
C3C C:HEM1305 4.4 73.7 1.0
C2A C:HEM1305 4.4 72.7 1.0
CG D:HIS79 4.4 48.7 1.0
C2C C:HEM1305 4.4 73.8 1.0
NE2 C:HIS45 4.6 52.2 1.0

Reference:

Q.Zhou, Y.Zhai, J.Lou, M.Liu, X.Pang, F.Sun. Thiabendazole Inhibits Ubiquinone Reduction Activity of Mitochondrial Respiratory Complex II Via A Water Molecule Mediated Binding Feature. Protein Cell V. 2 531 2011.
ISSN: ISSN 1674-800X
PubMed: 21822798
DOI: 10.1007/S13238-011-1079-1
Page generated: Sun Dec 13 15:21:10 2020

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