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Chlorine 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:

Iron (Fe) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Porcine Mitochondrial Respiratory Complex II Bound with Oxaloacetate and Pentachlorophenol, PDB code: 3sfd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 3sfd

Go back to Chlorine Binding Sites List in 3sfd
Chlorine binding site 1 out of 5 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 Chlorine with other atoms in the Cl 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
D:Cl1

b:35.1
occ:1.00
 CL1 D:PCI1 0.0 35.1 1.0
C2 D:PCI1 1.8 34.9 1.0
C3 D:PCI1 2.7 35.3 1.0
C1 D:PCI1 2.7 34.9 1.0
O1 D:PCI1 3.0 34.9 1.0
NE1 B:TRP173 3.1 49.7 1.0
CL2 D:PCI1 3.2 36.9 1.0
CZ2 B:TRP173 3.3 50.3 1.0
CE2 B:TRP173 3.6 50.3 1.0
CB B:PRO169 3.9 43.4 1.0
C4 D:PCI1 4.0 36.1 1.0
C6 D:PCI1 4.0 35.3 1.0
CD1 B:TRP173 4.4 49.4 1.0
C5 D:PCI1 4.5 36.1 1.0
CH2 B:TRP173 4.6 50.1 1.0
CG B:PRO169 4.7 43.2 1.0
CG2 C:ILE30 4.7 57.3 1.0
OH D:TYR91 4.8 60.8 1.0
CA B:PRO169 4.9 43.5 1.0
CD2 B:TRP173 4.9 49.8 1.0
CE3 B:TRP172 5.0 47.9 1.0

Chlorine binding site 2 out of 5 in 3sfd

Go back to Chlorine Binding Sites List in 3sfd
Chlorine binding site 2 out of 5 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 Chlorine with other atoms in the Cl 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
D:Cl1

b:36.9
occ:1.00
 CL2 D:PCI1 0.0 36.9 1.0
C3 D:PCI1 1.8 35.3 1.0
C4 D:PCI1 2.7 36.1 1.0
C2 D:PCI1 2.8 34.9 1.0
CL3 D:PCI1 3.1 38.2 1.0
CL1 D:PCI1 3.2 35.1 1.0
CH2 C:TRP35 3.6 52.6 1.0
CZ3 C:TRP35 3.9 52.9 1.0
CG B:PRO169 4.0 43.2 1.0
C5 D:PCI1 4.0 36.1 1.0
C1 D:PCI1 4.1 34.9 1.0
CB B:PRO169 4.3 43.4 1.0
CZ2 C:TRP35 4.4 52.7 1.0
C6 D:PCI1 4.5 35.3 1.0
CG C:MET39 4.6 54.5 1.0
SD C:MET39 4.6 54.7 1.0
CG1 C:ILE43 4.7 52.5 1.0
CG2 C:ILE43 4.8 51.5 1.0
CE3 C:TRP35 4.9 53.4 1.0

Chlorine binding site 3 out of 5 in 3sfd

Go back to Chlorine Binding Sites List in 3sfd
Chlorine binding site 3 out of 5 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 Chlorine with other atoms in the Cl 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
D:Cl1

b:38.2
occ:1.00
 CL3 D:PCI1 0.0 38.2 1.0
C4 D:PCI1 1.8 36.1 1.0
C3 D:PCI1 2.7 35.3 1.0
C5 D:PCI1 2.8 36.1 1.0
O C:MET39 2.9 54.4 1.0
CL2 D:PCI1 3.1 36.9 1.0
CL4 D:PCI1 3.2 38.6 1.0
CB C:SER42 3.7 52.3 1.0
CG C:MET39 3.7 54.5 1.0
CG1 C:ILE43 3.7 52.5 1.0
C C:MET39 3.9 54.3 1.0
N C:ILE43 3.9 52.3 1.0
CG2 B:ILE218 4.0 39.6 1.0
C2 D:PCI1 4.0 34.9 1.0
C6 D:PCI1 4.1 35.3 1.0
CA C:MET39 4.3 54.3 1.0
C C:SER42 4.4 52.3 1.0
CB C:ILE43 4.4 52.4 1.0
CA C:ILE43 4.5 52.5 1.0
CA C:SER42 4.6 52.4 1.0
CG2 C:ILE43 4.6 51.5 1.0
CD1 B:ILE218 4.6 37.8 1.0
C1 D:PCI1 4.6 34.9 1.0
CB C:MET39 4.6 54.1 1.0
CZ3 C:TRP35 4.6 52.9 1.0
CG1 B:ILE218 4.7 39.6 1.0
CG B:PRO169 4.7 43.2 1.0
OG C:SER42 4.8 52.0 1.0
CD1 C:ILE43 4.9 53.1 1.0
SD C:MET39 4.9 54.7 1.0
CB B:ILE218 5.0 40.5 1.0

Chlorine binding site 4 out of 5 in 3sfd

Go back to Chlorine Binding Sites List in 3sfd
Chlorine binding site 4 out of 5 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 Chlorine with other atoms in the Cl 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
D:Cl1

b:38.6
occ:1.00
 CL4 D:PCI1 0.0 38.6 1.0
C5 D:PCI1 1.8 36.1 1.0
C4 D:PCI1 2.7 36.1 1.0
C6 D:PCI1 2.8 35.3 1.0
CL5 D:PCI1 3.2 35.4 1.0
CL3 D:PCI1 3.2 38.2 1.0
CB C:SER42 3.2 52.3 1.0
C C:SER42 3.5 52.3 1.0
O C:SER42 3.5 52.2 1.0
CG1 B:ILE218 3.6 39.6 1.0
CD1 B:ILE218 3.7 37.8 1.0
N C:ILE43 3.8 52.3 1.0
OG C:SER42 3.9 52.0 1.0
CA C:SER42 4.0 52.4 1.0
C3 D:PCI1 4.0 35.3 1.0
C1 D:PCI1 4.0 34.9 1.0
CA C:ILE43 4.3 52.5 1.0
C2 D:PCI1 4.5 34.9 1.0
CB B:ILE218 4.7 40.5 1.0
CG2 B:ILE218 4.7 39.6 1.0
O C:HOH152 4.8 34.4 1.0
CG2 C:ILE43 4.9 51.5 1.0
CG C:ARG46 5.0 53.2 1.0

Chlorine binding site 5 out of 5 in 3sfd

Go back to Chlorine Binding Sites List in 3sfd
Chlorine binding site 5 out of 5 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 Chlorine with other atoms in the Cl 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
D:Cl1

b:35.4
occ:1.00
 CL5 D:PCI1 0.0 35.4 1.0
C6 D:PCI1 1.8 35.3 1.0
C1 D:PCI1 2.7 34.9 1.0
C5 D:PCI1 2.8 36.1 1.0
O1 D:PCI1 3.0 34.9 1.0
NH1 C:ARG46 3.1 54.6 1.0
CL4 D:PCI1 3.2 38.6 1.0
OH D:TYR91 3.6 60.8 1.0
CZ C:ARG46 3.7 54.8 1.0
CD2 B:HIS216 3.9 41.8 1.0
CG C:ARG46 4.0 53.2 1.0
C2 D:PCI1 4.0 34.9 1.0
C4 D:PCI1 4.1 36.1 1.0
NE C:ARG46 4.2 54.9 1.0
NH2 C:ARG46 4.3 54.8 1.0
CD C:ARG46 4.4 54.2 1.0
C3 D:PCI1 4.5 35.3 1.0
CD1 B:ILE218 4.5 37.8 1.0
OD2 D:ASP90 4.7 58.8 1.0
CG B:HIS216 4.7 41.6 1.0
CZ D:TYR91 4.7 61.2 1.0
NE2 B:HIS216 4.8 41.8 1.0
CB B:HIS216 4.9 41.0 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: Sat Dec 12 10:09:49 2020

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