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Fluorine 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:

Iron (Fe) 10 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Mitochondrial Respiratory Complex II Bound with 3-Nitropropionate and 2-Thenoyltrifluoroacetone, PDB code: 1zp0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1zp0

Go back to Fluorine Binding Sites List in 1zp0
Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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
C:F308

b:90.0
occ:1.00
F1 C:TTF308 0.0 90.0 1.0
C8 C:TTF308 1.3 79.9 1.0
F2 C:TTF308 2.1 92.5 1.0
F3 C:TTF308 2.1 84.5 1.0
C7 C:TTF308 2.3 69.2 1.0
C6 C:TTF308 2.8 49.8 1.0
CG B:PRO169 3.1 56.8 1.0
O2 C:TTF308 3.4 88.5 1.0
CB B:PRO169 3.6 68.3 1.0
CG C:MET39 3.7 56.1 1.0
SD C:MET39 4.0 60.2 1.0
C5 C:TTF308 4.3 53.1 1.0
CD B:PRO169 4.5 53.2 1.0
CG1 C:ILE43 4.6 63.9 1.0
S1 C:TTF308 4.6 59.8 1.0
C3 C:TTF308 4.8 50.7 1.0
OG C:SER42 4.9 92.6 1.0
CD1 C:ILE43 4.9 68.0 1.0
O C:MET39 4.9 69.4 1.0

Fluorine binding site 2 out of 6 in 1zp0

Go back to Fluorine Binding Sites List in 1zp0
Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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
C:F308

b:92.5
occ:1.00
F2 C:TTF308 0.0 92.5 1.0
C8 C:TTF308 1.3 79.9 1.0
F1 C:TTF308 2.1 90.0 1.0
F3 C:TTF308 2.2 84.5 1.0
C7 C:TTF308 2.3 69.2 1.0
C6 C:TTF308 2.8 49.8 1.0
O2 C:TTF308 3.4 88.5 1.0
CB B:PRO169 3.5 68.3 1.0
CG B:PRO169 3.6 56.8 1.0
CZ3 B:TRP172 3.9 85.9 1.0
CE3 B:TRP172 4.2 79.3 1.0
CG2 C:ILE30 4.3 75.1 1.0
C5 C:TTF308 4.3 53.1 1.0
CZ2 B:TRP173 4.5 81.6 1.0
CA B:PRO169 4.6 60.0 1.0
NE1 B:TRP173 4.7 81.7 1.0
CE2 B:TRP173 4.9 79.6 1.0
O1 C:TTF308 5.0 59.2 1.0
CH2 B:TRP172 5.0 87.6 1.0

Fluorine binding site 3 out of 6 in 1zp0

Go back to Fluorine Binding Sites List in 1zp0
Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F 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
C:F308

b:84.5
occ:1.00
F3 C:TTF308 0.0 84.5 1.0
C8 C:TTF308 1.4 79.9 1.0
F1 C:TTF308 2.1 90.0 1.0
F2 C:TTF308 2.2 92.5 1.0
C7 C:TTF308 2.6 69.2 1.0
O2 C:TTF308 3.1 88.5 1.0
CZ3 C:TRP35 3.4 0.5 1.0
CH2 C:TRP35 3.6 0.5 1.0
CD1 C:ILE43 3.8 68.0 1.0
C6 C:TTF308 3.8 49.8 1.0
CG1 C:ILE43 4.0 63.9 1.0
SD C:MET39 4.1 60.2 1.0
CG C:MET39 4.4 56.1 1.0
CE3 C:TRP35 4.6 0.7 1.0
CZ2 C:TRP35 4.9 0.8 1.0
CG B:PRO169 5.0 56.8 1.0

Fluorine binding site 4 out of 6 in 1zp0

Go back to Fluorine Binding Sites List in 1zp0
Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F 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
D:F309

b:0.9
occ:1.00
F1 D:TTF309 0.0 0.9 1.0
C8 D:TTF309 1.3 0.4 1.0
F2 D:TTF309 2.1 0.7 1.0
F3 D:TTF309 2.1 0.5 1.0
C7 D:TTF309 2.3 0.8 1.0
C6 D:TTF309 2.7 0.3 1.0
O D:ALA60 2.8 93.8 1.0
C D:ALA60 3.4 89.9 1.0
O2 D:TTF309 3.4 0.1 1.0
CA D:TYR61 3.6 96.5 1.0
N D:TYR61 3.7 94.6 1.0
CG D:PRO64 4.1 0.4 1.0
SG D:CYS127 4.2 0.7 1.0
C5 D:TTF309 4.2 0.9 1.0
CB D:ALA60 4.3 94.4 1.0
CB D:CYS127 4.4 99.3 1.0
CB D:TYR61 4.4 98.1 1.0
CA D:ALA60 4.4 84.6 1.0
C D:TYR61 4.6 97.3 1.0
O D:TYR61 4.6 1.0 1.0
CB D:PRO64 4.6 0.4 1.0
CA D:CYS127 4.6 98.3 1.0
O D:CYS127 4.7 98.1 1.0
CD1 D:TYR61 4.8 0.7 1.0
C D:CYS127 5.0 97.8 1.0

Fluorine binding site 5 out of 6 in 1zp0

Go back to Fluorine Binding Sites List in 1zp0
Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F 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
D:F309

b:0.7
occ:1.00
F2 D:TTF309 0.0 0.7 1.0
C8 D:TTF309 1.3 0.4 1.0
F1 D:TTF309 2.1 0.9 1.0
F3 D:TTF309 2.2 0.5 1.0
C7 D:TTF309 2.3 0.8 1.0
C6 D:TTF309 3.0 0.3 1.0
O2 D:TTF309 3.3 0.1 1.0
CG1 D:VAL130 3.6 75.4 1.0
S1 D:TTF309 3.8 0.3 1.0
CB D:VAL130 3.9 80.9 1.0
C5 D:TTF309 4.2 0.9 1.0
CG2 D:VAL130 4.4 86.4 1.0
O D:CYS127 4.4 98.1 1.0
C3 D:TTF309 4.4 0.8 1.0
O D:ALA60 4.7 93.8 1.0
CA D:CYS127 4.8 98.3 1.0
CA D:TYR61 4.9 96.5 1.0

Fluorine binding site 6 out of 6 in 1zp0

Go back to Fluorine Binding Sites List in 1zp0
Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F 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
D:F309

b:0.5
occ:1.00
F3 D:TTF309 0.0 0.5 1.0
C8 D:TTF309 1.4 0.4 1.0
F1 D:TTF309 2.1 0.9 1.0
F2 D:TTF309 2.2 0.7 1.0
C7 D:TTF309 2.6 0.8 1.0
O2 D:TTF309 3.1 0.1 1.0
N D:TYR61 3.2 94.6 1.0
CA D:TYR61 3.2 96.5 1.0
C D:ALA60 3.4 89.9 1.0
CB D:TYR61 3.5 98.1 1.0
O D:ALA60 3.5 93.8 1.0
O D:LEU57 3.8 75.2 1.0
CB D:ALA60 3.8 94.4 1.0
C6 D:TTF309 3.8 0.3 1.0
CA D:ALA60 4.2 84.6 1.0
CG D:TYR61 4.5 0.4 1.0
C D:TYR61 4.7 97.3 1.0
CD1 D:TYR61 4.7 0.7 1.0
C D:LEU57 4.9 72.3 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: Wed Jul 31 13:40:01 2024

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