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Fluorine in PDB 1g6c: Thiamin Phosphate Synthase

Enzymatic activity of Thiamin Phosphate Synthase

All present enzymatic activity of Thiamin Phosphate Synthase:
2.5.1.3;

Protein crystallography data

The structure of Thiamin Phosphate Synthase, PDB code: 1g6c was solved by D.H.Peapus, H.-J.Chiu, N.Campobasso, J.J.Reddick, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.86 / 1.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.650, 76.650, 140.070, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.7

Other elements in 1g6c:

The structure of Thiamin Phosphate Synthase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Thiamin Phosphate Synthase (pdb code 1g6c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Thiamin Phosphate Synthase, PDB code: 1g6c:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1g6c

Go back to Fluorine Binding Sites List in 1g6c
Fluorine binding site 1 out of 6 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:11.0
occ:1.00
 F1 A:IFP2001 0.0 11.0 1.0
CM2 A:IFP2001 1.3 10.1 1.0
F3 A:IFP2001 2.1 10.0 1.0
F2 A:IFP2001 2.1 11.3 1.0
C2A A:IFP2001 2.3 8.9 1.0
N1A A:IFP2001 3.0 9.2 1.0
N3A A:IFP2001 3.1 9.3 1.0
OG A:SER206 3.2 14.5 1.0
CB A:SER206 3.3 9.6 1.0
CD1 A:ILE31 3.6 10.3 1.0
CG1 A:VAL184 3.7 9.1 1.0
CD1 A:ILE186 3.7 12.8 1.0
CE2 A:TYR29 3.8 7.7 1.0
CD2 A:TYR29 3.8 6.3 1.0
C6A A:IFP2001 4.2 11.2 1.0
CB A:ILE186 4.3 8.8 1.0
C4A A:IFP2001 4.3 12.2 1.0
CG1 A:ILE186 4.5 10.1 1.0
CZ A:TYR29 4.5 7.5 1.0
CG2 A:VAL184 4.6 8.9 1.0
CG A:TYR29 4.6 5.6 1.0
NE2 A:GLN57 4.6 6.3 1.0
CG1 A:ILE31 4.8 6.2 1.0
CB A:VAL184 4.8 7.0 1.0
CG2 A:ILE186 4.8 9.7 1.0
CA A:GLY149 4.8 8.5 1.0
C5A A:IFP2001 4.8 12.2 1.0
CA A:SER206 4.8 7.1 1.0
CE1 A:HIS107 4.9 13.6 1.0

Fluorine binding site 2 out of 6 in 1g6c

Go back to Fluorine Binding Sites List in 1g6c
Fluorine binding site 2 out of 6 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:11.3
occ:1.00
 F2 A:IFP2001 0.0 11.3 1.0
CM2 A:IFP2001 1.3 10.1 1.0
F1 A:IFP2001 2.1 11.0 1.0
F3 A:IFP2001 2.2 10.0 1.0
C2A A:IFP2001 2.3 8.9 1.0
N3A A:IFP2001 2.6 9.3 1.0
CE2 A:TYR29 3.0 7.7 1.0
NE2 A:GLN57 3.0 6.3 1.0
CZ A:TYR29 3.3 7.5 1.0
OH A:TYR29 3.4 7.9 1.0
OH A:TYR147 3.4 10.7 1.0
ND1 A:HIS107 3.4 11.0 1.0
N1A A:IFP2001 3.5 9.2 1.0
CE1 A:HIS107 3.6 13.6 1.0
CD2 A:TYR29 3.7 6.3 1.0
CE1 A:TYR147 3.9 10.2 1.0
C4A A:IFP2001 4.0 12.2 1.0
CG A:HIS107 4.0 9.8 1.0
CD1 A:ILE31 4.0 10.3 1.0
CZ A:TYR147 4.1 10.0 1.0
NE2 A:HIS107 4.2 12.7 1.0
CD A:GLN57 4.2 6.4 1.0
CE1 A:TYR29 4.3 6.5 1.0
CD2 A:HIS107 4.4 14.1 1.0
OG A:SER206 4.6 14.5 1.0
C6A A:IFP2001 4.6 11.2 1.0
CG1 A:VAL184 4.6 9.1 1.0
CG A:TYR29 4.7 5.6 1.0
N4A A:IFP2001 4.7 11.2 1.0
CB A:HIS107 4.7 8.2 1.0
CG1 A:ILE31 4.8 6.2 1.0
C5A A:IFP2001 4.8 12.2 1.0
OE1 A:GLN57 4.9 7.7 1.0
CD1 A:TYR29 4.9 8.0 1.0

Fluorine binding site 3 out of 6 in 1g6c

Go back to Fluorine Binding Sites List in 1g6c
Fluorine binding site 3 out of 6 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:10.0
occ:1.00
 F3 A:IFP2001 0.0 10.0 1.0
CM2 A:IFP2001 1.3 10.1 1.0
F1 A:IFP2001 2.1 11.0 1.0
F2 A:IFP2001 2.2 11.3 1.0
C2A A:IFP2001 2.3 8.9 1.0
N1A A:IFP2001 2.6 9.2 1.0
CG1 A:VAL184 3.2 9.1 1.0
CE1 A:HIS107 3.3 13.6 1.0
CA A:GLY149 3.3 8.5 1.0
CE1 A:TYR147 3.3 10.2 1.0
N3A A:IFP2001 3.4 9.3 1.0
ND1 A:HIS107 3.8 11.0 1.0
N A:GLY149 3.9 8.5 1.0
C6A A:IFP2001 4.0 11.2 1.0
CE2 A:TYR29 4.1 7.7 1.0
NE2 A:HIS107 4.1 12.7 1.0
CD1 A:TYR147 4.2 9.9 1.0
OH A:TYR147 4.2 10.7 1.0
CZ A:TYR147 4.2 10.0 1.0
CD2 A:TYR29 4.5 6.3 1.0
C4A A:IFP2001 4.5 12.2 1.0
C A:GLY149 4.6 8.2 1.0
C A:VAL148 4.6 8.2 1.0
CB A:VAL184 4.6 7.0 1.0
CG A:HIS107 4.8 9.8 1.0
C5A A:IFP2001 4.8 12.2 1.0
O A:VAL148 4.8 9.3 1.0
O A:VAL184 4.9 7.6 1.0
CD2 A:HIS107 4.9 14.1 1.0
CZ A:TYR29 4.9 7.5 1.0
NE2 A:GLN57 5.0 6.3 1.0

Fluorine binding site 4 out of 6 in 1g6c

Go back to Fluorine Binding Sites List in 1g6c
Fluorine binding site 4 out of 6 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:11.9
occ:1.00
 F1 B:IFP2002 0.0 11.9 1.0
CM2 B:IFP2002 1.3 12.0 1.0
F2 B:IFP2002 2.1 10.6 1.0
F3 B:IFP2002 2.1 11.7 1.0
C2A B:IFP2002 2.3 9.8 1.0
N3A B:IFP2002 2.6 9.0 1.0
CE2 B:TYR1029 2.9 6.6 1.0
NE2 B:GLN1057 3.0 6.4 1.0
CZ B:TYR1029 3.3 6.7 1.0
OH B:TYR1029 3.4 7.1 1.0
OH B:TYR1147 3.4 9.5 1.0
ND1 B:HIS1107 3.5 9.9 1.0
N1A B:IFP2002 3.5 10.6 1.0
CE1 B:HIS1107 3.6 12.0 1.0
CD2 B:TYR1029 3.7 7.6 1.0
CE1 B:TYR1147 3.9 8.6 1.0
CD1 B:ILE1031 3.9 9.9 1.0
C4A B:IFP2002 4.0 11.9 1.0
CG B:HIS1107 4.0 8.5 1.0
CZ B:TYR1147 4.1 7.2 1.0
NE2 B:HIS1107 4.2 13.0 1.0
CD B:GLN1057 4.2 8.4 1.0
CE1 B:TYR1029 4.3 6.2 1.0
CD2 B:HIS1107 4.4 12.8 1.0
CG1 B:VAL1184 4.6 7.8 1.0
OG B:SER1206 4.6 13.9 1.0
C6A B:IFP2002 4.6 13.3 1.0
CG B:TYR1029 4.6 7.1 1.0
N4A B:IFP2002 4.8 11.9 1.0
CB B:HIS1107 4.8 7.3 1.0
CG1 B:ILE1031 4.8 7.2 1.0
OE1 B:GLN1057 4.9 8.5 1.0
CD1 B:TYR1029 4.9 7.3 1.0
C5A B:IFP2002 4.9 13.5 1.0

Fluorine binding site 5 out of 6 in 1g6c

Go back to Fluorine Binding Sites List in 1g6c
Fluorine binding site 5 out of 6 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:10.6
occ:1.00
 F2 B:IFP2002 0.0 10.6 1.0
CM2 B:IFP2002 1.3 12.0 1.0
F1 B:IFP2002 2.1 11.9 1.0
F3 B:IFP2002 2.2 11.7 1.0
C2A B:IFP2002 2.3 9.8 1.0
N1A B:IFP2002 2.7 10.6 1.0
CG1 B:VAL1184 3.2 7.8 1.0
CA B:GLY1149 3.3 7.8 1.0
CE1 B:HIS1107 3.3 12.0 1.0
CE1 B:TYR1147 3.3 8.6 1.0
N3A B:IFP2002 3.4 9.0 1.0
ND1 B:HIS1107 3.7 9.9 1.0
N B:GLY1149 3.9 7.0 1.0
C6A B:IFP2002 4.0 13.3 1.0
NE2 B:HIS1107 4.1 13.0 1.0
CE2 B:TYR1029 4.1 6.6 1.0
OH B:TYR1147 4.1 9.5 1.0
CD1 B:TYR1147 4.2 7.9 1.0
CZ B:TYR1147 4.2 7.2 1.0
C B:GLY1149 4.5 8.0 1.0
CD2 B:TYR1029 4.5 7.6 1.0
C4A B:IFP2002 4.5 11.9 1.0
C B:VAL1148 4.6 7.6 1.0
CB B:VAL1184 4.7 7.1 1.0
CG B:HIS1107 4.7 8.5 1.0
C5A B:IFP2002 4.8 13.5 1.0
O B:VAL1148 4.8 7.6 1.0
CD2 B:HIS1107 4.9 12.8 1.0
O B:VAL1184 4.9 8.0 1.0
NE2 B:GLN1057 5.0 6.4 1.0
CZ B:TYR1029 5.0 6.7 1.0

Fluorine binding site 6 out of 6 in 1g6c

Go back to Fluorine Binding Sites List in 1g6c
Fluorine binding site 6 out of 6 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2002

b:11.7
occ:1.00
 F3 B:IFP2002 0.0 11.7 1.0
CM2 B:IFP2002 1.3 12.0 1.0
F1 B:IFP2002 2.1 11.9 1.0
F2 B:IFP2002 2.2 10.6 1.0
C2A B:IFP2002 2.2 9.8 1.0
N1A B:IFP2002 3.0 10.6 1.0
N3A B:IFP2002 3.1 9.0 1.0
OG B:SER1206 3.2 13.9 1.0
CB B:SER1206 3.3 9.2 1.0
CD1 B:ILE1186 3.6 12.6 1.0
CD1 B:ILE1031 3.6 9.9 1.0
CG1 B:VAL1184 3.7 7.8 1.0
CE2 B:TYR1029 3.9 6.6 1.0
CD2 B:TYR1029 3.9 7.6 1.0
CB B:ILE1186 4.2 9.8 1.0
C6A B:IFP2002 4.2 13.3 1.0
C4A B:IFP2002 4.3 11.9 1.0
CG1 B:ILE1186 4.4 9.3 1.0
CG2 B:VAL1184 4.6 7.1 1.0
CZ B:TYR1029 4.6 6.7 1.0
NE2 B:GLN1057 4.6 6.4 1.0
CG B:TYR1029 4.7 7.1 1.0
CG2 B:ILE1186 4.7 10.0 1.0
CG1 B:ILE1031 4.8 7.2 1.0
C5A B:IFP2002 4.8 13.5 1.0
CA B:GLY1149 4.8 7.8 1.0
CB B:VAL1184 4.8 7.1 1.0
CA B:SER1206 4.9 8.3 1.0
CE1 B:HIS1107 4.9 12.0 1.0

Reference:

D.H.Peapus, H.J.Chiu, N.Campobasso, J.J.Reddick, T.P.Begley, S.E.Ealick. Structural Characterization of the Enzyme-Substrate, Enzyme-Intermediate, and Enzyme-Product Complexes of Thiamin Phosphate Synthase. Biochemistry V. 40 10103 2001.
ISSN: ISSN 0006-2960
PubMed: 11513589
DOI: 10.1021/BI0104726
Page generated: Wed Jul 31 11:23:27 2024

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