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Fluorine in PDB 1g4p: 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: 1g4p 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) 53.94 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.280, 76.280, 139.590, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 29.5

Other elements in 1g4p:

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 1g4p). 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: 1g4p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1g4p

Go back to Fluorine Binding Sites List in 1g4p
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:8.3
occ:1.00
 F1 A:FQP2001 0.0 8.3 1.0
CM2 A:FQP2001 1.3 6.3 1.0
F2 A:FQP2001 2.1 9.3 1.0
F3 A:FQP2001 2.1 6.2 1.0
C2A A:FQP2001 2.3 5.1 1.0
OG A:SER206 2.7 9.0 1.0
N1A A:FQP2001 3.1 5.6 1.0
N3A A:FQP2001 3.1 2.4 1.0
CB A:SER206 3.5 4.1 1.0
CD1 A:ILE31 3.5 4.5 1.0
CG1 A:VAL184 3.8 3.2 1.0
CD1 A:ILE186 3.9 2.9 1.0
CE2 A:TYR29 4.0 3.4 1.0
CD2 A:TYR29 4.1 4.1 1.0
CB A:ILE186 4.2 3.5 1.0
C6A A:FQP2001 4.3 4.8 1.0
C4A A:FQP2001 4.3 2.9 1.0
CG1 A:ILE186 4.4 2.4 1.0
NE2 A:GLN57 4.4 2.4 1.0
CG1 A:ILE31 4.6 2.8 1.0
CG2 A:VAL184 4.6 3.7 1.0
CZ A:TYR29 4.7 3.7 1.0
CE1 A:HIS107 4.8 2.4 1.0
CG A:TYR29 4.9 2.4 1.0
C5A A:FQP2001 4.9 4.2 1.0
CB A:VAL184 4.9 5.3 1.0
CA A:GLY149 4.9 4.0 1.0
CA A:SER206 4.9 3.5 1.0
O A:GLY185 5.0 4.0 1.0
CG2 A:ILE186 5.0 2.4 1.0

Fluorine binding site 2 out of 6 in 1g4p

Go back to Fluorine Binding Sites List in 1g4p
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:9.3
occ:1.00
 F2 A:FQP2001 0.0 9.3 1.0
CM2 A:FQP2001 1.3 6.3 1.0
F1 A:FQP2001 2.1 8.3 1.0
F3 A:FQP2001 2.1 6.2 1.0
C2A A:FQP2001 2.3 5.1 1.0
N3A A:FQP2001 2.6 2.4 1.0
NE2 A:GLN57 2.9 2.4 1.0
CE2 A:TYR29 3.2 3.4 1.0
ND1 A:HIS107 3.3 2.5 1.0
CE1 A:HIS107 3.4 2.4 1.0
N1A A:FQP2001 3.5 5.6 1.0
OH A:TYR29 3.6 2.4 1.0
CZ A:TYR29 3.6 3.7 1.0
OH A:TYR147 3.6 5.3 1.0
CG A:HIS107 3.9 2.4 1.0
NE2 A:HIS107 4.0 2.4 1.0
C4A A:FQP2001 4.0 2.9 1.0
CD2 A:TYR29 4.0 4.1 1.0
CE1 A:TYR147 4.2 5.2 1.0
CD1 A:ILE31 4.2 4.5 1.0
CD2 A:HIS107 4.2 2.4 1.0
CD A:GLN57 4.2 2.4 1.0
CZ A:TYR147 4.4 5.8 1.0
OG A:SER206 4.4 9.0 1.0
C6A A:FQP2001 4.6 4.8 1.0
CE1 A:TYR29 4.6 5.5 1.0
CG1 A:VAL184 4.6 3.2 1.0
CB A:HIS107 4.7 4.0 1.0
N4A A:FQP2001 4.7 2.4 1.0
OE1 A:GLN57 4.8 2.4 1.0
C5A A:FQP2001 4.9 4.2 1.0
CG1 A:ILE31 4.9 2.8 1.0
CG A:TYR29 5.0 2.4 1.0

Fluorine binding site 3 out of 6 in 1g4p

Go back to Fluorine Binding Sites List in 1g4p
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:6.2
occ:1.00
 F3 A:FQP2001 0.0 6.2 1.0
CM2 A:FQP2001 1.3 6.3 1.0
F1 A:FQP2001 2.1 8.3 1.0
F2 A:FQP2001 2.1 9.3 1.0
C2A A:FQP2001 2.3 5.1 1.0
N1A A:FQP2001 2.6 5.6 1.0
CE1 A:HIS107 3.1 2.4 1.0
CG1 A:VAL184 3.2 3.2 1.0
CA A:GLY149 3.4 4.0 1.0
N3A A:FQP2001 3.4 2.4 1.0
CE1 A:TYR147 3.6 5.2 1.0
ND1 A:HIS107 3.8 2.5 1.0
NE2 A:HIS107 3.8 2.4 1.0
N A:GLY149 3.9 4.5 1.0
C6A A:FQP2001 4.0 4.8 1.0
CE2 A:TYR29 4.3 3.4 1.0
OH A:TYR147 4.3 5.3 1.0
OG A:SER206 4.4 9.0 1.0
CZ A:TYR147 4.5 5.8 1.0
CD1 A:TYR147 4.5 5.0 1.0
C4A A:FQP2001 4.5 2.9 1.0
C A:VAL148 4.6 4.6 1.0
CB A:VAL184 4.6 5.3 1.0
C A:GLY149 4.7 5.2 1.0
CG A:HIS107 4.7 2.4 1.0
CD2 A:HIS107 4.7 2.4 1.0
CD2 A:TYR29 4.7 4.1 1.0
O A:VAL184 4.8 4.1 1.0
C5A A:FQP2001 4.8 4.2 1.0
O A:VAL148 4.8 4.7 1.0

Fluorine binding site 4 out of 6 in 1g4p

Go back to Fluorine Binding Sites List in 1g4p
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:6.1
occ:1.00
 F1 B:FQP2002 0.0 6.1 1.0
CM2 B:FQP2002 1.3 4.6 1.0
F3 B:FQP2002 2.1 2.4 1.0
F2 B:FQP2002 2.1 6.0 1.0
C2A B:FQP2002 2.3 4.8 1.0
N3A B:FQP2002 2.7 3.5 1.0
CE2 B:TYR1029 3.0 2.9 1.0
NE2 B:GLN1057 3.1 2.4 1.0
CZ B:TYR1029 3.3 3.4 1.0
OH B:TYR1029 3.4 2.4 1.0
N1A B:FQP2002 3.5 3.5 1.0
OH B:TYR1147 3.6 4.5 1.0
ND1 B:HIS1107 3.7 6.7 1.0
CD2 B:TYR1029 3.7 2.4 1.0
CE1 B:HIS1107 3.8 6.2 1.0
C4A B:FQP2002 4.0 3.2 1.0
CG B:HIS1107 4.1 6.7 1.0
CE1 B:TYR1029 4.1 3.9 1.0
CE1 B:TYR1147 4.2 4.2 1.0
CD1 B:ILE1031 4.3 3.2 1.0
NE2 B:HIS1107 4.3 5.6 1.0
CZ B:TYR1147 4.4 3.1 1.0
CD B:GLN1057 4.4 3.0 1.0
CD2 B:HIS1107 4.5 5.9 1.0
CG B:TYR1029 4.5 2.8 1.0
CG1 B:VAL1184 4.6 2.4 1.0
CD1 B:TYR1029 4.7 4.9 1.0
C6A B:FQP2002 4.7 3.9 1.0
N4A B:FQP2002 4.8 2.4 1.0
CG1 B:ILE1031 4.8 2.4 1.0
CB B:HIS1107 4.8 3.5 1.0
CB B:SER1206 4.9 4.1 1.0
C5A B:FQP2002 4.9 3.3 1.0
OE1 B:GLN1057 4.9 3.2 1.0

Fluorine binding site 5 out of 6 in 1g4p

Go back to Fluorine Binding Sites List in 1g4p
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:6.0
occ:1.00
 F2 B:FQP2002 0.0 6.0 1.0
CM2 B:FQP2002 1.3 4.6 1.0
F1 B:FQP2002 2.1 6.1 1.0
F3 B:FQP2002 2.2 2.4 1.0
C2A B:FQP2002 2.3 4.8 1.0
N1A B:FQP2002 2.7 3.5 1.0
CG1 B:VAL1184 3.1 2.4 1.0
CE1 B:HIS1107 3.3 6.2 1.0
N3A B:FQP2002 3.4 3.5 1.0
CA B:GLY1149 3.5 2.8 1.0
CE1 B:TYR1147 3.5 4.2 1.0
ND1 B:HIS1107 3.7 6.7 1.0
NE2 B:HIS1107 3.9 5.6 1.0
C6A B:FQP2002 4.1 3.9 1.0
CE2 B:TYR1029 4.1 2.9 1.0
N B:GLY1149 4.1 2.4 1.0
OH B:TYR1147 4.1 4.5 1.0
CZ B:TYR1147 4.3 3.1 1.0
CD1 B:TYR1147 4.4 4.4 1.0
CD2 B:TYR1029 4.5 2.4 1.0
C4A B:FQP2002 4.6 3.2 1.0
C B:VAL1148 4.6 2.4 1.0
O B:VAL1148 4.6 3.0 1.0
CB B:VAL1184 4.6 3.3 1.0
CG B:HIS1107 4.6 6.7 1.0
CD2 B:HIS1107 4.7 5.9 1.0
C B:GLY1149 4.8 3.6 1.0
O B:VAL1184 4.8 2.4 1.0
C5A B:FQP2002 4.9 3.3 1.0
CZ B:TYR1029 4.9 3.4 1.0

Fluorine binding site 6 out of 6 in 1g4p

Go back to Fluorine Binding Sites List in 1g4p
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:2.4
occ:1.00
 F3 B:FQP2002 0.0 2.4 1.0
CM2 B:FQP2002 1.3 4.6 1.0
F1 B:FQP2002 2.1 6.1 1.0
F2 B:FQP2002 2.2 6.0 1.0
C2A B:FQP2002 2.3 4.8 1.0
N1A B:FQP2002 3.0 3.5 1.0
N3A B:FQP2002 3.1 3.5 1.0
OG B:SER1206 3.2 8.1 1.0
CB B:SER1206 3.3 4.1 1.0
CD1 B:ILE1186 3.7 5.0 1.0
CD1 B:ILE1031 3.7 3.2 1.0
CG1 B:VAL1184 3.8 2.4 1.0
CB B:ILE1186 4.0 3.7 1.0
CE2 B:TYR1029 4.1 2.9 1.0
CD2 B:TYR1029 4.1 2.4 1.0
C6A B:FQP2002 4.2 3.9 1.0
CG1 B:ILE1186 4.3 4.0 1.0
C4A B:FQP2002 4.3 3.2 1.0
CG2 B:ILE1186 4.6 2.6 1.0
CG1 B:ILE1031 4.7 2.4 1.0
NE2 B:GLN1057 4.7 2.4 1.0
CZ B:TYR1029 4.7 3.4 1.0
CG B:TYR1029 4.7 2.8 1.0
CG2 B:VAL1184 4.8 2.4 1.0
C5A B:FQP2002 4.8 3.3 1.0
CA B:SER1206 4.9 4.3 1.0
CA B:GLY1149 4.9 2.8 1.0
CB B:VAL1184 5.0 3.3 1.0
CE1 B:HIS1107 5.0 6.2 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 11:22:14 2024

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