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Fluorine in PDB 1njs: Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid

Enzymatic activity of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid

All present enzymatic activity of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid:
2.1.2.2;

Protein crystallography data

The structure of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid, PDB code: 1njs was solved by Y.Zhang, J.Desharnais, T.H.Marsilje, C.Li, M.P.Hedrick, L.T.Gooljarsingh, A.Tavassoli, S.J.Benkovic, A.J.Olson, D.L.Boger, I.A.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.32 / 1.98
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 126.235, 126.235, 94.419, 90.00, 90.00, 120.00
R / Rfree (%) 22.7 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid (pdb code 1njs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid, PDB code: 1njs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 1njs

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Fluorine binding site 1 out of 6 in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:25.2
occ:1.00
 F2 A:KEU510 0.0 25.2 1.0
C6 A:KEU510 1.4 24.9 1.0
F1 A:KEU510 2.1 24.8 1.0
F A:KEU510 2.2 25.3 1.0
C5 A:KEU510 2.5 25.5 1.0
OA1 A:KEU510 2.7 23.7 1.0
CE A:MET89 3.2 30.7 1.0
C10 A:KEU510 3.2 23.7 1.0
C11 A:KEU510 3.2 21.9 1.0
C16 A:KEU510 3.4 20.5 1.0
CA A:SER118 3.5 22.5 1.0
SD A:MET89 3.5 30.4 1.0
OA2 A:KEU510 3.5 26.1 1.0
CB A:SER118 3.6 22.3 1.0
O A:HOH562 3.6 29.6 1.0
C1 A:KEU510 3.9 23.2 1.0
C12 A:KEU510 4.1 21.6 1.0
C15 A:KEU510 4.3 22.8 1.0
N A:SER118 4.3 22.4 1.0
O A:HOH550 4.4 26.7 1.0
O A:HOH652 4.5 30.4 1.0
O A:GLY117 4.5 22.5 1.0
C A:SER118 4.6 22.6 1.0
O A:SER118 4.6 23.8 1.0
C A:GLY117 4.6 22.7 1.0
O A:PHE88 4.8 22.3 1.0
C13 A:KEU510 4.9 22.6 1.0
O A:HOH525 4.9 24.1 1.0
C14 A:KEU510 4.9 23.1 1.0

Fluorine binding site 2 out of 6 in 1njs

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Fluorine binding site 2 out of 6 in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:24.8
occ:1.00
 F1 A:KEU510 0.0 24.8 1.0
C6 A:KEU510 1.3 24.9 1.0
F2 A:KEU510 2.1 25.2 1.0
C5 A:KEU510 2.2 25.5 1.0
F A:KEU510 2.2 25.3 1.0
C1 A:KEU510 2.8 23.2 1.0
OA2 A:KEU510 2.9 26.1 1.0
C10 A:KEU510 2.9 23.7 1.0
O A:HOH529 3.1 23.2 1.0
O A:HOH525 3.2 24.1 1.0
CE A:MET89 3.5 30.7 1.0
OA1 A:KEU510 3.5 23.7 1.0
C11 A:KEU510 3.7 21.9 1.0
C16 A:KEU510 3.7 20.5 1.0
O A:PHE88 3.7 22.3 1.0
O A:HOH652 3.9 30.4 1.0
OD1 A:ASN106 4.1 20.4 1.0
O A:ILE107 4.2 18.5 1.0
ND2 A:ASN106 4.3 16.9 1.0
SD A:MET89 4.5 30.4 1.0
C2 A:KEU510 4.5 24.8 1.0
CG A:ASN106 4.6 20.8 1.0
O A:HOH562 4.7 29.6 1.0
C A:PHE88 4.9 22.4 1.0
O A:HOH563 4.9 27.6 1.0
C15 A:KEU510 5.0 22.8 1.0

Fluorine binding site 3 out of 6 in 1njs

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Fluorine binding site 3 out of 6 in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F510

b:25.3
occ:1.00
 F A:KEU510 0.0 25.3 1.0
C6 A:KEU510 1.3 24.9 1.0
F1 A:KEU510 2.2 24.8 1.0
F2 A:KEU510 2.2 25.2 1.0
C5 A:KEU510 2.4 25.5 1.0
OA2 A:KEU510 2.6 26.1 1.0
OA1 A:KEU510 2.8 23.7 1.0
O A:HOH562 3.2 29.6 1.0
O A:HOH652 3.3 30.4 1.0
CD A:PRO109 3.4 18.7 1.0
ND1 A:HIS108 3.5 17.9 1.0
O A:HOH550 3.6 26.7 1.0
C10 A:KEU510 3.8 23.7 1.0
O A:HOH525 3.9 24.1 1.0
O A:ILE107 4.1 18.5 1.0
CE1 A:HIS108 4.3 20.3 1.0
CA A:HIS108 4.3 18.2 1.0
CG A:PRO109 4.3 20.0 1.0
CE A:MET89 4.4 30.7 1.0
C1 A:KEU510 4.4 23.2 1.0
CG A:HIS108 4.5 19.2 1.0
O A:GLY117 4.5 22.5 1.0
N A:PRO109 4.6 18.3 1.0
CA A:SER118 4.6 22.5 1.0
CB A:HIS108 4.6 17.7 1.0
C11 A:KEU510 4.7 21.9 1.0
ND2 A:ASN106 5.0 16.9 1.0
O A:HOH529 5.0 23.2 1.0
C A:HIS108 5.0 17.9 1.0
O A:HOH567 5.0 33.1 1.0

Fluorine binding site 4 out of 6 in 1njs

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Fluorine binding site 4 out of 6 in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F610

b:34.1
occ:1.00
 F2 B:KEU610 0.0 34.1 1.0
C6 B:KEU610 1.4 34.1 1.0
F1 B:KEU610 2.2 34.2 1.0
F B:KEU610 2.3 35.5 1.0
C5 B:KEU610 2.6 34.3 1.0
OA1 B:KEU610 2.8 31.5 1.0
CE B:MET89 3.2 39.9 1.0
C11 B:KEU610 3.2 35.9 1.0
C10 B:KEU610 3.2 35.2 1.0
C16 B:KEU610 3.4 37.8 1.0
SD B:MET89 3.5 40.0 1.0
OA2 B:KEU610 3.6 31.7 1.0
O B:HOH673 3.6 40.0 1.0
CA B:SER118 3.8 33.3 1.0
CB B:SER118 3.8 34.5 1.0
C12 B:KEU610 3.9 38.2 1.0
C1 B:KEU610 4.0 38.9 1.0
C15 B:KEU610 4.3 39.1 1.0
O B:HOH630 4.3 27.2 1.0
N B:SER118 4.5 32.7 1.0
C13 B:KEU610 4.7 39.5 1.0
O B:GLY117 4.8 30.1 1.0
C B:SER118 4.8 33.1 1.0
C B:GLY117 4.8 31.5 1.0
O B:SER118 4.8 34.1 1.0
C14 B:KEU610 4.9 40.5 1.0

Fluorine binding site 5 out of 6 in 1njs

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Fluorine binding site 5 out of 6 in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F610

b:34.2
occ:1.00
 F1 B:KEU610 0.0 34.2 1.0
C6 B:KEU610 1.3 34.1 1.0
F2 B:KEU610 2.2 34.1 1.0
C5 B:KEU610 2.2 34.3 1.0
F B:KEU610 2.2 35.5 1.0
OA2 B:KEU610 2.8 31.7 1.0
C1 B:KEU610 2.8 38.9 1.0
C10 B:KEU610 2.9 35.2 1.0
CE B:MET89 3.2 39.9 1.0
O B:HOH665 3.3 32.1 1.0
O B:HOH635 3.3 27.8 1.0
OA1 B:KEU610 3.5 31.5 1.0
C11 B:KEU610 3.7 35.9 1.0
C16 B:KEU610 3.8 37.8 1.0
OD1 B:ASN106 4.0 26.6 1.0
O B:PHE88 4.1 31.3 1.0
O B:ILE107 4.1 24.3 1.0
ND2 B:ASN106 4.3 26.8 1.0
SD B:MET89 4.4 40.0 1.0
C2 B:KEU610 4.5 37.2 1.0
CG B:ASN106 4.6 27.4 1.0
O B:HOH673 4.7 40.0 1.0
ND1 B:HIS108 5.0 25.0 1.0
C12 B:KEU610 5.0 38.2 1.0

Fluorine binding site 6 out of 6 in 1njs

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Fluorine binding site 6 out of 6 in the Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Human Gar Tfase in Complex with Hydrolyzed Form of 10- Trifluoroacetyl-5,10-Dideaza-Acyclic-5,6,7,8- Tetrahydrofolic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F610

b:35.5
occ:1.00
 F B:KEU610 0.0 35.5 1.0
C6 B:KEU610 1.4 34.1 1.0
F1 B:KEU610 2.2 34.2 1.0
F2 B:KEU610 2.3 34.1 1.0
C5 B:KEU610 2.4 34.3 1.0
OA2 B:KEU610 2.6 31.7 1.0
OA1 B:KEU610 2.8 31.5 1.0
O B:HOH673 3.1 40.0 1.0
O B:HOH630 3.5 27.2 1.0
CD B:PRO109 3.5 21.8 1.0
ND1 B:HIS108 3.5 25.0 1.0
C10 B:KEU610 3.8 35.2 1.0
O B:ILE107 4.1 24.3 1.0
O B:HOH665 4.2 32.1 1.0
CE1 B:HIS108 4.2 25.2 1.0
CA B:HIS108 4.3 22.2 1.0
CG B:HIS108 4.4 23.6 1.0
CE B:MET89 4.4 39.9 1.0
CG B:PRO109 4.4 21.8 1.0
C1 B:KEU610 4.5 38.9 1.0
CB B:HIS108 4.6 22.3 1.0
C11 B:KEU610 4.6 35.9 1.0
O B:GLY117 4.6 30.1 1.0
N B:PRO109 4.7 21.3 1.0
CA B:SER118 4.8 33.3 1.0

Reference:

Y.Zhang, J.Desharnais, T.H.Marsilje, C.Li, M.P.Hedrick, L.T.Gooljarsingh, A.Tavassoli, S.J.Benkovic, A.J.Olson, D.L.Boger, I.A.Wilson. Rational Design, Synthesis, Evaluation, and Crystal Structure of A Potent Inhibitor of Human Gar Tfase: 10-(Trifluoroacetyl)-5,10-Dideazaacyclic-5,6,7,8- Tetrahydrofolic Acid Biochemistry V. 42 6043 2003.
ISSN: ISSN 0006-2960
PubMed: 12755606
DOI: 10.1021/BI034219C
Page generated: Wed Jul 31 12:08:14 2024

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