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Fluorine in PDB 6ygx: Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One

Enzymatic activity of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One

All present enzymatic activity of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One:
2.4.2.29;

Protein crystallography data

The structure of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One, PDB code: 6ygx was solved by A.Nguyen, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.60 / 1.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.083, 64.980, 71.374, 90.00, 93.78, 90.00
R / Rfree (%) 13.5 / 15.6

Other elements in 6ygx:

The structure of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One (pdb code 6ygx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One, PDB code: 6ygx:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ygx

Go back to Fluorine Binding Sites List in 6ygx
Fluorine binding site 1 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F95

b:27.8
occ:1.00
 F A:FTR95 0.0 27.8 1.0
CZ3 A:FTR95 1.4 23.4 1.0
CE3 A:FTR95 2.4 21.9 1.0
CH2 A:FTR95 2.4 21.9 1.0
HH2 A:FTR95 2.5 26.3 1.0
HE3 A:FTR95 2.5 26.3 1.0
HH21 A:ARG97 3.3 35.1 0.5
HH22 A:ARG97 3.4 35.1 0.5
NH2 A:ARG97 3.4 29.2 0.5
CD2 A:FTR95 3.6 18.7 1.0
O A:HOH555 3.6 52.3 1.0
CZ2 A:FTR95 3.6 19.5 1.0
CE2 A:FTR95 4.1 18.3 1.0
CZ A:ARG97 4.1 28.9 0.5
HH11 A:ARG97 4.4 35.3 0.5
HG21 A:ILE67 4.4 21.3 1.0
HZ2 A:FTR95 4.4 23.4 1.0
HD3 A:ARG97 4.5 29.2 0.5
HE A:ARG97 4.6 32.6 0.5
NE A:ARG97 4.7 27.1 0.5
HG23 A:ILE67 4.7 21.3 1.0
HH12 A:ARG97 4.7 36.3 0.5
NH1 A:ARG97 4.7 30.3 0.5
O A:ALA64 4.8 20.3 1.0
HB3 A:ALA64 4.8 25.3 1.0
CG2 A:ILE67 5.0 17.8 1.0
CG A:FTR95 5.0 18.3 1.0
HD13 A:ILE67 5.0 25.2 1.0

Fluorine binding site 2 out of 4 in 6ygx

Go back to Fluorine Binding Sites List in 6ygx
Fluorine binding site 2 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F178

b:21.3
occ:1.00
 F A:FTR178 0.0 21.3 1.0
CZ3 A:FTR178 1.4 18.5 1.0
CH2 A:FTR178 2.4 18.5 1.0
CE3 A:FTR178 2.4 16.2 1.0
HH2 A:FTR178 2.5 22.3 1.0
HE3 A:FTR178 2.6 19.5 1.0
HB2 A:GLU157 2.7 29.8 1.0
O A:HOH679 3.1 37.7 1.0
O A:ASP156 3.2 18.4 1.0
HE2 A:PHE155 3.3 23.3 1.0
C A:ASP156 3.4 17.1 1.0
HA A:GLU157 3.4 25.9 1.0
CB A:GLU157 3.5 24.8 1.0
N A:GLU157 3.5 18.6 1.0
CE2 A:PHE155 3.6 19.4 1.0
CD2 A:FTR178 3.6 15.6 1.0
CZ2 A:FTR178 3.6 18.2 1.0
CA A:GLU157 3.7 21.6 1.0
O A:HOH747 3.7 57.2 1.0
H A:GLU157 4.0 22.3 1.0
CZ A:PHE155 4.0 20.3 1.0
HG3 A:GLU157 4.0 34.2 1.0
HZ A:PHE155 4.0 24.3 1.0
CE2 A:FTR178 4.1 16.9 1.0
HG13 A:VAL122 4.1 40.5 1.0
CD2 A:PHE155 4.2 17.8 1.0
HB3 A:GLU157 4.2 29.8 1.0
OE1 A:GLU157 4.2 31.1 1.0
HA A:ASP156 4.2 18.4 1.0
CG A:GLU157 4.3 28.5 1.0
HD2 A:PHE155 4.3 21.4 1.0
CA A:ASP156 4.3 15.3 1.0
HZ2 A:FTR178 4.4 21.9 1.0
HG2 A:ARG174 4.6 26.1 1.0
HG12 A:VAL122 4.6 40.5 1.0
HD3 A:ARG174 4.6 29.9 1.0
N A:ASP156 4.7 14.4 1.0
CD A:GLU157 4.7 29.7 1.0
CG1 A:VAL122 4.8 33.8 1.0
CE1 A:PHE155 4.8 20.5 1.0
H A:ASP156 4.9 17.3 1.0
CG A:FTR178 5.0 15.5 1.0
CG A:PHE155 5.0 15.6 1.0

Fluorine binding site 3 out of 4 in 6ygx

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Fluorine binding site 3 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F296

b:37.2
occ:1.00
 F A:FTR296 0.0 37.2 1.0
CZ3 A:FTR296 1.4 33.9 1.0
CH2 A:FTR296 2.4 33.3 1.0
CE3 A:FTR296 2.4 30.1 1.0
HD13 A:LEU357 2.5 22.8 1.0
HH2 A:FTR296 2.5 40.0 1.0
HD1 A:PHE377 2.6 31.1 1.0
HE3 A:FTR296 2.6 36.2 1.0
HZ A:PHE373 2.7 29.3 1.0
HD12 A:LEU357 3.1 22.8 1.0
CD1 A:LEU357 3.2 19.0 1.0
CD1 A:PHE377 3.3 25.9 1.0
HE1 A:PHE377 3.3 33.2 1.0
CZ A:PHE373 3.5 24.4 1.0
HA A:LEU357 3.6 19.3 1.0
HE1 A:PHE373 3.6 29.7 1.0
CE1 A:PHE377 3.6 27.7 1.0
CZ2 A:FTR296 3.6 32.2 1.0
CD2 A:FTR296 3.6 28.6 1.0
HD11 A:LEU357 3.7 22.8 1.0
CE1 A:PHE373 3.9 24.7 1.0
HB2 A:LEU357 4.0 20.4 1.0
CE2 A:FTR296 4.1 30.1 1.0
HB2 A:PHE377 4.2 28.1 1.0
CG A:PHE377 4.4 24.4 1.0
HZ2 A:FTR296 4.4 38.6 1.0
HB2 A:LYS360 4.4 22.5 1.0
CA A:LEU357 4.4 16.1 1.0
CG A:LEU357 4.4 17.5 1.0
CB A:LEU357 4.5 17.0 1.0
HZ A:PHE353 4.6 29.5 1.0
CE2 A:PHE373 4.6 23.4 1.0
HE2 A:PHE373 4.7 28.1 1.0
O A:HOH785 4.7 64.3 1.0
O A:HOH585 4.7 23.3 1.0
O A:HOH756 4.8 45.1 1.0
CB A:PHE377 4.8 23.4 1.0
CZ A:PHE377 4.9 27.1 1.0
CZ A:PHE353 5.0 24.6 1.0
CG A:FTR296 5.0 26.4 1.0
HB3 A:LYS360 5.0 22.5 1.0

Fluorine binding site 4 out of 4 in 6ygx

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Fluorine binding site 4 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S, 5R,6S)-3,4,5,6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H- Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F326

b:34.5
occ:1.00
 F A:FTR326 0.0 34.5 1.0
CZ3 A:FTR326 1.4 32.4 1.0
CE3 A:FTR326 2.4 30.4 1.0
CH2 A:FTR326 2.4 32.2 1.0
HH2 A:FTR326 2.5 38.7 1.0
HE3 A:FTR326 2.6 36.5 1.0
HD22 A:LEU345 2.8 30.4 1.0
HA A:VAL322 2.8 44.1 1.0
HD21 A:LEU345 3.1 30.4 1.0
HG22 A:VAL322 3.2 44.6 1.0
CD2 A:LEU345 3.4 25.4 1.0
CD2 A:FTR326 3.6 29.2 1.0
CZ2 A:FTR326 3.6 31.1 1.0
CA A:VAL322 3.7 36.7 1.0
HD23 A:LEU345 3.8 30.4 1.0
HB3 A:LYS325 3.8 45.3 1.0
O A:ALA321 3.9 39.0 1.0
HG13 A:VAL322 4.0 44.3 1.0
CG2 A:VAL322 4.0 37.1 1.0
N A:VAL322 4.0 37.5 1.0
CE2 A:FTR326 4.1 29.7 1.0
C A:ALA321 4.1 39.1 1.0
HG23 A:VAL322 4.2 44.6 1.0
HB1 A:ALA321 4.2 48.4 1.0
CB A:VAL322 4.3 37.0 1.0
HD13 A:LEU345 4.3 28.3 1.0
HZ2 A:FTR326 4.4 37.3 1.0
H A:VAL322 4.5 45.1 1.0
HB3 A:ALA321 4.5 48.4 1.0
CG1 A:VAL322 4.6 36.9 1.0
CG A:LEU345 4.6 23.5 1.0
CB A:LYS325 4.6 37.7 1.0
HB2 A:LYS325 4.7 45.3 1.0
HD11 A:LEU345 4.7 28.3 1.0
HG21 A:VAL322 4.7 44.6 1.0
CB A:ALA321 4.8 40.3 1.0
CD1 A:LEU345 4.8 23.6 1.0
C A:VAL322 4.8 36.0 1.0
O A:VAL322 4.9 35.9 1.0
CG A:FTR326 5.0 28.3 1.0

Reference:

A.Nguyen, A.Heine, G.Klebe. Co-Crystallization, Nanoesi-Ms and 19F uc(Nmr) Reveal Dimer Disturbing Inhibitors and Conformational Changes at Dimer Contacts To Be Published.
Page generated: Tue Jul 15 17:44:14 2025

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