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Fluorine in PDB 6yh3: Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One

Enzymatic activity of Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One

All present enzymatic activity of Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One:
2.4.2.29;

Protein crystallography data

The structure of Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One, PDB code: 6yh3 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) 42.78 / 1.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.934, 65.196, 71.597, 90.00, 94.22, 90.00
R / Rfree (%) 13.4 / 16.5

Other elements in 6yh3:

The structure of Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-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) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One (pdb code 6yh3). 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) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One, PDB code: 6yh3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6yh3

Go back to Fluorine Binding Sites List in 6yh3
Fluorine binding site 1 out of 4 in the Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-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) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F95

b:30.2
occ:1.00
 F A:FTR95 0.0 30.2 1.0
CZ3 A:FTR95 1.4 26.2 1.0
CE3 A:FTR95 2.4 24.2 1.0
CH2 A:FTR95 2.4 24.0 1.0
HH2 A:FTR95 2.5 28.8 1.0
HE3 A:FTR95 2.6 29.0 1.0
HH21 A:ARG97 3.1 31.1 0.4
HH22 A:ARG97 3.3 31.1 0.4
NH2 A:ARG97 3.3 26.0 0.4
O A:HOH623 3.5 48.7 1.0
CD2 A:FTR95 3.6 21.1 1.0
CZ2 A:FTR95 3.6 21.6 1.0
CE2 A:FTR95 4.1 20.5 1.0
CZ A:ARG97 4.1 26.2 0.4
HZ2 A:FTR95 4.4 26.0 1.0
HH21 A:ARG97 4.4 39.6 0.6
HD3 A:ARG97 4.4 31.4 0.6
HE A:ARG97 4.5 30.8 0.4
HG21 A:ILE67 4.6 23.2 1.0
HG23 A:ILE67 4.6 23.2 1.0
NE A:ARG97 4.7 25.7 0.4
O A:ALA64 4.8 23.1 1.0
HH12 A:ARG97 4.8 32.9 0.4
NH1 A:ARG97 4.8 27.4 0.4
HB3 A:ALA64 4.9 27.4 1.0
CG A:FTR95 5.0 20.2 1.0
HD13 A:ILE67 5.0 30.9 1.0

Fluorine binding site 2 out of 4 in 6yh3

Go back to Fluorine Binding Sites List in 6yh3
Fluorine binding site 2 out of 4 in the Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-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) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F178

b:21.4
occ:1.00
 F A:FTR178 0.0 21.4 1.0
CZ3 A:FTR178 1.3 19.5 1.0
CE3 A:FTR178 2.3 17.4 1.0
CH2 A:FTR178 2.4 19.9 1.0
HE3 A:FTR178 2.5 20.9 1.0
HH2 A:FTR178 2.6 23.8 1.0
HB2 A:GLU157 2.6 26.2 1.0
O A:HOH667 3.1 27.0 1.0
O A:ASP156 3.2 17.9 1.0
HA A:GLU157 3.3 23.6 1.0
HE2 A:PHE155 3.3 24.6 1.0
C A:ASP156 3.3 17.6 1.0
O A:HOH701 3.3 43.4 1.0
CB A:GLU157 3.4 21.9 1.0
N A:GLU157 3.4 17.6 1.0
CE2 A:PHE155 3.5 20.5 1.0
CA A:GLU157 3.6 19.7 1.0
CD2 A:FTR178 3.6 16.4 1.0
CZ2 A:FTR178 3.6 18.5 1.0
H A:GLU157 3.9 21.2 1.0
CZ A:PHE155 3.9 20.9 1.0
HZ A:PHE155 4.0 25.1 1.0
HB3 A:GLU157 4.0 26.2 1.0
CE2 A:FTR178 4.1 18.2 1.0
CD2 A:PHE155 4.1 18.9 1.0
HG3 A:GLU157 4.1 30.4 1.0
HA A:ASP156 4.2 20.6 1.0
OE1 A:GLU157 4.3 30.6 1.0
HD2 A:PHE155 4.3 22.7 1.0
CA A:ASP156 4.3 17.2 1.0
CG A:GLU157 4.3 25.4 1.0
HZ2 A:FTR178 4.4 22.1 1.0
N A:ASP156 4.6 16.4 1.0
HG2 A:ARG174 4.6 28.4 1.0
CD A:GLU157 4.8 27.7 1.0
CE1 A:PHE155 4.8 20.3 1.0
H A:ASP156 4.9 19.7 1.0
HD3 A:ARG174 4.9 32.1 1.0
CG A:PHE155 4.9 17.1 1.0
HA3 A:GLY105 4.9 27.3 1.0
CG A:FTR178 4.9 16.9 1.0
O A:PHE155 5.0 17.2 1.0

Fluorine binding site 3 out of 4 in 6yh3

Go back to Fluorine Binding Sites List in 6yh3
Fluorine binding site 3 out of 4 in the Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-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) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F296

b:38.6
occ:1.00
 F A:FTR296 0.0 38.6 1.0
CZ3 A:FTR296 1.4 34.2 1.0
CE3 A:FTR296 2.4 29.1 1.0
CH2 A:FTR296 2.4 33.8 1.0
HD1 A:PHE377 2.5 32.8 1.0
HH2 A:FTR296 2.5 40.5 1.0
HE3 A:FTR296 2.6 34.9 1.0
HD13 A:LEU357 2.7 28.8 1.0
HZ A:PHE373 2.7 31.4 1.0
HD12 A:LEU357 2.9 28.8 1.0
CD1 A:LEU357 3.2 24.0 1.0
CD1 A:PHE377 3.2 27.4 1.0
HE1 A:PHE377 3.3 34.5 1.0
CZ A:PHE373 3.5 26.2 1.0
HE1 A:PHE373 3.5 32.4 1.0
CD2 A:FTR296 3.6 28.2 1.0
CZ2 A:FTR296 3.6 33.1 1.0
CE1 A:PHE377 3.6 28.8 1.0
HD11 A:LEU357 3.7 28.8 1.0
HA A:LEU357 3.7 22.5 1.0
CE1 A:PHE373 3.9 27.0 1.0
HB2 A:PHE377 4.0 29.7 1.0
CE2 A:FTR296 4.1 30.2 1.0
HB2 A:LEU357 4.1 25.5 1.0
CG A:PHE377 4.3 25.9 1.0
HZ2 A:FTR296 4.4 39.7 1.0
CD A:LYS360 4.4 30.6 1.0
HZ A:PHE353 4.5 35.0 1.0
CG A:LEU357 4.5 21.5 1.0
HB2 A:LYS360 4.5 25.8 1.0
CA A:LEU357 4.6 18.8 1.0
CB A:LEU357 4.6 21.2 1.0
CE2 A:PHE373 4.6 25.0 1.0
O A:HOH597 4.6 25.6 1.0
O A:HOH760 4.6 39.7 1.0
CB A:PHE377 4.7 24.8 1.0
HE2 A:PHE373 4.7 30.0 1.0
CZ A:PHE377 4.9 28.2 1.0
HA A:PHE377 5.0 30.2 1.0
CG A:FTR296 5.0 26.2 1.0
CZ A:PHE353 5.0 29.2 1.0
HA A:FTR296 5.0 28.6 1.0

Fluorine binding site 4 out of 4 in 6yh3

Go back to Fluorine Binding Sites List in 6yh3
Fluorine binding site 4 out of 4 in the Trna-Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-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) in Co-Crystallized Complex with 6- Amino-2-(Methylamino)-4-Phenethyl-1,7-Dihydro-8H-Imidazo[4,5- G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F326

b:31.8
occ:1.00
 F A:FTR326 0.0 31.8 1.0
CZ3 A:FTR326 1.4 30.0 1.0
CH2 A:FTR326 2.4 29.8 1.0
CE3 A:FTR326 2.4 27.8 1.0
HH2 A:FTR326 2.5 35.8 1.0
HE3 A:FTR326 2.6 33.4 1.0
HA A:VAL322 2.8 34.9 1.0
HD22 A:LEU345 2.8 33.8 1.0
HG22 A:VAL322 3.1 33.6 1.0
HD21 A:LEU345 3.1 33.8 1.0
CD2 A:LEU345 3.4 28.1 1.0
CD2 A:FTR326 3.6 26.9 1.0
CZ2 A:FTR326 3.6 29.1 1.0
CA A:VAL322 3.7 29.1 1.0
HD23 A:LEU345 3.8 33.8 1.0
HB3 A:LYS325 3.8 41.7 1.0
O A:ALA321 3.9 32.7 1.0
CG2 A:VAL322 3.9 28.0 1.0
N A:VAL322 3.9 30.5 1.0
C A:ALA321 4.1 31.4 1.0
CE2 A:FTR326 4.1 27.0 1.0
HG13 A:VAL322 4.1 31.9 1.0
HG23 A:VAL322 4.2 33.6 1.0
HB1 A:ALA321 4.2 41.4 1.0
CB A:VAL322 4.3 27.8 1.0
HB3 A:ALA321 4.3 41.4 1.0
HZ2 A:FTR326 4.4 34.9 1.0
H A:VAL322 4.4 36.6 1.0
HD13 A:LEU345 4.5 32.5 1.0
CB A:LYS325 4.6 34.7 1.0
HG21 A:VAL322 4.7 33.6 1.0
CG A:LEU345 4.7 25.9 1.0
CB A:ALA321 4.7 34.5 1.0
HD11 A:LEU345 4.7 32.5 1.0
CG1 A:VAL322 4.7 26.6 1.0
HB2 A:LYS325 4.8 41.7 1.0
C A:VAL322 4.8 29.4 1.0
CD1 A:LEU345 4.9 27.1 1.0
O A:VAL322 4.9 29.5 1.0
CG A:FTR326 5.0 25.7 1.0

Reference:

A.Nguyen, A.Heine, G.Klebe. Co-Crystallization, 19F uc(Nmr) and Nanoesi-Ms Reveal Dimer Disturbing Inhibitors and Conformational Changes at Dimer Contacts To Be Published.
Page generated: Tue Jul 15 17:45:52 2025

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