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

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

All present enzymatic activity of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-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-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-One, PDB code: 6yhd 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) 22.52 / 1.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.579, 65.369, 70.564, 90.00, 96.13, 90.00
R / Rfree (%) 12.1 / 14.4

Other elements in 6yhd:

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

Zinc (Zn) 1 atom
Chlorine (Cl) 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-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-One (pdb code 6yhd). 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-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-One, PDB code: 6yhd:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6yhd

Go back to Fluorine Binding Sites List in 6yhd
Fluorine binding site 1 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- 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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F95

b:17.0
occ:1.00
 F A:FTR95 0.0 17.0 1.0
CZ3 A:FTR95 1.4 15.0 1.0
CH2 A:FTR95 2.3 14.4 1.0
CE3 A:FTR95 2.4 14.1 1.0
HH2 A:FTR95 2.5 17.2 1.0
HB2 A:ARG60 2.6 17.8 1.0
HE3 A:FTR95 2.6 17.0 1.0
HB A:VAL59 2.7 17.9 1.0
HG12 A:VAL59 2.7 19.3 1.0
H A:ARG60 2.8 16.5 1.0
N A:ARG60 2.8 13.8 1.0
HA A:ARG60 2.9 16.9 1.0
O A:PRO56 3.1 14.6 1.0
CA A:ARG60 3.2 14.1 1.0
CB A:ARG60 3.3 14.8 1.0
CG1 A:VAL59 3.3 16.1 1.0
CB A:VAL59 3.3 14.9 1.0
C A:VAL59 3.4 13.9 1.0
HG11 A:VAL59 3.5 19.3 1.0
CZ2 A:FTR95 3.6 13.6 1.0
CD2 A:FTR95 3.6 13.2 1.0
HB3 A:ARG60 3.8 17.8 1.0
HB3 A:ALA64 3.9 18.1 1.0
CA A:VAL59 3.9 14.0 1.0
HD3 A:ARG60 3.9 18.4 1.0
O A:VAL59 4.0 14.2 1.0
CE2 A:FTR95 4.1 13.5 1.0
HA A:PRO56 4.2 17.7 1.0
C A:PRO56 4.2 14.4 1.0
HG13 A:VAL59 4.2 19.3 1.0
HD2 A:ARG60 4.3 18.4 1.0
HZ2 A:FTR95 4.4 16.3 1.0
C3 A:GOL402 4.4 30.2 1.0
HG23 A:ILE67 4.4 16.3 1.0
O A:ALA64 4.4 14.1 1.0
CG A:ARG60 4.4 14.7 1.0
CD A:ARG60 4.4 15.4 1.0
C1 A:GOL402 4.4 30.6 1.0
HB3 A:PRO56 4.5 19.3 1.0
HD2 A:ARG97 4.6 21.8 1.0
CG2 A:VAL59 4.6 15.4 1.0
CA A:PRO56 4.6 14.7 1.0
N A:VAL59 4.6 13.5 1.0
HG21 A:ILE67 4.6 16.3 1.0
H A:VAL59 4.6 16.2 1.0
HG21 A:VAL59 4.7 18.5 1.0
C A:ARG60 4.7 14.6 1.0
HA A:VAL59 4.7 16.8 1.0
HG2 A:ARG60 4.8 17.7 1.0
CB A:ALA64 4.8 15.1 1.0
CG2 A:ILE67 4.9 13.6 1.0
HB1 A:ALA64 5.0 18.1 1.0
HG23 A:VAL59 5.0 18.5 1.0
CB A:PRO56 5.0 16.1 1.0

Fluorine binding site 2 out of 4 in 6yhd

Go back to Fluorine Binding Sites List in 6yhd
Fluorine binding site 2 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- 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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F178

b:18.7
occ:1.00
 F A:FTR178 0.0 18.7 1.0
CZ3 A:FTR178 1.4 16.8 1.0
CE3 A:FTR178 2.4 15.8 1.0
CH2 A:FTR178 2.4 16.4 1.0
HB2 A:GLU157 2.5 25.9 0.4
HH2 A:FTR178 2.5 19.7 1.0
HE3 A:FTR178 2.5 19.0 1.0
HB2 A:GLU157 2.8 25.9 0.6
O A:ASP156 3.1 15.7 1.0
HG11 A:VAL108 3.2 31.1 1.0
HG21 A:VAL108 3.3 30.6 1.0
HE2 A:PHE155 3.3 20.0 1.0
C A:ASP156 3.4 15.7 1.0
CB A:GLU157 3.4 21.6 0.4
N A:GLU157 3.5 16.8 0.6
CE2 A:PHE155 3.5 16.7 1.0
HA A:GLU157 3.6 23.3 0.4
HA A:GLU157 3.6 22.5 0.6
CD2 A:FTR178 3.6 14.7 1.0
CB A:GLU157 3.6 21.5 0.6
CZ2 A:FTR178 3.6 16.1 1.0
N A:GLU157 3.7 17.6 0.4
CA A:GLU157 3.8 19.4 0.4
CA A:GLU157 3.8 18.7 0.6
HG23 A:VAL122 3.9 29.2 1.0
H A:GLU157 3.9 20.2 0.6
HB3 A:GLU157 3.9 25.9 0.4
CZ A:PHE155 4.0 16.8 1.0
HB3 A:GLU157 4.0 25.9 0.6
HG21 A:VAL122 4.0 29.2 1.0
HZ A:PHE155 4.1 20.1 1.0
CE2 A:FTR178 4.1 15.6 1.0
CD2 A:PHE155 4.1 15.3 1.0
CG1 A:VAL108 4.1 25.9 1.0
CG2 A:VAL108 4.2 25.5 1.0
HD2 A:PHE155 4.2 18.4 1.0
H A:GLU157 4.3 21.1 0.4
HG3 A:GLU157 4.3 27.8 0.4
HA A:ASP156 4.3 16.8 1.0
OE2 A:GLU157 4.3 23.9 0.4
HZ2 A:FTR178 4.4 19.3 1.0
CA A:ASP156 4.4 14.0 1.0
CG2 A:VAL122 4.4 24.4 1.0
CG A:GLU157 4.4 23.2 0.4
HB A:VAL108 4.5 29.6 1.0
CB A:VAL108 4.5 24.7 1.0
HG12 A:VAL108 4.6 31.1 1.0
HG2 A:ARG174 4.6 22.2 1.0
HG22 A:VAL108 4.6 30.6 1.0
HG13 A:VAL108 4.6 31.1 1.0
HA2 A:GLY105 4.7 22.0 1.0
HG22 A:VAL122 4.7 29.2 1.0
HD3 A:ARG174 4.7 24.7 1.0
N A:ASP156 4.7 13.6 1.0
HG23 A:VAL108 4.8 30.6 1.0
CG A:GLU157 4.8 23.7 0.6
HG3 A:GLU157 4.8 28.4 0.6
CD A:GLU157 4.8 23.9 0.4
CE1 A:PHE155 4.8 16.4 1.0
CG A:PHE155 4.9 14.9 1.0
CG A:FTR178 5.0 14.6 1.0

Fluorine binding site 3 out of 4 in 6yhd

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

b:26.8
occ:1.00
 F A:FTR296 0.0 26.8 1.0
CZ3 A:FTR296 1.4 23.3 1.0
CE3 A:FTR296 2.4 20.8 1.0
CH2 A:FTR296 2.4 23.6 1.0
HH2 A:FTR296 2.5 28.4 1.0
HE3 A:FTR296 2.6 25.0 1.0
HD13 A:LEU357 2.6 19.9 1.0
HD1 A:PHE377 2.8 25.2 1.0
HE1 A:PHE377 2.9 26.1 1.0
HZ A:PHE373 3.2 24.0 1.0
HD12 A:LEU357 3.2 19.9 1.0
CD1 A:LEU357 3.3 16.6 1.0
HD2 A:LYS360 3.3 26.4 1.0
CD1 A:PHE377 3.3 21.0 1.0
CE1 A:PHE377 3.4 21.8 1.0
HA A:LEU357 3.4 16.9 1.0
HB2 A:LEU357 3.5 17.8 1.0
CD2 A:FTR296 3.6 19.4 1.0
CZ2 A:FTR296 3.6 23.1 1.0
HD11 A:LEU357 3.9 19.9 1.0
HZ A:PHE353 4.0 24.5 1.0
CZ A:PHE373 4.0 20.0 1.0
CB A:LEU357 4.1 14.8 1.0
CE2 A:FTR296 4.1 20.9 1.0
HD3 A:LYS360 4.1 26.4 1.0
CD A:LYS360 4.1 22.0 1.0
CA A:LEU357 4.1 14.1 1.0
HE3 A:LYS360 4.2 29.8 1.0
CG A:LEU357 4.3 15.6 1.0
HE1 A:PHE373 4.3 24.6 1.0
CZ A:PHE353 4.4 20.4 1.0
HZ2 A:FTR296 4.4 27.7 1.0
C1 A:GOL403 4.5 37.8 1.0
CG A:PHE377 4.5 19.7 1.0
CZ A:PHE377 4.6 22.1 1.0
CE1 A:PHE373 4.6 20.5 1.0
HD22 A:LEU357 4.6 19.7 1.0
HB2 A:PHE377 4.7 23.2 1.0
HB2 A:LYS360 4.7 20.7 1.0
CE A:LYS360 4.7 24.9 1.0
O A:HOH591 4.8 19.8 1.0
N A:LEU357 4.8 14.1 1.0
HA A:FTR296 4.9 21.9 1.0
CE2 A:PHE353 4.9 18.9 1.0
HE2 A:PHE353 4.9 22.7 1.0
CE1 A:PHE353 4.9 20.5 1.0
HE1 A:PHE353 4.9 24.6 1.0
CG A:FTR296 4.9 18.4 1.0
HB3 A:LEU357 5.0 17.8 1.0
HZ A:PHE377 5.0 26.5 1.0
HG A:LEU357 5.0 18.7 1.0

Fluorine binding site 4 out of 4 in 6yhd

Go back to Fluorine Binding Sites List in 6yhd
Fluorine binding site 4 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- 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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((2R,3S,4R,5R)-3,4- Dihydroxy-5-Methoxytetrahydrofuran-2-Yl)Ethyl)-2-(Methylamino)-3,7- Dihydro-8H-Imidazo[4,5-G]Quinazolin-8-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F326

b:15.3
occ:1.00
 F A:FTR326 0.0 15.3 1.0
CZ3 A:FTR326 1.3 14.3 1.0
CE3 A:FTR326 2.4 13.9 1.0
CH2 A:FTR326 2.4 14.2 1.0
HH2 A:FTR326 2.5 17.1 1.0
HE3 A:FTR326 2.5 16.6 1.0
HA A:VAL322 2.6 16.5 1.0
HD22 A:LEU345 2.9 17.5 1.0
HD2 A:LYS325 3.0 33.7 1.0
HG22 A:VAL322 3.0 16.8 1.0
HD21 A:LEU345 3.3 17.5 1.0
CA A:VAL322 3.5 13.8 1.0
HB2 A:LYS325 3.5 22.7 1.0
CD2 A:LEU345 3.5 14.6 1.0
O A:ALA321 3.5 15.6 1.0
CD2 A:FTR326 3.6 13.4 1.0
CZ2 A:FTR326 3.6 14.5 1.0
N A:VAL322 3.7 14.0 1.0
C A:ALA321 3.7 14.3 1.0
CG2 A:VAL322 3.9 14.0 1.0
HD23 A:LEU345 3.9 17.5 1.0
HB1 A:ALA321 4.0 19.6 1.0
O A:HOH508 4.0 24.1 1.0
HG13 A:VAL322 4.0 17.4 1.0
CD A:LYS325 4.0 28.1 1.0
HZ3 A:LYS325 4.0 40.7 1.0
HB3 A:ALA321 4.0 19.6 1.0
CE2 A:FTR326 4.1 14.2 1.0
CB A:VAL322 4.2 13.6 1.0
HG23 A:VAL322 4.2 16.8 1.0
H A:VAL322 4.2 16.8 1.0
HE3 A:LYS325 4.3 38.3 1.0
CB A:LYS325 4.4 18.9 1.0
HZ2 A:FTR326 4.4 17.4 1.0
CB A:ALA321 4.4 16.4 1.0
HD3 A:LYS325 4.5 33.7 1.0
C A:VAL322 4.6 13.8 1.0
CE A:LYS325 4.6 31.9 1.0
CG1 A:VAL322 4.6 14.5 1.0
HG21 A:VAL322 4.6 16.8 1.0
HB3 A:LYS325 4.6 22.7 1.0
HD13 A:LEU345 4.7 17.4 1.0
CG A:LYS325 4.7 23.4 1.0
O A:VAL322 4.7 14.8 1.0
NZ A:LYS325 4.7 34.0 1.0
CA A:ALA321 4.7 14.9 1.0
HD11 A:LEU345 4.8 17.4 1.0
OE1 A:GLU348 4.8 14.2 1.0
HG3 A:LYS325 4.8 28.1 1.0
CG A:LEU345 4.8 13.7 1.0
CG A:FTR326 5.0 13.7 1.0
CD1 A:LEU345 5.0 14.5 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 17:50:06 2025

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