Fluorine in PDB 6yyz: Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-1,7-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-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-1,7-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-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-1,7-Dihydro-8H- Imidazo[4,5-G]Quinazolin-8-One, PDB code: 6yyz 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) 37.12 / 1.21
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.723, 65.036, 71.568, 90.00, 93.71, 90.00
R / Rfree (%) 13.4 / 15.9

Other elements in 6yyz:

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

Fluorine binding site 1 out of 4 in 6yyz

Go back to Fluorine Binding Sites List in 6yyz
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,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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:25.9
occ:1.00
 F A:FTR95 0.0 25.9 1.0
CZ3 A:FTR95 1.4 22.2 1.0
CE3 A:FTR95 2.4 20.1 1.0
CH2 A:FTR95 2.4 21.5 1.0
HH2 A:FTR95 2.5 25.8 1.0
HE3 A:FTR95 2.6 24.1 1.0
O A:HOH506 3.3 57.2 1.0
O A:HOH567 3.4 36.7 1.0
CD2 A:FTR95 3.6 17.9 1.0
CZ2 A:FTR95 3.6 19.6 1.0
CE2 A:FTR95 4.1 17.6 1.0
HZ2 A:FTR95 4.4 23.5 1.0
HH21 A:ARG97 4.4 37.4 1.0
HD3 A:ARG97 4.5 30.9 1.0
HG23 A:ILE67 4.5 20.3 1.0
O A:HOH555 4.6 54.9 1.0
HG21 A:ILE67 4.6 20.3 1.0
HB3 A:ALA64 4.8 24.2 1.0
O A:ALA64 4.8 18.7 1.0
HD13 A:ILE67 4.9 25.0 1.0
CG A:FTR95 5.0 16.9 1.0

Fluorine binding site 2 out of 4 in 6yyz

Go back to Fluorine Binding Sites List in 6yyz
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,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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:16.6
occ:1.00
 F A:FTR178 0.0 16.6 1.0
CZ3 A:FTR178 1.4 15.3 1.0
CE3 A:FTR178 2.4 14.4 1.0
CH2 A:FTR178 2.4 15.5 1.0
HH2 A:FTR178 2.5 18.6 1.0
HB2 A:GLU157 2.5 21.3 1.0
HE3 A:FTR178 2.6 17.2 1.0
O A:HOH696 3.1 22.2 1.0
O A:ASP156 3.2 14.4 1.0
C A:ASP156 3.3 13.9 1.0
HA A:GLU157 3.3 18.9 1.0
HE2 A:PHE155 3.3 19.8 1.0
CB A:GLU157 3.4 17.7 1.0
N A:GLU157 3.4 14.5 1.0
CE2 A:PHE155 3.5 16.5 1.0
CA A:GLU157 3.5 15.7 1.0
CD2 A:FTR178 3.6 13.7 1.0
CZ2 A:FTR178 3.6 15.4 1.0
CZ A:PHE155 3.9 17.1 1.0
H A:GLU157 3.9 17.4 1.0
HZ A:PHE155 3.9 20.5 1.0
HB3 A:GLU157 4.0 21.3 1.0
CE2 A:FTR178 4.1 15.0 1.0
HG3 A:GLU157 4.1 24.8 1.0
CD2 A:PHE155 4.1 14.8 1.0
HA A:ASP156 4.1 16.0 1.0
CA A:ASP156 4.2 13.3 1.0
CG A:GLU157 4.3 20.6 1.0
OE1 A:GLU157 4.3 23.5 1.0
HD2 A:PHE155 4.3 17.8 1.0
HZ2 A:FTR178 4.4 18.5 1.0
N A:ASP156 4.6 12.6 1.0
HG2 A:ARG174 4.6 21.4 1.0
CE1 A:PHE155 4.7 16.7 1.0
CD A:GLU157 4.7 21.8 1.0
HD3 A:ARG174 4.8 25.7 1.0
H A:ASP156 4.8 15.1 1.0
CG A:PHE155 4.9 13.7 1.0
CG A:FTR178 4.9 14.0 1.0

Fluorine binding site 3 out of 4 in 6yyz

Go back to Fluorine Binding Sites List in 6yyz
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,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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:31.9
occ:1.00
 F A:FTR296 0.0 31.9 1.0
CZ3 A:FTR296 1.4 29.2 1.0
CE3 A:FTR296 2.4 26.4 1.0
CH2 A:FTR296 2.4 28.7 1.0
HD1 A:PHE377 2.5 28.6 1.0
HH2 A:FTR296 2.6 34.4 1.0
HE3 A:FTR296 2.6 31.6 1.0
HZ A:PHE373 2.7 28.9 1.0
HD13 A:LEU357 2.7 24.7 1.0
HD12 A:LEU357 3.0 24.7 1.0
CD1 A:PHE377 3.2 23.8 1.0
CD1 A:LEU357 3.3 20.6 1.0
HE1 A:PHE377 3.4 30.4 1.0
CZ A:PHE373 3.4 24.1 1.0
HE1 A:PHE373 3.5 30.2 1.0
CD2 A:FTR296 3.6 24.9 1.0
CZ2 A:FTR296 3.6 28.3 1.0
CE1 A:PHE377 3.7 25.4 1.0
HD11 A:LEU357 3.8 24.7 1.0
HA A:LEU357 3.8 20.5 1.0
CE1 A:PHE373 3.8 25.1 1.0
HB2 A:PHE377 4.0 28.2 1.0
CE2 A:FTR296 4.1 26.5 1.0
HB2 A:LEU357 4.2 22.3 1.0
CG A:PHE377 4.3 23.3 1.0
HZ2 A:FTR296 4.4 34.0 1.0
HZ A:PHE353 4.5 29.5 1.0
CG A:LEU357 4.5 19.8 1.0
CE2 A:PHE373 4.5 22.7 1.0
O A:HOH602 4.6 23.6 1.0
HB2 A:LYS360 4.6 23.1 1.0
CA A:LEU357 4.6 17.1 1.0
CB A:LEU357 4.6 18.6 1.0
CB A:PHE377 4.6 23.5 1.0
O A:HOH814 4.7 37.3 1.0
HE2 A:PHE373 4.7 27.3 1.0
HA A:PHE377 4.9 29.1 1.0
CG A:FTR296 5.0 23.6 1.0
HA A:FTR296 5.0 26.1 1.0
CZ A:PHE353 5.0 24.6 1.0
CZ A:PHE377 5.0 25.5 1.0

Fluorine binding site 4 out of 4 in 6yyz

Go back to Fluorine Binding Sites List in 6yyz
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,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4R, 5R)-3,4,5-Trimethoxytetrahydrofuran-2-Yl)Ethyl)-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:29.1
occ:1.00
 F A:FTR326 0.0 29.1 1.0
CZ3 A:FTR326 1.4 27.4 1.0
CE3 A:FTR326 2.4 25.9 1.0
CH2 A:FTR326 2.4 27.6 1.0
HH2 A:FTR326 2.5 33.1 1.0
HE3 A:FTR326 2.6 31.1 1.0
HD22 A:LEU345 2.7 34.6 1.0
HA A:VAL322 2.8 31.2 1.0
HG22 A:VAL322 3.0 32.0 1.0
HD21 A:LEU345 3.1 34.6 1.0
CD2 A:LEU345 3.3 28.9 1.0
CD2 A:FTR326 3.6 24.7 1.0
CZ2 A:FTR326 3.7 26.9 1.0
CA A:VAL322 3.7 26.0 1.0
HD23 A:LEU345 3.7 34.6 1.0
CG2 A:VAL322 3.9 26.7 1.0
O A:ALA321 3.9 29.8 1.0
HG13 A:VAL322 3.9 30.0 1.0
N A:VAL322 4.0 27.6 1.0
C A:ALA321 4.1 28.8 1.0
CE2 A:FTR326 4.1 25.6 1.0
HG23 A:VAL322 4.2 32.0 1.0
CB A:VAL322 4.2 26.1 1.0
HB1 A:ALA321 4.4 37.4 1.0
HZ2 A:FTR326 4.4 32.3 1.0
HD11 A:LEU345 4.4 33.6 1.0
H A:VAL322 4.5 33.1 1.0
HB3 A:ALA321 4.5 37.4 1.0
HG21 A:VAL322 4.5 32.0 1.0
HD13 A:LEU345 4.6 33.6 1.0
CG1 A:VAL322 4.6 25.0 1.0
CG A:LEU345 4.6 27.9 1.0
CB A:LYS325 4.7 30.6 1.0
C A:VAL322 4.8 24.9 1.0
CD1 A:LEU345 4.8 28.0 1.0
CB A:ALA321 4.8 31.2 1.0
O A:VAL322 4.9 25.8 1.0
CG A:FTR326 5.0 23.2 1.0
CD A:LYS325 5.0 34.8 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: Sun Dec 13 13:43:00 2020

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