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Fluorine in PDB 6yhe: Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 6-Amino-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-1H-Imidazo[4,5-G]Quinazolin-8(7H)-One, PDB code: 6yhe 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) 42.63 / 1.54
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 84.657, 64.820, 71.808, 90.00, 93.96, 90.00
R / Rfree (%) 14.9 / 18.3

Other elements in 6yhe:

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

Fluorine binding site 1 out of 4 in 6yhe

Go back to Fluorine Binding Sites List in 6yhe
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-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-1H-Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F95

b:32.9
occ:1.00
 F A:FTR95 0.0 32.9 1.0
CZ3 A:FTR95 1.4 29.2 1.0
CH2 A:FTR95 2.4 28.3 1.0
CE3 A:FTR95 2.4 27.1 1.0
HH2 A:FTR95 2.5 34.0 1.0
HE3 A:FTR95 2.6 32.5 1.0
CZ2 A:FTR95 3.6 25.9 1.0
CD2 A:FTR95 3.6 24.3 1.0
CE2 A:FTR95 4.1 24.0 1.0
HH11 A:ARG97 4.2 53.1 1.0
HZ2 A:FTR95 4.4 31.1 1.0
HD3 A:ARG97 4.5 42.7 1.0
HG21 A:ILE67 4.6 26.6 1.0
HB3 A:ALA64 4.7 30.9 1.0
NH1 A:ARG97 4.7 44.2 1.0
HG23 A:ILE67 4.8 26.6 1.0
O A:ALA64 4.8 26.4 1.0
HH12 A:ARG97 4.8 53.1 1.0
CG A:FTR95 5.0 24.3 1.0

Fluorine binding site 2 out of 4 in 6yhe

Go back to Fluorine Binding Sites List in 6yhe
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-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-1H-Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F178

b:27.1
occ:1.00
 F A:FTR178 0.0 27.1 1.0
CZ3 A:FTR178 1.4 25.2 1.0
CE3 A:FTR178 2.4 22.7 1.0
CH2 A:FTR178 2.4 24.0 1.0
HH2 A:FTR178 2.5 28.9 1.0
HE3 A:FTR178 2.6 27.2 1.0
HB2 A:GLU157 2.7 41.4 1.0
O A:HOH628 3.2 37.5 1.0
O A:ASP156 3.2 24.5 1.0
HE2 A:PHE155 3.2 29.5 1.0
C A:ASP156 3.4 24.8 1.0
HA A:GLU157 3.4 36.9 1.0
CE2 A:PHE155 3.5 24.6 1.0
N A:GLU157 3.5 27.0 1.0
CB A:GLU157 3.5 34.5 1.0
CD2 A:FTR178 3.6 20.9 1.0
CZ2 A:FTR178 3.7 23.1 1.0
CA A:GLU157 3.7 30.7 1.0
CZ A:PHE155 3.9 25.8 1.0
H A:GLU157 3.9 32.4 1.0
HG3 A:GLU157 4.0 46.6 1.0
HZ A:PHE155 4.0 31.0 1.0
CD2 A:PHE155 4.1 22.7 1.0
CE2 A:FTR178 4.1 22.5 1.0
HG23 A:VAL122 4.1 46.7 1.0
HA A:ASP156 4.2 27.1 1.0
HD2 A:PHE155 4.2 27.2 1.0
HB3 A:GLU157 4.2 41.4 1.0
CG A:GLU157 4.3 38.8 1.0
CA A:ASP156 4.3 22.5 1.0
HG21 A:VAL122 4.3 46.7 1.0
OE1 A:GLU157 4.4 42.8 1.0
HZ2 A:FTR178 4.4 27.7 1.0
CG2 A:VAL122 4.6 38.9 1.0
HG22 A:VAL122 4.6 46.7 1.0
N A:ASP156 4.6 21.0 1.0
HD3 A:ARG174 4.7 36.7 1.0
HG2 A:ARG174 4.7 33.1 1.0
CD A:GLU157 4.8 41.8 1.0
CE1 A:PHE155 4.8 25.7 1.0
H A:ASP156 4.9 25.2 1.0
CG A:PHE155 4.9 21.1 1.0
CG A:FTR178 5.0 20.3 1.0
HA3 A:GLY105 5.0 44.3 1.0

Fluorine binding site 3 out of 4 in 6yhe

Go back to Fluorine Binding Sites List in 6yhe
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-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-1H-Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F296

b:41.6
occ:1.00
 F A:FTR296 0.0 41.6 1.0
CZ3 A:FTR296 1.4 39.1 1.0
CH2 A:FTR296 2.4 38.5 1.0
CE3 A:FTR296 2.4 35.1 1.0
HH2 A:FTR296 2.5 46.2 1.0
HE3 A:FTR296 2.6 42.1 1.0
HD13 A:LEU357 2.6 30.4 1.0
HD1 A:PHE377 2.6 36.7 1.0
HZ A:PHE373 2.7 37.3 1.0
HD12 A:LEU357 2.9 30.4 1.0
CD1 A:LEU357 3.2 25.3 1.0
HE1 A:PHE377 3.3 37.1 1.0
CD1 A:PHE377 3.3 30.6 1.0
CZ A:PHE373 3.5 31.1 1.0
HA A:LEU357 3.6 24.6 1.0
HE1 A:PHE373 3.6 37.5 1.0
CE1 A:PHE377 3.6 30.9 1.0
CZ2 A:FTR296 3.6 37.5 1.0
CD2 A:FTR296 3.6 32.9 1.0
HD11 A:LEU357 3.8 30.4 1.0
HB2 A:LEU357 3.9 27.7 1.0
CE1 A:PHE373 3.9 31.3 1.0
CE2 A:FTR296 4.1 34.3 1.0
HB2 A:PHE377 4.2 35.8 1.0
CB A:LEU357 4.4 23.1 1.0
CA A:LEU357 4.4 20.5 1.0
HZ2 A:FTR296 4.4 45.0 1.0
CG A:LEU357 4.4 25.0 1.0
CG A:PHE377 4.4 30.0 1.0
HB2 A:LYS360 4.4 27.2 1.0
HZ A:PHE353 4.4 37.0 1.0
CE2 A:PHE373 4.6 29.0 1.0
HE2 A:PHE373 4.7 34.8 1.0
O A:HOH726 4.7 43.1 1.0
O A:HOH611 4.7 31.5 1.0
CB A:PHE377 4.8 29.9 1.0
CZ A:PHE377 4.9 30.8 1.0
CZ A:PHE353 4.9 30.8 1.0
HB3 A:LYS360 5.0 27.2 1.0
CG A:FTR296 5.0 32.0 1.0

Fluorine binding site 4 out of 4 in 6yhe

Go back to Fluorine Binding Sites List in 6yhe
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-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-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-4-(2-((3AR,4R,6R,6AR)-6-Methoxy- 2,2-Dimethyltetrahydrofuro[3,4-D][1,3]Dioxol-4-Yl)Ethyl)-2- (Methylamino)-1H-Imidazo[4,5-G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F326

b:39.8
occ:1.00
 F A:FTR326 0.0 39.8 1.0
CZ3 A:FTR326 1.4 37.7 1.0
CE3 A:FTR326 2.4 35.8 1.0
CH2 A:FTR326 2.4 37.9 1.0
HH2 A:FTR326 2.5 45.5 1.0
HE3 A:FTR326 2.6 42.9 1.0
HD22 A:LEU345 2.7 36.4 1.0
HA A:VAL322 2.9 43.4 1.0
HD21 A:LEU345 3.0 36.4 1.0
HG22 A:VAL322 3.2 41.9 1.0
CD2 A:LEU345 3.3 30.3 1.0
CD2 A:FTR326 3.6 34.3 1.0
CZ2 A:FTR326 3.7 36.3 1.0
HD23 A:LEU345 3.7 36.4 1.0
CA A:VAL322 3.8 36.1 1.0
HB3 A:LYS325 3.9 46.2 1.0
O A:ALA321 3.9 38.5 1.0
N A:VAL322 4.1 36.4 1.0
CG2 A:VAL322 4.1 34.9 1.0
CE2 A:FTR326 4.1 34.8 1.0
C A:ALA321 4.1 38.0 1.0
HG13 A:VAL322 4.2 44.1 1.0
HG23 A:VAL322 4.4 41.9 1.0
HB1 A:ALA321 4.4 47.6 1.0
HZ2 A:FTR326 4.4 43.6 1.0
CB A:VAL322 4.4 35.6 1.0
HD13 A:LEU345 4.4 35.1 1.0
HB3 A:ALA321 4.6 47.6 1.0
HD11 A:LEU345 4.6 35.1 1.0
H A:VAL322 4.6 43.7 1.0
CG A:LEU345 4.6 28.2 1.0
CD1 A:LEU345 4.8 29.3 1.0
CB A:LYS325 4.8 38.5 1.0
CG1 A:VAL322 4.8 36.8 1.0
HG21 A:VAL322 4.8 41.9 1.0
C A:VAL322 4.9 36.4 1.0
CB A:ALA321 4.9 39.7 1.0
O A:VAL322 4.9 36.3 1.0
HB2 A:LYS325 5.0 46.2 1.0
CG A:FTR326 5.0 33.5 1.0
HB3 A:FTR326 5.0 39.7 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: Fri Aug 2 04:42:19 2024

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