Atomistry » Fluorine » PDB 6yhc-6z4b » 6yhe
Atomistry »
  Fluorine »
    PDB 6yhc-6z4b »
      6yhe »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy