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Fluorine in PDB 6yh2: Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 2-(Methylamino)-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 2-(Methylamino)-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 2-(Methylamino)-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 2-(Methylamino)-1,7-Dihydro-8H- Imidazo[4,5-G]Quinazolin-8-One, PDB code: 6yh2 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) 45.10 / 1.19
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.724, 65.338, 70.909, 90.00, 96.13, 90.00
R / Rfree (%) 11.9 / 13.5

Other elements in 6yh2:

The structure of Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 2-(Methylamino)-1,7-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 2-(Methylamino)-1,7-Dihydro-8H- Imidazo[4,5-G]Quinazolin-8-One (pdb code 6yh2). 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 2-(Methylamino)-1,7-Dihydro-8H- Imidazo[4,5-G]Quinazolin-8-One, PDB code: 6yh2:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6yh2

Go back to Fluorine Binding Sites List in 6yh2
Fluorine binding site 1 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 2-(Methylamino)-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 2-(Methylamino)-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:14.5
occ:1.00
 F A:FTR95 0.0 14.5 1.0
CZ3 A:FTR95 1.4 12.6 1.0
CE3 A:FTR95 2.4 12.5 1.0
CH2 A:FTR95 2.4 11.9 1.0
HH2 A:FTR95 2.5 14.3 1.0
HB2 A:ARG60 2.5 15.6 1.0
HE3 A:FTR95 2.6 15.0 1.0
HG12 A:VAL59 2.7 16.0 1.0
HB A:VAL59 2.7 14.8 1.0
H A:ARG60 2.8 13.6 1.0
N A:ARG60 2.9 11.3 1.0
HA A:ARG60 2.9 14.4 1.0
O A:PRO56 3.2 12.6 1.0
CA A:ARG60 3.2 12.0 1.0
CB A:ARG60 3.3 13.0 1.0
CG1 A:VAL59 3.3 13.3 1.0
CB A:VAL59 3.4 12.3 1.0
C A:VAL59 3.4 11.8 1.0
HG11 A:VAL59 3.5 16.0 1.0
CD2 A:FTR95 3.6 11.5 1.0
CZ2 A:FTR95 3.6 11.5 1.0
HB3 A:ARG60 3.8 15.6 1.0
HB3 A:ALA64 3.9 14.9 1.0
CA A:VAL59 3.9 11.8 1.0
HD3 A:ARG60 3.9 15.9 1.0
O A:VAL59 4.0 12.5 1.0
CE2 A:FTR95 4.1 11.3 1.0
HG13 A:VAL59 4.2 16.0 1.0
C A:PRO56 4.2 12.3 1.0
HA A:PRO56 4.2 14.9 1.0
C1 A:GOL402 4.3 25.5 1.0
HD2 A:ARG60 4.3 15.9 1.0
O A:ALA64 4.3 11.8 1.0
HZ2 A:FTR95 4.4 13.8 1.0
C3 A:GOL402 4.4 26.0 1.0
CG A:ARG60 4.4 12.4 1.0
CD A:ARG60 4.4 13.3 1.0
HB3 A:PRO56 4.5 17.3 1.0
HG23 A:ILE67 4.5 13.9 1.0
HD2 A:ARG97 4.5 19.0 1.0
N A:VAL59 4.6 11.6 1.0
CA A:PRO56 4.7 12.4 1.0
CG2 A:VAL59 4.7 13.5 1.0
C A:ARG60 4.7 12.1 1.0
H A:VAL59 4.7 13.9 1.0
HG21 A:VAL59 4.7 16.2 1.0
HA A:VAL59 4.7 14.2 1.0
HG2 A:ARG60 4.7 14.9 1.0
CB A:ALA64 4.8 12.4 1.0
HG21 A:ILE67 4.8 13.9 1.0
HB1 A:ALA64 4.9 14.9 1.0
CG A:FTR95 5.0 11.9 1.0

Fluorine binding site 2 out of 4 in 6yh2

Go back to Fluorine Binding Sites List in 6yh2
Fluorine binding site 2 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 2-(Methylamino)-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 2-(Methylamino)-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:17.6
occ:1.00
 F A:FTR178 0.0 17.6 1.0
CZ3 A:FTR178 1.4 16.1 1.0
CH2 A:FTR178 2.4 16.2 1.0
CE3 A:FTR178 2.4 14.8 1.0
HH2 A:FTR178 2.5 19.4 1.0
HE3 A:FTR178 2.6 17.7 1.0
HB2 A:GLU157 2.6 22.5 1.0
O A:ASP156 3.0 14.6 1.0
O A:HOH729 3.1 22.9 1.0
HE2 A:PHE155 3.1 20.3 1.0
C A:ASP156 3.3 14.3 1.0
O A:HOH774 3.3 38.9 1.0
CB A:GLU157 3.4 18.7 1.0
HA A:GLU157 3.5 19.1 1.0
CE2 A:PHE155 3.5 16.9 1.0
N A:GLU157 3.6 15.1 1.0
CZ2 A:FTR178 3.6 15.6 1.0
CD2 A:FTR178 3.6 14.0 1.0
CA A:GLU157 3.7 15.9 1.0
HB3 A:GLU157 4.0 22.5 1.0
HG23 A:VAL122 4.0 26.3 0.7
HD2 A:PHE155 4.1 18.5 1.0
H A:GLU157 4.1 18.1 1.0
CD2 A:PHE155 4.1 15.4 1.0
CE2 A:FTR178 4.1 14.9 1.0
HA A:ASP156 4.1 16.0 1.0
OE1 A:GLU157 4.2 26.5 1.0
CZ A:PHE155 4.2 17.2 1.0
HG22 A:VAL122 4.3 26.3 0.7
HZ A:PHE155 4.3 20.6 1.0
CA A:ASP156 4.3 13.3 1.0
HG3 A:GLU157 4.3 26.5 1.0
HZ2 A:FTR178 4.4 18.7 1.0
CG A:GLU157 4.4 22.0 1.0
HG2 A:ARG174 4.5 20.3 1.0
CG2 A:VAL122 4.5 21.9 0.7
HD3 A:ARG174 4.6 24.2 1.0
HG21 A:VAL122 4.6 26.3 0.7
N A:ASP156 4.7 12.9 1.0
CD A:GLU157 4.7 24.0 1.0
CD A:GLN117 4.9 34.4 1.0
H A:ASP156 4.9 15.5 1.0
CG A:FTR178 5.0 13.5 1.0

Fluorine binding site 3 out of 4 in 6yh2

Go back to Fluorine Binding Sites List in 6yh2
Fluorine binding site 3 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 2-(Methylamino)-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 2-(Methylamino)-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:25.4
occ:1.00
 F A:FTR296 0.0 25.4 1.0
CZ3 A:FTR296 1.3 22.6 1.0
CE3 A:FTR296 2.4 19.3 1.0
CH2 A:FTR296 2.4 22.4 1.0
HH2 A:FTR296 2.5 26.9 1.0
HE3 A:FTR296 2.6 23.2 1.0
HD13 A:LEU357 2.6 17.6 1.0
HD1 A:PHE377 2.8 22.3 1.0
HE1 A:PHE377 2.8 23.3 1.0
HD12 A:LEU357 3.1 17.6 1.0
HZ A:PHE373 3.2 21.9 1.0
CD1 A:LEU357 3.3 14.7 1.0
HD2 A:LYS360 3.3 24.4 1.0
HA A:LEU357 3.3 14.2 1.0
CD1 A:PHE377 3.3 18.6 1.0
CE1 A:PHE377 3.3 19.4 1.0
HB2 A:LEU357 3.4 15.2 1.0
CD2 A:FTR296 3.6 17.9 1.0
CZ2 A:FTR296 3.6 21.7 1.0
HZ A:PHE353 3.9 22.8 1.0
HD11 A:LEU357 4.0 17.6 1.0
CB A:LEU357 4.0 12.7 1.0
CZ A:PHE373 4.1 18.2 1.0
CD A:LYS360 4.1 20.4 1.0
CA A:LEU357 4.1 11.9 1.0
HD3 A:LYS360 4.1 24.4 1.0
CE2 A:FTR296 4.1 19.3 1.0
HE3 A:LYS360 4.1 27.7 1.0
CG A:LEU357 4.2 13.6 1.0
HE1 A:PHE373 4.3 22.5 1.0
CZ A:PHE353 4.3 19.0 1.0
HZ2 A:FTR296 4.4 26.0 1.0
C3 A:GOL403 4.5 34.2 1.0
CG A:PHE377 4.6 17.2 1.0
CZ A:PHE377 4.6 19.4 1.0
CE1 A:PHE373 4.6 18.8 1.0
HB2 A:LYS360 4.6 17.9 1.0
CE A:LYS360 4.7 23.1 1.0
HD22 A:LEU357 4.7 18.3 1.0
HB2 A:PHE377 4.7 20.5 1.0
N A:LEU357 4.8 11.9 1.0
CE1 A:PHE353 4.8 19.2 1.0
HE1 A:PHE353 4.8 23.1 1.0
O A:HOH559 4.8 18.1 1.0
CE2 A:PHE353 4.9 17.6 1.0
HA A:FTR296 4.9 19.2 1.0
HE2 A:PHE353 4.9 21.2 1.0
HB3 A:LEU357 4.9 15.2 1.0
HZ A:PHE377 4.9 23.3 1.0
CG A:FTR296 5.0 17.2 1.0
H A:LEU357 5.0 14.3 1.0
HG A:LEU357 5.0 16.3 1.0

Fluorine binding site 4 out of 4 in 6yh2

Go back to Fluorine Binding Sites List in 6yh2
Fluorine binding site 4 out of 4 in the Trna-Guanine Transglycosylase (Tgt) Labeled with 5-Fluorotryptophan in Co-Crystallized Complex with 2-(Methylamino)-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 2-(Methylamino)-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:13.8
occ:1.00
 F A:FTR326 0.0 13.8 1.0
CZ3 A:FTR326 1.4 12.5 1.0
CH2 A:FTR326 2.4 12.8 1.0
CE3 A:FTR326 2.4 11.8 1.0
HH2 A:FTR326 2.5 15.4 1.0
HE3 A:FTR326 2.6 14.2 1.0
HA A:VAL322 2.6 14.1 1.0
HD22 A:LEU345 2.9 14.9 1.0
HD2 A:LYS325 3.1 28.4 1.0
HG22 A:VAL322 3.1 14.3 1.0
HD21 A:LEU345 3.2 14.9 1.0
HB2 A:LYS325 3.5 20.5 1.0
CD2 A:LEU345 3.5 12.4 1.0
CA A:VAL322 3.5 11.8 1.0
O A:ALA321 3.6 14.0 1.0
CD2 A:FTR326 3.6 11.6 1.0
CZ2 A:FTR326 3.6 13.0 1.0
N A:VAL322 3.7 12.4 1.0
C A:ALA321 3.8 12.9 1.0
CG2 A:VAL322 3.9 11.9 1.0
HD23 A:LEU345 3.9 14.9 1.0
HB1 A:ALA321 4.0 17.9 1.0
HG23 A:VAL322 4.0 14.3 1.0
CD A:LYS325 4.0 23.7 1.0
HG13 A:VAL322 4.1 14.5 1.0
CE2 A:FTR326 4.1 12.8 1.0
HB3 A:ALA321 4.1 17.9 1.0
CB A:VAL322 4.2 11.6 1.0
H A:VAL322 4.2 14.9 1.0
CB A:LYS325 4.3 17.1 1.0
HZ2 A:FTR326 4.4 15.6 1.0
CB A:ALA321 4.4 14.9 1.0
HD3 A:LYS325 4.5 28.4 1.0
C A:VAL322 4.6 12.2 1.0
HB3 A:LYS325 4.6 20.5 1.0
HD13 A:LEU345 4.6 14.9 1.0
CG1 A:VAL322 4.7 12.1 1.0
HG21 A:VAL322 4.7 14.3 1.0
CG A:LYS325 4.7 20.7 1.0
O A:VAL322 4.7 13.6 1.0
OE1 A:GLU348 4.7 12.6 1.0
CA A:ALA321 4.8 13.7 1.0
HD11 A:LEU345 4.8 14.9 1.0
CG A:LEU345 4.8 12.4 1.0
CE A:LYS325 4.8 26.2 1.0
HG3 A:LYS325 4.9 24.8 1.0
CG A:FTR326 5.0 11.9 1.0
CD1 A:LEU345 5.0 12.4 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: Fri Aug 2 04:35:07 2024

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