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Chlorine 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:

Fluorine (F) 4 atoms
Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine was 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:

Chlorine binding site 1 out of 1 in 6yhd

Go back to Chlorine Binding Sites List in 6yhd
Chlorine binding site 1 out of 1 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 Chlorine with other atoms in the Cl 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:Cl404

b:18.0
occ:0.78
 HH12 A:ARG289 2.4 21.1 1.0
O A:HOH750 2.7 36.1 1.0
HG1 A:THR285 3.0 18.4 1.0
OG1 A:THR285 3.1 15.3 1.0
O A:HOH541 3.1 18.1 1.0
HB A:VAL282 3.1 19.8 1.0
HB A:THR285 3.1 18.3 1.0
HH22 A:ARG289 3.1 23.9 1.0
HB2 A:ARG286 3.2 19.7 0.6
NH1 A:ARG289 3.3 17.6 1.0
HB2 A:ARG286 3.3 21.6 0.4
HD2 A:LYS52 3.4 21.6 1.0
H A:ARG286 3.5 18.7 0.4
H A:ARG286 3.6 17.9 0.6
CB A:THR285 3.6 15.2 1.0
HE2 A:LYS52 3.6 24.0 1.0
O A:HOH798 3.8 36.2 1.0
N A:ARG286 3.8 15.6 0.4
N A:ARG286 3.8 14.9 0.6
HH11 A:ARG289 3.8 21.1 1.0
HG12 A:VAL282 3.8 22.6 1.0
NH2 A:ARG289 3.8 19.9 1.0
O A:HOH755 3.9 26.5 1.0
HG3 A:LYS52 3.9 19.1 1.0
HA A:ARG286 4.0 19.7 0.4
CB A:VAL282 4.0 16.5 1.0
HA A:ARG286 4.0 18.5 0.6
CZ A:ARG289 4.0 18.4 1.0
CB A:ARG286 4.1 16.4 0.6
HB2 A:LYS52 4.1 17.7 1.0
HG11 A:VAL282 4.1 22.6 1.0
CB A:ARG286 4.1 18.0 0.4
CD A:LYS52 4.1 18.0 1.0
CG1 A:VAL282 4.2 18.8 1.0
CA A:ARG286 4.2 16.4 0.4
CA A:ARG286 4.2 15.4 0.6
HE A:ARG286 4.2 29.6 0.4
CE A:LYS52 4.3 20.0 1.0
HA A:VAL282 4.3 18.1 1.0
C A:THR285 4.3 15.1 1.0
O A:VAL282 4.3 15.4 1.0
CG A:LYS52 4.4 15.9 1.0
HE3 A:LYS52 4.5 24.0 1.0
CA A:THR285 4.6 15.3 1.0
HG21 A:THR285 4.6 19.6 1.0
HH21 A:ARG289 4.6 23.9 1.0
HB3 A:ARG286 4.6 19.7 0.6
HB3 A:ARG286 4.6 21.6 0.4
CA A:VAL282 4.7 15.1 1.0
HD3 A:ARG286 4.7 24.3 0.6
CG2 A:THR285 4.7 16.3 1.0
HB A:VAL45 4.7 18.0 1.0
CB A:LYS52 4.8 14.8 1.0
H A:LYS52 4.8 16.4 1.0
HH21 A:ARG286 4.8 32.7 0.4
NE A:ARG286 4.9 24.7 0.4
HG3 A:ARG286 4.9 23.7 0.4
HG3 A:ARG286 4.9 21.3 0.6
HG12 A:VAL45 5.0 19.2 1.0
O A:HOH642 5.0 16.1 1.0
HD3 A:LYS52 5.0 21.6 1.0
O A:VAL45 5.0 16.2 1.0
C A:VAL282 5.0 14.8 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: Sat Jul 12 22:06:04 2025

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