Zinc 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:

Fluorine (F) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 1 in 6yyz

Go back to Zinc Binding Sites List in 6yyz
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn401

b:21.8
occ:1.00
ND1 A:HIS349 2.1 19.4 1.0
SG A:CYS323 2.3 21.6 1.0
SG A:CYS318 2.3 24.4 1.0
SG A:CYS320 2.3 25.2 1.0
CE1 A:HIS349 2.9 19.9 1.0
HE1 A:HIS349 3.0 23.9 1.0
HB2 A:CYS323 3.0 28.3 1.0
HB3 A:CYS318 3.0 30.1 1.0
HB3 A:CYS320 3.2 32.8 1.0
CB A:CYS318 3.2 25.1 1.0
CB A:CYS323 3.3 23.6 1.0
CG A:HIS349 3.3 19.9 1.0
H A:CYS323 3.3 28.9 1.0
HB2 A:HIS349 3.4 25.9 1.0
CB A:CYS320 3.4 27.3 1.0
H A:CYS320 3.4 36.2 1.0
HA A:HIS349 3.6 27.0 1.0
HB2 A:CYS318 3.6 30.1 1.0
CB A:HIS349 3.7 21.6 1.0
HB A:VAL322 3.9 31.3 1.0
N A:CYS323 3.9 24.1 1.0
HB3 A:CYS323 4.0 28.3 1.0
N A:CYS320 4.1 30.2 1.0
NE2 A:HIS349 4.1 19.8 1.0
HB2 A:LEU314 4.1 21.9 1.0
HB2 A:CYS320 4.1 32.8 1.0
CA A:HIS349 4.1 22.5 1.0
CA A:CYS323 4.2 24.6 1.0
CA A:CYS320 4.2 28.7 1.0
CD2 A:HIS349 4.3 19.7 1.0
HE22 A:GLN356 4.5 36.2 1.0
HB3 A:ASP315 4.5 27.5 1.0
H A:ASP315 4.5 24.1 1.0
HD12 A:LEU314 4.5 23.8 1.0
HB3 A:ALA352 4.5 32.5 1.0
O A:HIS349 4.6 22.6 1.0
CA A:CYS318 4.6 26.9 1.0
HA A:CYS323 4.6 29.5 1.0
HB3 A:HIS349 4.6 25.9 1.0
C A:CYS320 4.7 29.4 1.0
O A:CYS320 4.7 29.6 1.0
C A:CYS318 4.7 28.6 1.0
C A:HIS349 4.8 22.7 1.0
H A:VAL322 4.8 33.1 1.0
CB A:VAL322 4.9 26.1 1.0
HE2 A:HIS349 4.9 23.8 1.0
O A:CYS318 4.9 28.1 1.0
C A:VAL322 5.0 24.9 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: Wed Dec 16 13:19:19 2020

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