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Zinc in PDB 5lpt: Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One

Enzymatic activity of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One

All present enzymatic activity of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One:
2.4.2.29;

Protein crystallography data

The structure of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One, PDB code: 5lpt was solved by F.R.Ehrmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.51 / 2.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.745, 78.866, 84.891, 90.00, 108.72, 90.00
R / Rfree (%) 20.1 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One (pdb code 5lpt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One, PDB code: 5lpt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5lpt

Go back to Zinc Binding Sites List in 5lpt
Zinc binding site 1 out of 2 in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-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) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.2
occ:1.00
 ND1 A:HIS349 2.0 29.1 1.0
SG A:CYS323 2.2 28.1 1.0
SG A:CYS320 2.2 28.3 1.0
SG A:CYS318 2.3 24.9 1.0
CE1 A:HIS349 2.9 30.5 1.0
CB A:CYS323 3.1 27.9 1.0
CG A:HIS349 3.2 29.1 1.0
CB A:CYS318 3.3 27.4 1.0
CB A:CYS320 3.5 26.9 1.0
CB A:HIS349 3.6 27.8 1.0
N A:CYS323 3.8 28.3 1.0
CA A:CYS323 4.0 27.9 1.0
CA A:HIS349 4.1 27.7 1.0
NE2 A:HIS349 4.1 30.6 1.0
CD2 A:HIS349 4.2 29.6 1.0
N A:CYS320 4.3 30.0 1.0
CA A:CYS320 4.4 28.4 1.0
O A:HIS349 4.5 27.3 1.0
CA A:CYS318 4.6 28.2 1.0
CB A:VAL322 4.7 24.8 1.0
C A:HIS349 4.7 26.0 1.0
O A:CYS320 4.7 28.7 1.0
C A:CYS320 4.8 28.5 1.0
C A:CYS318 4.8 29.8 1.0
C A:VAL322 4.8 27.9 1.0

Zinc binding site 2 out of 2 in 5lpt

Go back to Zinc Binding Sites List in 5lpt
Zinc binding site 2 out of 2 in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) with 6-Amino-2-(Methylamino)-4-(2-((2R,3R,4S,5R,6S)-3,4,5, 6-Tetramethoxytetrahydro-2H-Pyran-2-Yl)Ethyl)-1H-Imidazo[4,5- G]Quinazolin-8(7H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:23.7
occ:1.00
 ND1 B:HIS349 2.1 23.4 1.0
SG B:CYS323 2.2 32.7 1.0
SG B:CYS318 2.3 27.2 1.0
SG B:CYS320 2.3 24.0 1.0
CE1 B:HIS349 2.9 24.9 1.0
CG B:HIS349 3.2 22.1 1.0
CB B:CYS318 3.2 28.9 1.0
CB B:CYS323 3.2 32.0 1.0
CB B:CYS320 3.5 25.0 1.0
CB B:HIS349 3.6 20.9 1.0
N B:CYS323 3.9 29.7 1.0
NE2 B:HIS349 4.1 25.2 1.0
CA B:HIS349 4.1 23.3 1.0
CA B:CYS323 4.1 30.9 1.0
N B:CYS320 4.2 29.1 1.0
CD2 B:HIS349 4.2 23.6 1.0
CA B:CYS320 4.3 27.1 1.0
CA B:CYS318 4.5 30.7 1.0
O B:HIS349 4.6 19.1 1.0
C B:CYS318 4.7 32.2 1.0
C B:HIS349 4.8 21.4 1.0
C B:CYS320 4.8 28.9 1.0
O B:CYS320 4.8 30.0 1.0
CB B:VAL322 4.8 28.9 1.0
C B:VAL322 5.0 30.0 1.0
O B:HOH539 5.0 27.7 1.0

Reference:

F.R.Ehrmann, T.Botzanowski, T.Pfaffender, A.Heine, F.Diederich, S.Sanglier-Cianferani, G.Klebe. Carbohydrate-Based Inhibitors Targeting the Ribose-34 Pocket of Z.Mobilis Tgt and Changing the Oligomeric State of the Homodimer To Be Published.
Page generated: Sun Oct 27 21:14:31 2024

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