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Zinc in PDB 5lpq: Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) 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) in Co-Crystallized Complex (Space Group P21) 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) in Co-Crystallized Complex (Space Group P21) 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) in Co-Crystallized Complex (Space Group P21) 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: 5lpq 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) 43.67 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.900, 78.851, 84.943, 90.00, 109.72, 90.00
R / Rfree (%) 22.7 / 26.2

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-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 5lpq). 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-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: 5lpq:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5lpq

Go back to Zinc Binding Sites List in 5lpq
Zinc binding site 1 out of 2 in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) 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 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-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:Zn401

b:26.8
occ:1.00
 ND1 A:HIS349 2.0 26.5 1.0
SG A:CYS318 2.2 29.5 1.0
SG A:CYS323 2.2 25.1 1.0
SG A:CYS320 2.3 28.6 1.0
CE1 A:HIS349 2.9 25.3 1.0
CB A:CYS318 3.2 32.4 1.0
CG A:HIS349 3.2 25.7 1.0
CB A:CYS323 3.3 28.5 1.0
CB A:CYS320 3.5 27.1 1.0
CB A:HIS349 3.6 27.1 1.0
N A:CYS323 3.9 29.8 1.0
NE2 A:HIS349 4.0 25.1 1.0
CA A:HIS349 4.1 26.5 1.0
CD2 A:HIS349 4.2 24.0 1.0
CA A:CYS323 4.2 31.0 1.0
N A:CYS320 4.2 29.6 1.0
CA A:CYS320 4.4 29.7 1.0
O A:HIS349 4.5 24.6 1.0
CA A:CYS318 4.5 34.1 1.0
C A:HIS349 4.7 25.5 1.0
C A:CYS318 4.7 36.1 1.0
CB A:VAL322 4.8 26.1 1.0
C A:CYS320 4.8 33.3 1.0
O A:CYS320 4.9 36.4 1.0
C A:VAL322 4.9 29.6 1.0

Zinc binding site 2 out of 2 in 5lpq

Go back to Zinc Binding Sites List in 5lpq
Zinc binding site 2 out of 2 in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex (Space Group P21) 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 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-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
B:Zn401

b:25.8
occ:1.00
 ND1 B:HIS349 2.1 25.9 1.0
SG B:CYS318 2.2 25.5 1.0
SG B:CYS323 2.2 26.0 1.0
SG B:CYS320 2.2 22.2 1.0
CE1 B:HIS349 2.9 26.4 1.0
CG B:HIS349 3.2 22.9 1.0
CB B:CYS318 3.2 29.7 1.0
CB B:CYS323 3.4 30.5 1.0
CB B:CYS320 3.5 26.0 1.0
CB B:HIS349 3.6 22.6 1.0
N B:CYS323 3.9 28.0 1.0
CA B:HIS349 4.0 25.7 1.0
NE2 B:HIS349 4.1 23.7 1.0
CD2 B:HIS349 4.2 22.1 1.0
N B:CYS320 4.2 33.8 1.0
CA B:CYS323 4.3 29.1 1.0
CA B:CYS320 4.4 30.8 1.0
O B:HIS349 4.5 29.9 1.0
CA B:CYS318 4.6 35.1 1.0
C B:HIS349 4.7 26.3 1.0
C B:CYS318 4.8 37.9 1.0
CB B:VAL322 4.8 24.5 1.0
C B:CYS320 4.8 30.7 1.0
O B:CYS320 4.9 31.7 1.0
C B:VAL322 4.9 28.7 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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