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Zinc in PDB 5j9o: Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine

Enzymatic activity of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine

All present enzymatic activity of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine:
2.4.2.29;

Protein crystallography data

The structure of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine, PDB code: 5j9o 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) 19.45 / 1.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.102, 63.798, 70.955, 90.00, 92.95, 90.00
R / Rfree (%) 14 / 16.9

Other elements in 5j9o:

The structure of Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine (pdb code 5j9o). 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) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine, PDB code: 5j9o:

Zinc binding site 1 out of 1 in 5j9o

Go back to Zinc Binding Sites List in 5j9o
Zinc binding site 1 out of 1 in the Trna Guanine Transglycosylase (Tgt) in Co-Crystallized Complex with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine


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 with 1- (2-(Methylamino)-1H-Benzo[D]Imidazol-6-Yl)Guanidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:18.8
occ:1.00
ND1 A:HIS349 2.1 17.6 1.0
SG A:CYS323 2.3 18.9 1.0
SG A:CYS318 2.3 20.8 1.0
SG A:CYS320 2.3 17.9 1.0
CE1 A:HIS349 3.0 18.4 1.0
CB A:CYS318 3.2 21.4 1.0
CG A:HIS349 3.2 17.0 1.0
CB A:CYS323 3.3 18.5 1.0
CB A:CYS320 3.4 19.1 1.0
CB A:HIS349 3.7 16.5 1.0
N A:CYS323 3.9 18.4 1.0
CA A:HIS349 4.1 15.8 1.0
N A:CYS320 4.1 20.8 1.0
NE2 A:HIS349 4.1 17.9 1.0
CA A:CYS323 4.2 18.9 1.0
CA A:CYS320 4.2 19.4 1.0
CD2 A:HIS349 4.3 17.3 1.0
O A:HIS349 4.5 17.1 1.0
CA A:CYS318 4.6 22.8 1.0
O A:CYS320 4.6 19.1 1.0
C A:CYS320 4.7 19.8 1.0
C A:CYS318 4.7 23.8 1.0
C A:HIS349 4.8 16.2 1.0
CB A:VAL322 4.8 17.4 1.0
O A:CYS318 4.9 24.5 1.0
C A:VAL322 4.9 18.3 1.0

Reference:

F.R.Ehrmann, C.Hohn, A.Heine, F.Diederich, G.Klebe. Benzimidazole-Based Inhibitors As A Novel Scaffold to Inhibit Z.Mobilis Tgt and Study Protein Flexibility and the Contributions of Active Site Residues to Binding Affinity of Lin-Benzopurines. To Be Published.
Page generated: Wed Dec 16 06:24:35 2020

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