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Zinc in PDB 4dy1: Trna-Guanine Transglycosylase F92C C158S C281S Mutant

Enzymatic activity of Trna-Guanine Transglycosylase F92C C158S C281S Mutant

All present enzymatic activity of Trna-Guanine Transglycosylase F92C C158S C281S Mutant:
2.4.2.29;

Protein crystallography data

The structure of Trna-Guanine Transglycosylase F92C C158S C281S Mutant, PDB code: 4dy1 was solved by S.Jakobi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.16 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.828, 64.601, 71.092, 90.00, 96.39, 90.00
R / Rfree (%) 16.6 / 22

Other elements in 4dy1:

The structure of Trna-Guanine Transglycosylase F92C C158S C281S Mutant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Trna-Guanine Transglycosylase F92C C158S C281S Mutant (pdb code 4dy1). 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 F92C C158S C281S Mutant, PDB code: 4dy1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4dy1

Go back to Zinc Binding Sites List in 4dy1
Zinc binding site 1 out of 2 in the Trna-Guanine Transglycosylase F92C C158S C281S Mutant


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 F92C C158S C281S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:14.2
occ:1.00
ND1 A:HIS349 2.2 10.4 1.0
SG A:CYS323 2.3 14.6 1.0
SG A:CYS318 2.4 14.1 1.0
SG A:CYS320 2.4 12.7 1.0
CE1 A:HIS349 3.0 16.7 1.0
CB A:CYS318 3.3 12.8 1.0
CG A:HIS349 3.3 9.0 1.0
CB A:CYS323 3.3 11.8 1.0
CB A:CYS320 3.4 10.1 1.0
CB A:HIS349 3.7 7.9 1.0
N A:CYS323 3.9 9.5 1.0
N A:CYS320 4.0 10.1 1.0
CA A:CYS320 4.2 13.2 1.0
CA A:HIS349 4.2 8.4 1.0
CA A:CYS323 4.2 13.2 1.0
NE2 A:HIS349 4.2 11.0 1.0
CD2 A:HIS349 4.4 9.8 1.0
O A:HIS349 4.5 9.1 1.0
CA A:CYS318 4.6 12.8 1.0
O A:CYS320 4.6 13.8 1.0
C A:CYS320 4.6 17.0 1.0
C A:CYS318 4.7 16.3 1.0
CB A:VAL322 4.8 11.5 1.0
C A:HIS349 4.8 9.3 1.0
C A:VAL322 4.9 11.8 1.0
O A:CYS318 5.0 17.2 1.0

Zinc binding site 2 out of 2 in 4dy1

Go back to Zinc Binding Sites List in 4dy1
Zinc binding site 2 out of 2 in the Trna-Guanine Transglycosylase F92C C158S C281S Mutant


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 F92C C158S C281S Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:28.5
occ:1.00
NE2 A:HIS73 2.2 28.7 1.0
CL A:CL403 2.2 29.9 1.0
CE1 A:HIS73 3.2 29.4 1.0
CD2 A:HIS73 3.3 23.8 1.0
ND1 A:HIS73 4.3 30.6 1.0
CG A:HIS73 4.4 26.6 1.0
NZ A:LYS52 4.5 31.2 1.0
O A:ARG77 4.8 25.0 0.5
CD2 A:LEU74 4.8 17.6 1.0
CG2 A:THR47 4.9 31.8 1.0
O A:ARG77 4.9 25.0 0.5

Reference:

S.Jakobi, P.T.Nguyen, F.Debaene, S.Cianferani, K.Reuter, G.Klebe. What Glues A Homodimer Together: Systematic Analysis of the Stabilizing Effect of An Aromatic Hot Spot in the Protein-Protein Interface of the Trna-Modifying Enzyme Tgt. Acs Chem.Biol. V. 10 1897 2015.
ISSN: ISSN 1554-8929
PubMed: 25951081
DOI: 10.1021/ACSCHEMBIO.5B00028
Page generated: Wed Dec 16 05:15:11 2020

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