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Zinc in PDB 1it8: Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0

Enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0

All present enzymatic activity of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0:
2.4.2.29;

Protein crystallography data

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0, PDB code: 1it8 was solved by R.Ishitani, O.Nureki, S.Fukai, T.Kijimoto, N.Nameki, M.Watanabe, H.Kondo, M.Sekine, N.Okada, S.Nishimura, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.87 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.467, 100.467, 366.168, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 27.8

Other elements in 1it8:

The structure of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 (pdb code 1it8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0, PDB code: 1it8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1it8

Go back to Zinc Binding Sites List in 1it8
Zinc binding site 1 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn600

b:30.9
occ:1.00
 ND1 A:HIS307 2.1 15.4 1.0
SG A:CYS284 2.3 30.1 1.0
SG A:CYS281 2.4 21.3 1.0
SG A:CYS279 2.4 18.8 1.0
CE1 A:HIS307 2.8 13.8 1.0
CB A:CYS284 3.2 27.2 1.0
CG A:HIS307 3.2 16.2 1.0
CB A:CYS279 3.3 17.9 1.0
CB A:CYS281 3.4 20.4 1.0
CB A:HIS307 3.7 17.0 1.0
N A:CYS284 4.0 26.5 1.0
NE2 A:HIS307 4.0 14.9 1.0
OH A:TYR262 4.0 13.6 1.0
N A:CYS281 4.1 20.0 1.0
CD2 A:HIS307 4.2 16.1 1.0
CA A:CYS284 4.2 26.7 1.0
CA A:HIS307 4.3 16.9 1.0
CA A:CYS281 4.3 20.6 1.0
CA A:CYS279 4.6 18.8 1.0
CZ A:TYR262 4.7 11.6 1.0
CE1 A:TYR262 4.7 13.1 1.0
O A:HIS307 4.8 18.1 1.0
C A:CYS279 4.8 18.3 1.0
N A:SER280 4.8 18.4 1.0
CB A:VAL283 4.8 24.0 1.0
C A:HIS307 4.9 17.0 1.0
C A:CYS281 4.9 20.4 1.0
CG2 A:VAL311 4.9 19.7 1.0

Zinc binding site 2 out of 2 in 1it8

Go back to Zinc Binding Sites List in 1it8
Zinc binding site 2 out of 2 in the Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Archaeosine Trna-Guanine Transglycosylase From Pyrococcus Horikoshii Complexed with Archaeosine Precursor, PREQ0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn600

b:26.4
occ:1.00
 ND1 B:HIS307 2.1 15.7 1.0
SG B:CYS284 2.3 27.6 1.0
SG B:CYS281 2.4 23.9 1.0
SG B:CYS279 2.4 25.1 1.0
CE1 B:HIS307 2.9 14.6 1.0
CB B:CYS281 3.1 20.7 1.0
CB B:CYS284 3.3 27.6 1.0
CB B:CYS279 3.3 23.4 1.0
CG B:HIS307 3.3 15.8 1.0
CB B:HIS307 3.8 14.6 1.0
N B:CYS281 3.9 20.2 1.0
N B:CYS284 4.0 27.4 1.0
CA B:CYS281 4.1 22.3 1.0
NE2 B:HIS307 4.1 15.3 1.0
OH B:TYR262 4.1 20.5 1.0
CA B:HIS307 4.2 17.2 1.0
CA B:CYS284 4.3 27.5 1.0
CD2 B:HIS307 4.3 15.1 1.0
O B:HIS307 4.6 17.0 1.0
CA B:CYS279 4.6 23.6 1.0
CE1 B:TYR262 4.7 18.0 1.0
CZ B:TYR262 4.7 19.2 1.0
C B:HIS307 4.7 17.4 1.0
C B:CYS279 4.8 23.3 1.0
C B:CYS281 4.8 23.8 1.0
N B:SER280 4.9 22.1 1.0
O B:CYS281 4.9 23.5 1.0
CG2 B:VAL311 4.9 20.6 1.0
CB B:VAL283 5.0 27.2 1.0

Reference:

R.Ishitani, O.Nureki, S.Fukai, T.Kijimoto, N.Nameki, M.Watanabe, H.Kondo, M.Sekine, N.Okada, S.Nishimura, S.Yokoyama. Crystal Structure of Archaeosine Trna-Guanine Transglycosylase. J.Mol.Biol. V. 318 665 2002.
ISSN: ISSN 0022-2836
PubMed: 12054814
DOI: 10.1016/S0022-2836(02)00090-6
Page generated: Sun Oct 13 03:12:17 2024

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