Zinc in PDB 1ww1: Crystal Structure of Trnase Z From Thermotoga Maritima

All present enzymatic activity of Crystal Structure of Trnase Z From Thermotoga Maritima:
3.1.26.11;

The structure of Crystal Structure of Trnase Z From Thermotoga Maritima, PDB code: 1ww1 was solved by R.Ishii, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative(Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.80 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.902, 73.642, 91.994, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.9

The binding sites of Zinc atom in the Crystal Structure of Trnase Z From Thermotoga Maritima (pdb code 1ww1). 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 Trnase Z From Thermotoga Maritima, PDB code: 1ww1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Trnase Z From Thermotoga Maritima


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 Trnase Z From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:0.3 occ:1.00 NE2 A:HIS244 3.0 54.4 1.0 O A:ALA9 3.1 74.7 1.0 OD1 A:ASP190 3.3 71.0 1.0 OD2 A:ASP52 3.5 50.3 1.0 CE1 A:HIS244 3.8 60.9 1.0 OD2 A:ASP190 4.0 75.9 1.0 CD2 A:HIS244 4.0 52.5 1.0 CG A:ASP190 4.1 69.6 1.0 NE2 A:HIS53 4.1 60.3 1.0 CD2 A:LEU10 4.1 43.9 1.0 C A:ALA9 4.3 60.7 1.0 CG A:ASP52 4.4 47.3 1.0 CE1 A:HIS222 4.5 88.0 1.0 OD1 A:ASP52 4.5 44.6 1.0 CA A:LEU10 4.6 41.8 1.0 O A:HOH310 4.7 51.9 1.0 CD2 A:HIS53 4.7 58.3 1.0 NE2 A:HIS222 4.8 86.3 1.0 ND1 A:HIS244 4.9 59.3 1.0 N A:LEU10 5.0 43.8 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Trnase Z From Thermotoga Maritima


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 Trnase Z From Thermotoga Maritima within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.3 occ:1.00 OD1 B:ASP190 2.7 92.6 1.0 OD2 B:ASP52 3.2 50.2 1.0 NE2 B:HIS244 3.3 73.5 1.0 CG B:ASP190 3.6 99.2 1.0 NE2 B:HIS53 3.8 72.1 1.0 OD2 B:ASP190 3.8 97.3 1.0 CE1 B:HIS244 4.0 75.3 1.0 CG B:ASP52 4.1 56.2 1.0 OD1 B:ASP52 4.1 59.7 1.0 CD2 B:HIS244 4.2 68.7 1.0 N B:LEU10 4.4 42.2 1.0 CD2 B:HIS53 4.4 72.7 1.0 ND1 B:HIS50 4.5 89.6 1.0 CD2 B:LEU10 4.6 49.8 1.0 CA B:LEU10 4.7 46.5 1.0 CE1 B:HIS53 4.9 71.5 1.0

R.Ishii, A.Minagawa, H.Takaku, M.Takagi, M.Nashimoto, S.Yokoyama. Crystal Structure of the Trna 3' Processing Endoribonuclease Trnase Z From Thermotoga Maritima J.Biol.Chem. V. 280 14138 2005.
ISSN: ISSN 0021-9258
PubMed: 15701599
DOI: 10.1074/JBC.M500355200