Zinc in PDB 2e7y: High Resolution Structure of T. Maritima Trnase Z

All present enzymatic activity of High Resolution Structure of T. Maritima Trnase Z:
3.1.26.11;

The structure of High Resolution Structure of T. Maritima Trnase Z, PDB code: 2e7y was solved by R.Ishii, S.Yokoyama, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.44 / 1.97
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	150.299, 172.694, 64.886, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.9

The binding sites of Zinc atom in the High Resolution Structure of T. Maritima Trnase Z (pdb code 2e7y). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the High Resolution Structure of T. Maritima Trnase Z, PDB code: 2e7y:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the High Resolution Structure of T. Maritima Trnase Z


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Structure of T. Maritima Trnase Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1301 b:43.5 occ:1.00 OD1 A:ASP190 2.0 39.9 1.0 NE2 A:HIS244 2.1 36.6 1.0 NE2 A:HIS53 2.2 31.9 1.0 O A:HOH1416 2.2 51.7 1.0 OD2 A:ASP52 2.8 30.8 1.0 CG A:ASP190 2.8 36.8 1.0 CE1 A:HIS244 3.0 35.6 1.0 CD2 A:HIS244 3.0 30.4 1.0 CD2 A:HIS53 3.0 26.4 1.0 OD2 A:ASP190 3.1 47.6 1.0 ZN A:ZN1302 3.2 65.0 1.0 CE1 A:HIS53 3.2 29.0 1.0 CG A:ASP52 3.7 30.3 1.0 OD1 A:ASP52 4.0 30.2 1.0 ND1 A:HIS244 4.0 40.5 1.0 NE2 A:HIS48 4.0 40.4 1.0 O A:HOH1311 4.0 29.9 1.0 CG A:HIS244 4.0 45.2 1.0 CG A:HIS53 4.2 35.3 1.0 CB A:ASP190 4.2 37.6 1.0 ND1 A:HIS53 4.2 32.2 1.0 CE1 A:HIS48 4.3 44.6 1.0 O A:HOH1449 4.3 67.5 1.0 N A:LEU10 4.7 29.5 1.0 CE1 A:HIS222 4.7 80.9 1.0 O A:HOH1390 4.7 49.2 1.0

Zinc binding site 2 out of 4 in the High Resolution Structure of T. Maritima Trnase Z


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Structure of T. Maritima Trnase Z within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:65.0 occ:1.00 NE2 A:HIS48 2.4 40.4 1.0 O A:HOH1416 2.4 51.7 1.0 ND1 A:HIS50 2.5 84.9 1.0 OD1 A:ASP190 2.5 39.9 1.0 NE2 A:HIS134 2.6 87.3 1.0 CD2 A:HIS48 3.1 43.1 1.0 ZN A:ZN1301 3.2 43.5 1.0 CE1 A:HIS50 3.3 70.4 1.0 O A:HOH1449 3.3 67.5 1.0 CG A:HIS50 3.3 49.1 1.0 CE1 A:HIS134 3.4 58.6 1.0 CE1 A:HIS48 3.5 44.6 1.0 CG A:ASP190 3.5 36.8 1.0 CD2 A:HIS134 3.6 65.8 1.0 CB A:HIS50 3.7 34.1 1.0 CB A:ASP190 4.0 37.6 1.0 CD2 A:HIS53 4.1 26.4 1.0 NE2 A:HIS53 4.1 31.9 1.0 NE2 A:HIS50 4.3 89.3 1.0 CG A:HIS48 4.3 42.2 1.0 CD2 A:HIS50 4.4 72.7 1.0 OD1 A:ASP52 4.4 30.2 1.0 ND1 A:HIS48 4.5 53.6 1.0 OD2 A:ASP190 4.5 47.6 1.0 ND1 A:HIS134 4.5 76.3 1.0 O A:HOH1396 4.6 47.7 1.0 CG A:HIS134 4.7 76.1 1.0 OD2 A:ASP52 4.8 30.8 1.0 CE1 A:HIS222 4.8 80.9 1.0

Zinc binding site 3 out of 4 in the High Resolution Structure of T. Maritima Trnase Z


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Structure of T. Maritima Trnase Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2301 b:47.8 occ:1.00 OD1 B:ASP190 2.0 39.8 1.0 O B:HOH2373 2.0 48.5 1.0 NE2 B:HIS53 2.2 43.3 1.0 NE2 B:HIS244 2.2 38.0 1.0 CG B:ASP190 2.9 52.7 1.0 OD2 B:ASP52 2.9 37.9 1.0 CD2 B:HIS53 2.9 35.2 1.0 CD2 B:HIS244 3.0 37.5 1.0 OD2 B:ASP190 3.1 44.6 1.0 CE1 B:HIS244 3.2 43.2 1.0 ZN B:ZN2302 3.3 72.2 1.0 CE1 B:HIS53 3.3 34.2 1.0 CG B:ASP52 3.8 46.4 1.0 OD1 B:ASP52 3.9 26.4 1.0 O B:HOH2309 3.9 27.2 1.0 NE2 B:HIS48 4.0 40.0 1.0 CG B:HIS244 4.2 39.8 1.0 CG B:HIS53 4.2 28.8 1.0 ND1 B:HIS244 4.2 44.6 1.0 CE1 B:HIS48 4.3 66.7 1.0 CB B:ASP190 4.3 46.3 1.0 ND1 B:HIS53 4.3 38.2 1.0 CE1 B:HIS222 4.6 98.7 1.0 N B:LEU10 4.7 31.4 1.0 O B:HOH2424 4.7 58.6 1.0

Zinc binding site 4 out of 4 in the High Resolution Structure of T. Maritima Trnase Z


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Structure of T. Maritima Trnase Z within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn2302 b:72.2 occ:1.00 NE2 B:HIS48 2.4 40.0 1.0 ND1 B:HIS50 2.5 56.4 1.0 OD1 B:ASP190 2.5 39.8 1.0 O B:HOH2373 2.9 48.5 1.0 CD2 B:HIS48 3.0 40.3 1.0 ZN B:ZN2301 3.3 47.8 1.0 CE1 B:HIS50 3.3 52.5 1.0 CG B:HIS50 3.4 56.0 1.0 CG B:ASP190 3.5 52.7 1.0 CE1 B:HIS48 3.6 66.7 1.0 CB B:HIS50 3.7 41.6 1.0 O B:HOH2377 3.9 72.6 1.0 CB B:ASP190 4.0 46.3 1.0 CD2 B:HIS53 4.1 35.2 1.0 NE2 B:HIS53 4.2 43.3 1.0 CG B:HIS48 4.3 49.1 1.0 NE2 B:HIS50 4.4 86.3 1.0 CD2 B:HIS50 4.4 51.2 1.0 ND1 B:HIS48 4.5 62.3 1.0 OD2 B:ASP190 4.6 44.6 1.0 OD1 B:ASP52 4.6 26.4 1.0 O B:HOH2428 4.8 62.0 1.0 O B:HOH2383 4.8 76.5 1.0 CE1 B:HIS222 4.9 98.7 1.0

R.Ishii, A.Minagawa, H.Takaku, M.Takagi, M.Nashimoto, S.Yokoyama. The Structure of the Flexible Arm of Thermotoga Maritima Trnase Z Differs From Those of Homologous Enzymes Acta Crystallogr.,Sect.F V. 63 637 2007.
ISSN: ESSN 1744-3091
PubMed: 17671357
DOI: 10.1107/S1744309107033623