Calcium in PDB 2a8k: Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease

The structure of Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease, PDB code: 2a8k was solved by Y.L.Lin, Y.Elias, R.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	65.220, 65.220, 100.740, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 23.4

The binding sites of Calcium atom in the Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease (pdb code 2a8k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease, PDB code: 2a8k:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:14.9 occ:1.00 O A:HOH405 2.3 13.2 1.0 O D:GLU24 2.4 11.6 1.0 O D:HOH405 2.4 13.4 1.0 OE2 A:GLU24 2.4 13.5 1.0 OG1 D:THR90 2.5 12.5 1.0 O D:HOH436 2.6 22.8 1.0 O D:HOH432 2.7 22.6 1.0 OE1 A:GLU24 3.0 13.2 1.0 CD A:GLU24 3.1 13.1 1.0 C D:GLU24 3.5 10.8 1.0 CB D:THR90 3.6 10.8 1.0 CA D:GLU24 4.1 12.0 1.0 CG2 D:THR90 4.1 11.1 1.0 OD1 D:ASP88 4.3 9.4 1.0 O D:HOH406 4.3 13.2 1.0 OD2 D:ASP88 4.4 9.7 1.0 CG A:GLU24 4.6 10.9 1.0 N D:ARG25 4.6 11.8 1.0 O A:HOH404 4.7 10.9 1.0 O A:HOH420 4.7 19.4 1.0 CB D:GLU24 4.7 12.5 1.0 O A:HOH412 4.8 12.7 1.0 CG D:ASP88 4.8 9.2 1.0 CA D:ARG25 4.9 11.3 1.0 CA D:THR90 4.9 11.5 1.0 O D:THR90 5.0 12.1 1.0

Calcium binding site 2 out of 4 in the Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:15.2 occ:1.00 O B:HOH410 2.3 14.7 1.0 O C:GLU24 2.4 11.8 1.0 O C:HOH432 2.4 26.0 1.0 O C:HOH407 2.4 14.7 1.0 OE2 B:GLU24 2.5 13.2 1.0 OG1 C:THR90 2.5 12.1 1.0 OE1 B:GLU24 3.0 12.9 1.0 CD B:GLU24 3.1 11.4 1.0 C C:GLU24 3.5 10.9 1.0 CB C:THR90 3.6 10.9 1.0 CG2 C:THR90 4.1 11.9 1.0 CA C:GLU24 4.1 12.0 1.0 OD1 C:ASP88 4.3 9.8 1.0 O C:HOH406 4.3 13.1 1.0 OD2 C:ASP88 4.4 10.0 1.0 CG B:GLU24 4.6 10.1 1.0 N C:ARG25 4.6 12.2 1.0 O B:HOH423 4.7 18.9 1.0 O B:HOH407 4.7 10.6 1.0 CB C:GLU24 4.7 12.8 1.0 O B:HOH412 4.8 13.0 1.0 CG C:ASP88 4.8 9.8 1.0 CA C:THR90 4.9 11.9 1.0 CA C:ARG25 4.9 11.8 1.0 O C:THR90 5.0 12.2 1.0

Calcium binding site 3 out of 4 in the Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca403 b:13.0 occ:1.00 O B:HOH417 2.4 15.9 1.0 O B:HOH413 2.4 14.0 1.0 O B:GLU24 2.4 11.2 1.0 O C:HOH410 2.4 16.1 1.0 OE2 C:GLU24 2.5 13.7 1.0 OG1 B:THR90 2.6 16.0 1.0 OE1 C:GLU24 3.3 13.6 1.0 CD C:GLU24 3.3 12.3 1.0 C B:GLU24 3.5 10.6 1.0 CB B:THR90 3.6 13.9 1.0 CG2 B:THR90 4.0 15.8 1.0 CA B:GLU24 4.1 9.4 1.0 OD1 B:ASP88 4.4 11.7 1.0 O C:HOH414 4.5 15.6 1.0 OD2 B:ASP88 4.6 12.9 1.0 O C:HOH417 4.6 14.5 1.0 N B:ARG25 4.6 10.8 1.0 O B:PRO23 4.7 12.9 1.0 CG C:GLU24 4.7 12.2 1.0 CB B:GLU24 4.9 10.3 1.0 CG B:ASP88 4.9 10.8 1.0 CA B:THR90 5.0 14.4 1.0 O C:HOH404 5.0 12.0 1.0 CA B:ARG25 5.0 9.7 1.0

Calcium binding site 4 out of 4 in the Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Mutational Studies of the Catalytic Domain of Colicin E5A Trna-Specific Ribonuclease within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:13.1 occ:1.00 O A:HOH426 2.4 21.6 1.0 O A:HOH414 2.4 14.7 1.0 O A:HOH408 2.4 13.4 1.0 O A:GLU24 2.4 11.4 1.0 O D:HOH409 2.5 16.1 1.0 OE2 D:GLU24 2.5 13.5 1.0 OG1 A:THR90 2.6 15.2 1.0 OE1 D:GLU24 3.3 13.3 1.0 CD D:GLU24 3.3 12.3 1.0 C A:GLU24 3.5 11.6 1.0 CB A:THR90 3.6 13.8 1.0 CG2 A:THR90 4.0 16.1 1.0 O A:HOH417 4.1 14.5 1.0 CA A:GLU24 4.1 9.7 1.0 OD1 A:ASP88 4.4 11.6 1.0 O D:HOH421 4.5 16.7 1.0 OD2 A:ASP88 4.6 12.0 1.0 O D:HOH416 4.6 15.2 1.0 N A:ARG25 4.6 11.3 1.0 O A:PRO23 4.7 13.2 1.0 CG D:GLU24 4.7 11.9 1.0 CB A:GLU24 4.9 11.0 1.0 CG A:ASP88 4.9 10.4 1.0 CA A:THR90 5.0 14.1 1.0 CA A:ARG25 5.0 9.4 1.0 O D:HOH403 5.0 11.4 1.0

Y.L.Lin, Y.Elias, R.H.Huang. Structural and Mutational Studies of the Catalytic Domain of Colicin E5: A Trna-Specific Ribonuclease Biochemistry V. 44 10494 2005.
ISSN: ISSN 0006-2960
PubMed: 16060658
DOI: 10.1021/BI050749S