Calcium in PDB 8ux2: Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+

The structure of Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+, PDB code: 8ux2 was solved by Z.Zhang, H.Rondon, C.Das, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.47 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.656, 82.937, 151.212, 90, 90, 90
R / Rfree (%)	19.2 / 22.7

The binding sites of Calcium atom in the Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+ (pdb code 8ux2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+, PDB code: 8ux2:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:17.2 occ:1.00 OD1 A:ASP134 2.3 26.1 1.0 O A:HOH419 2.3 20.6 1.0 O3D A:NAD301 2.4 21.3 1.0 O2D A:NAD301 2.5 19.4 1.0 O A:ALA135 2.5 26.1 1.0 O A:HOH503 2.5 21.1 1.0 C2D A:NAD301 3.4 18.2 1.0 C3D A:NAD301 3.4 20.1 1.0 CG A:ASP134 3.4 33.7 1.0 C A:ALA135 3.6 25.6 1.0 OD2 A:ASP134 3.9 42.8 1.0 N A:ALA135 4.0 28.8 1.0 C1D A:NAD301 4.0 19.5 1.0 OE2 A:GLU220 4.1 26.2 1.0 C A:ASP134 4.2 29.6 1.0 OE1 A:GLU220 4.3 24.4 1.0 O A:THR137 4.3 23.1 1.0 CA A:ALA135 4.5 28.2 1.0 O A:HOH435 4.5 31.3 1.0 CD A:GLU220 4.5 29.8 1.0 N A:ALA136 4.6 21.2 1.0 O A:ASP134 4.6 28.4 1.0 CB A:ASP134 4.6 31.3 1.0 CA A:ASP134 4.7 29.3 1.0 C4D A:NAD301 4.7 20.0 1.0 CA A:ALA136 4.7 27.1 1.0 C A:ALA136 4.8 21.8 1.0 N A:THR137 4.8 22.9 1.0 O A:HOH441 4.9 33.8 1.0 O4D A:NAD301 4.9 19.3 1.0

Calcium binding site 2 out of 3 in the Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:16.3 occ:1.00 OD1 B:ASP134 2.3 24.2 1.0 O B:HOH401 2.3 20.6 1.0 O B:HOH509 2.4 21.5 1.0 O2D B:NAD301 2.4 20.2 1.0 O B:ALA135 2.4 26.8 1.0 O3D B:NAD301 2.4 17.2 1.0 C2D B:NAD301 3.3 19.9 1.0 CG B:ASP134 3.4 29.6 1.0 C3D B:NAD301 3.4 22.5 1.0 C B:ALA135 3.6 30.6 1.0 OD2 B:ASP134 3.9 33.2 1.0 C1D B:NAD301 4.0 19.4 1.0 OE1 B:GLU220 4.0 21.6 1.0 O B:THR137 4.3 23.8 1.0 C B:ASP134 4.3 34.0 1.0 N B:ALA135 4.3 30.1 1.0 OE2 B:GLU220 4.4 22.8 1.0 N B:ALA136 4.5 26.8 1.0 CA B:ALA136 4.5 26.2 1.0 CA B:ALA135 4.6 28.8 1.0 O B:HOH518 4.6 33.5 1.0 O B:ASP134 4.6 32.7 1.0 CD B:GLU220 4.6 21.1 1.0 CB B:ASP134 4.6 35.1 1.0 C4D B:NAD301 4.7 21.3 1.0 CA B:ASP134 4.7 33.9 1.0 C B:ALA136 4.7 24.8 1.0 O4D B:NAD301 4.8 18.5 1.0 N B:THR137 4.9 23.1 1.0

Calcium binding site 3 out of 3 in the Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Chromobacterium Violaceum Mono-Adp-Ribosyltransferase Ctec in Complex with Nad+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:28.2 occ:1.00 O C:HOH443 2.2 21.4 1.0 O C:HOH507 2.3 28.5 1.0 OD1 C:ASP134 2.3 46.0 1.0 O2D C:NAD302 2.4 26.5 1.0 O3D C:NAD302 2.5 18.9 1.0 O C:HOH416 2.5 30.8 1.0 O C:ALA135 2.5 39.0 1.0 C2D C:NAD302 3.3 20.6 1.0 C3D C:NAD302 3.4 24.1 1.0 CG C:ASP134 3.5 54.5 1.0 C C:ALA135 3.7 42.3 1.0 OE2 C:GLU220 3.9 31.7 1.0 OD2 C:ASP134 4.0 59.8 1.0 C1D C:NAD302 4.1 18.3 1.0 C C:ASP134 4.4 47.9 1.0 N C:ALA135 4.4 45.5 1.0 CA C:ALA136 4.4 37.1 1.0 OE1 C:GLU220 4.5 26.1 1.0 O C:THR137 4.5 35.5 1.0 N C:ALA136 4.5 33.4 1.0 O C:ASP134 4.5 44.7 1.0 CD C:GLU220 4.6 32.2 1.0 C4D C:NAD302 4.7 19.4 1.0 C C:ALA136 4.7 34.5 1.0 CA C:ALA135 4.7 55.6 1.0 CB C:ASP134 4.7 51.8 1.0 N C:THR137 4.7 32.0 1.0 CA C:ASP134 4.8 44.9 1.0 O4D C:NAD302 4.9 17.6 1.0

Z.Zhang, H.M.Rondon-Cordero, C.Das. Crystal Structure of Bacterial Ubiquitin Adp-Ribosyltransferase Ctec Reveals A Substrate-Recruiting Insertion. J.Biol.Chem. 05604 2023.
ISSN: ESSN 1083-351X
PubMed: 38159861
DOI: 10.1016/J.JBC.2023.105604