Calcium in PDB 6k4r: Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A

The structure of Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A, PDB code: 6k4r was solved by S.Y.Ouyang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.09 / 3.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.846, 159.178, 135.032, 90.00, 101.78, 90.00
R / Rfree (%)	23.9 / 27.9

The structure of Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A (pdb code 6k4r). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A, PDB code: 6k4r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:71.7 occ:1.00 OD1 C:ASP23 2.3 65.0 1.0 O C:THR27 2.3 69.9 1.0 OD1 C:ASP25 2.3 67.6 1.0 OD2 C:ASP23 2.4 67.2 1.0 OD2 C:ASP25 2.4 68.8 1.0 CG C:ASP23 2.7 65.8 1.0 CG C:ASP25 2.7 67.5 1.0 OD1 C:ASP21 3.2 64.9 1.0 C C:THR27 3.4 71.0 1.0 OG1 C:THR27 3.6 72.8 1.0 CB C:ASP23 4.2 63.8 1.0 CB C:ASP25 4.2 66.4 1.0 N C:ILE28 4.2 76.8 1.0 CA C:ILE28 4.2 75.2 1.0 CA C:THR27 4.4 70.6 1.0 CG C:ASP21 4.5 64.5 1.0 N C:THR27 4.5 68.5 1.0 CB C:THR27 4.6 72.5 1.0 N C:ASP23 4.7 65.4 1.0 N C:ASP25 4.8 64.5 1.0 C C:ILE28 4.9 77.4 1.0 CG2 C:THR29 4.9 80.5 1.0 CA C:ASP23 4.9 64.9 1.0 N C:THR29 5.0 78.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Sidj-Cam-Amp Ternary Complex at 3.11 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:73.9 occ:1.00 N D:ILE28 2.2 78.4 1.0 OD1 D:ASP21 2.3 66.7 1.0 OD1 D:ASP23 2.3 73.1 1.0 OD2 D:ASP23 2.3 71.1 1.0 OG1 D:THR27 2.4 79.1 1.0 CG D:ASP23 2.6 71.5 1.0 CA D:ILE28 2.9 75.2 1.0 CG D:ASP21 3.1 66.5 1.0 C D:THR27 3.2 81.5 1.0 N D:THR29 3.3 78.0 1.0 CB D:THR27 3.5 80.6 1.0 N D:THR27 3.5 79.5 1.0 CA D:THR27 3.5 82.1 1.0 C D:ILE28 3.6 78.4 1.0 OD2 D:ASP21 3.7 68.6 1.0 CB D:ASP21 4.0 65.1 1.0 CA D:ASP21 4.0 63.5 1.0 CB D:ASP23 4.1 67.5 1.0 C D:ASP25 4.2 68.5 1.0 O D:ASP25 4.2 71.7 1.0 O D:THR27 4.2 81.9 1.0 CB D:ILE28 4.2 72.7 1.0 C D:GLY26 4.3 78.6 1.0 CG2 D:THR27 4.3 77.1 1.0 N D:ASP23 4.3 65.3 1.0 C D:ASP21 4.4 62.5 1.0 N D:GLY26 4.5 72.4 1.0 CA D:ASP25 4.5 67.9 1.0 N D:LYS22 4.6 64.2 1.0 CA D:THR29 4.6 76.8 1.0 CA D:ASP23 4.7 64.0 1.0 OD1 D:ASP25 4.8 66.7 1.0 O D:ILE28 4.8 82.1 1.0 C D:ASP23 4.9 63.8 1.0 CA D:GLY26 5.0 77.2 1.0 O D:ASP23 5.0 65.2 1.0 OG1 D:THR29 5.0 73.6 1.0

N.Gan, X.Zhen, Y.Liu, X.Xu, C.He, J.Qiu, Y.Liu, G.M.Fujimoto, E.S.Nakayasu, B.Zhou, L.Zhao, K.Puvar, C.Das, S.Ouyang, Z.Q.Luo. Regulation of Phosphoribosyl Ubiquitination By A Calmodulin-Dependent Glutamylase. Nature V. 572 387 2019.
ISSN: ESSN 1476-4687
PubMed: 31330531
DOI: 10.1038/S41586-019-1439-1