Calcium in PDB 6k4k: Crystal Structure of Sidj-Cam Binary Complex at 2.71 A

The structure of Crystal Structure of Sidj-Cam Binary Complex at 2.71 A, PDB code: 6k4k 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)	55.87 / 2.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.955, 159.533, 135.611, 90.00, 101.89, 90.00
R / Rfree (%)	20.5 / 24.3

The binding sites of Calcium atom in the Crystal Structure of Sidj-Cam Binary Complex at 2.71 A (pdb code 6k4k). 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 Binary Complex at 2.71 A, PDB code: 6k4k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Sidj-Cam Binary Complex at 2.71 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 Binary Complex at 2.71 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:99.2 occ:1.00 CB C:ASP25 2.0 92.6 1.0 OD2 C:ASP23 2.4 81.3 1.0 O C:THR27 2.5 65.5 1.0 OD1 C:ASP23 2.6 84.8 1.0 CG C:ASP25 2.6 0.5 1.0 OD1 C:ASP21 2.7 63.0 1.0 CG C:ASP23 2.8 77.0 1.0 OD1 C:ASP25 2.8 0.4 1.0 CA C:ASP25 3.4 65.2 1.0 OG1 C:THR27 3.4 72.6 1.0 OD2 C:ASP25 3.5 0.9 1.0 C C:THR27 3.6 62.5 1.0 N C:ASP25 3.7 63.8 1.0 CG C:ASP21 3.8 63.4 1.0 N C:THR27 4.0 54.2 1.0 CA C:THR27 4.2 64.2 1.0 CB C:ASP23 4.3 65.8 1.0 OD2 C:ASP21 4.3 48.5 1.0 C C:ASP25 4.3 56.7 1.0 CB C:THR27 4.4 64.0 1.0 N C:GLY26 4.6 56.4 1.0 N C:ILE28 4.7 62.1 1.0 N C:ASP23 4.9 50.0 1.0 CA C:ASP23 4.9 58.0 1.0 C C:ASP23 5.0 59.0 1.0 CA C:ILE28 5.0 66.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Sidj-Cam Binary Complex at 2.71 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 Binary Complex at 2.71 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:0.6 occ:1.00 O D:ASP25 2.1 0.7 1.0 OD1 D:ASP21 2.1 0.1 1.0 O D:THR27 2.3 0.9 1.0 C D:THR27 2.7 0.3 1.0 OD1 D:ASP25 2.8 80.4 1.0 C D:ASP25 2.9 0.3 1.0 CG D:ASP21 2.9 82.9 1.0 OD2 D:ASP21 3.0 63.8 1.0 OD2 D:ASP23 3.0 0.7 1.0 CA D:ASP25 3.1 0.4 1.0 OD1 D:ASP23 3.1 0.1 1.0 CA D:ILE28 3.1 98.9 1.0 CG D:ASP23 3.2 96.6 1.0 N D:ILE28 3.2 0.8 1.0 N D:THR27 3.5 0.6 1.0 CG D:ASP25 3.7 80.2 1.0 CA D:THR27 3.7 0.9 1.0 OG1 D:THR27 3.9 0.7 1.0 CB D:ASP25 3.9 99.1 1.0 O D:ASP23 3.9 45.8 1.0 CB D:ILE28 4.0 83.6 1.0 C D:ILE28 4.0 96.9 1.0 N D:GLY26 4.1 0.2 1.0 N D:ASP25 4.2 0.3 1.0 O D:GLY24 4.3 73.4 1.0 C D:ASP23 4.3 59.4 1.0 CB D:ASP23 4.3 68.2 1.0 CB D:ASP21 4.3 64.0 1.0 C D:GLY24 4.4 0.3 1.0 C D:GLY26 4.4 0.4 1.0 CB D:THR27 4.5 0.6 1.0 O D:ILE28 4.6 0.8 1.0 N D:THR29 4.7 76.0 1.0 CA D:GLY26 4.7 0.5 1.0 CA D:ASP23 4.7 61.1 1.0 OD2 D:ASP25 4.7 76.5 1.0 CG1 D:ILE28 4.7 56.7 1.0 N D:ASP23 4.8 65.4 1.0 CA D:ASP21 4.9 50.5 1.0 N D:GLY24 4.9 81.0 1.0 C D:ASP21 4.9 59.2 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