Calcium in PDB 6k4l: Crystal Structure of Se-Labelled Sidj Complex with Cam at 2.95 A

The structure of Crystal Structure of Se-Labelled Sidj Complex with Cam at 2.95 A, PDB code: 6k4l 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)	68.32 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.060, 159.246, 135.809, 90.00, 101.68, 90.00
R / Rfree (%)	24.3 / 26.9

The structure of Crystal Structure of Se-Labelled Sidj Complex with Cam at 2.95 A also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Se-Labelled Sidj Complex with Cam at 2.95 A (pdb code 6k4l). 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 Se-Labelled Sidj Complex with Cam at 2.95 A, PDB code: 6k4l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Se-Labelled Sidj Complex with Cam at 2.95 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 Se-Labelled Sidj Complex with Cam at 2.95 A within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:0.1 occ:1.00 OG1 C:THR27 2.0 0.0 1.0 OD1 C:ASP23 2.3 58.3 1.0 O C:THR27 2.4 0.7 1.0 C C:THR27 2.7 1.0 1.0 OD1 C:ASP21 2.7 73.2 1.0 CB C:THR27 3.0 0.2 1.0 CA C:THR27 3.1 0.4 1.0 CG C:ASP21 3.2 67.6 1.0 N C:THR27 3.2 0.9 1.0 OD2 C:ASP21 3.4 73.9 1.0 N C:ILE28 3.5 0.8 1.0 CG C:ASP23 3.5 57.9 1.0 CA C:ILE28 4.0 92.6 1.0 N C:ASP23 4.1 66.7 1.0 CB C:ASP21 4.2 62.4 1.0 CA C:ASP21 4.2 63.1 1.0 OD2 C:ASP23 4.2 54.9 1.0 CG2 C:THR27 4.3 0.2 1.0 N C:LYS22 4.3 60.8 1.0 C C:GLY26 4.4 94.6 1.0 C C:ASP21 4.4 64.3 1.0 CB C:ASP23 4.5 61.5 1.0 CA C:ASP23 4.6 61.3 1.0 N C:GLY24 4.6 60.5 1.0 C C:ASP23 4.7 61.3 1.0 OE1 C:GLU32 4.8 0.8 1.0 O C:ASP25 4.8 92.1 1.0 CB C:ILE28 4.9 89.0 1.0 C C:ASP25 4.9 83.8 1.0 C C:GLY24 4.9 73.2 1.0 N C:GLY26 4.9 92.7 1.0 N C:ASP25 4.9 72.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Se-Labelled Sidj Complex with Cam at 2.95 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 Se-Labelled Sidj Complex with Cam at 2.95 A within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:0.8 occ:1.00 OD1 D:ASP21 2.3 73.9 1.0 OD1 D:ASP23 2.4 61.6 1.0 OG1 D:THR27 2.4 0.9 1.0 N D:ILE28 2.5 0.8 1.0 N D:THR27 2.5 0.1 1.0 N D:GLY26 2.9 0.6 1.0 CG D:ASP21 2.9 71.1 1.0 CA D:ASP25 2.9 79.5 1.0 C D:ASP25 2.9 97.4 1.0 OD2 D:ASP21 2.9 70.9 1.0 CA D:THR27 3.1 0.1 1.0 C D:THR27 3.2 0.1 1.0 C D:GLY26 3.2 0.9 1.0 CB D:THR27 3.3 0.9 1.0 OD1 D:ASP25 3.4 84.8 1.0 CG D:ASP23 3.5 57.2 1.0 CA D:ILE28 3.5 0.5 1.0 CA D:GLY26 3.6 0.9 1.0 N D:ASP25 3.7 67.7 1.0 O D:ASP25 3.8 96.4 1.0 O D:ASP23 4.0 56.0 1.0 OD2 D:ASP23 4.0 56.6 1.0 O D:GLY26 4.0 0.1 1.0 C D:GLY24 4.1 60.8 1.0 CB D:ASP25 4.1 77.0 1.0 CG D:ASP25 4.1 81.7 1.0 C D:ASP23 4.2 51.4 1.0 CB D:ASP21 4.3 66.7 1.0 O D:GLY24 4.3 67.1 1.0 CB D:ILE28 4.4 0.9 1.0 O D:THR27 4.4 0.4 1.0 CG2 D:THR27 4.4 0.5 1.0 N D:GLY24 4.6 49.5 1.0 C D:ILE28 4.7 0.4 1.0 CB D:ASP23 4.7 50.6 1.0 N D:THR29 4.7 0.2 1.0 N D:ASP23 4.7 57.4 1.0 CA D:ASP23 4.8 50.8 1.0 CA D:ASP21 4.9 61.1 1.0 CA D:GLY24 5.0 55.4 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