Calcium in PDB 6vat: Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium

The structure of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vat was solved by U.Gabale, S.Ressl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.65 / 2.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.799, 113.799, 299.777, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 24.9

The structure of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Calcium atom in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium (pdb code 6vat). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium, PDB code: 6vat:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca604 b:60.2 occ:1.00 OH B:TYR553 3.1 43.3 1.0 CB B:LEU570 3.9 41.9 1.0 CE2 B:TYR553 3.9 40.6 1.0 CZ B:TYR553 3.9 40.0 1.0 CD1 B:LEU570 4.0 34.4 1.0 CA B:LEU570 4.1 44.9 1.0 N B:LEU570 4.1 45.9 1.0 CB B:PRO568 4.2 43.0 1.0 CD1 B:LEU573 4.4 37.8 1.0 N B:GLN569 4.4 43.5 1.0 CG B:LEU570 4.6 35.5 1.0 C B:GLN569 4.6 41.6 1.0 CA B:PRO568 4.7 42.8 1.0

Calcium binding site 2 out of 3 in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca608 b:53.0 occ:1.00 OH C:TYR553 2.9 42.2 1.0 CE2 C:TYR553 3.7 41.3 1.0 CZ C:TYR553 3.8 40.0 1.0 CB C:PRO568 4.0 59.4 1.0 N C:GLN569 4.1 48.0 1.0 CD1 C:LEU570 4.2 40.5 1.0 CD1 C:LEU573 4.2 35.7 1.0 N C:LEU570 4.2 46.5 1.0 CA C:LEU570 4.2 39.5 1.0 CB C:LEU570 4.2 41.5 1.0 CA C:PRO568 4.4 58.1 1.0 C C:GLN569 4.5 44.5 1.0 C C:PRO568 4.7 52.4 1.0 CG C:LEU570 4.8 45.1 1.0 CA C:GLN569 5.0 48.4 1.0 O C:GLN569 5.0 40.6 1.0

Calcium binding site 3 out of 3 in the Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Periplasmic Domain of Yejm From Salmonella Typhimurium within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca603 b:0.7 occ:1.00 CA E:LEU570 3.6 99.7 1.0 N E:LEU570 3.8 0.1 1.0 CB E:LEU570 3.8 0.5 1.0 CD1 E:LEU570 4.1 91.4 1.0 C E:GLN569 4.2 95.4 1.0 OH E:TYR553 4.3 0.1 1.0 N E:GLN569 4.4 97.9 1.0 CE2 E:TYR553 4.4 0.6 1.0 O E:GLN569 4.5 89.2 1.0 CG E:LEU570 4.6 89.9 1.0 CZ E:TYR553 4.9 0.5 1.0 CB E:PRO568 4.9 0.7 1.0 CD1 E:LEU573 4.9 80.6 1.0 CA E:GLN569 4.9 94.5 1.0

U.Gabale, P.A.Pena Palomino, H.Kim, W.Chen, S.Ressl. The Essential Inner Membrane Protein Yejm Is A Metalloenzyme. Sci Rep V. 10 17794 2020.
ISSN: ESSN 2045-2322
PubMed: 33082366
DOI: 10.1038/S41598-020-73660-6