Calcium in PDB 5hkv: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin, PDB code: 5hkv was solved by A.Yonath, D.Matzov, Z.Eyal, R.Ben Hamou, E.Zimmerman, H.Rozenberg, A.Bashan, M.Fridman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.66
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	280.885, 280.885, 873.522, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 23.4

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin also contains other interesting chemical elements:

Magnesium	(Mg)	162 atoms
Manganese	(Mn)	338 atoms

The binding sites of Calcium atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin (pdb code 5hkv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin, PDB code: 5hkv:

Calcium binding site 1 out of 1 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ Y:Ca203 b:0.8 occ:1.00 OP2 Y:C79 2.2 79.1 1.0 P Y:C79 3.6 78.8 1.0 C3' Y:C78 3.9 67.3 1.0 C7 Y:SPD213 4.0 0.7 1.0 C6 Y:C78 4.2 68.0 1.0 O5' Y:C79 4.2 78.9 1.0 O3' Y:C78 4.3 67.0 1.0 C2' Y:C78 4.3 67.6 1.0 C5 Y:C79 4.4 79.6 1.0 C5 Y:C78 4.5 68.4 1.0 N7 Y:A80 4.5 67.8 1.0 N10 Y:SPD213 4.6 0.7 1.0 N1 Y:C78 4.6 68.1 1.0 OP1 Y:C79 4.7 78.7 1.0 N6 Y:A80 4.7 68.7 1.0 C9 Y:SPD213 4.9 0.7 1.0 C4 Y:SPD213 4.9 0.7 1.0 O5' Y:C78 4.9 67.4 1.0 N6 Y:SPD213 5.0 0.7 1.0 C6 Y:C79 5.0 79.5 1.0

D.Matzov, Z.Eyal, R.I.Benhamou, M.Shalev-Benami, Y.Halfon, M.Krupkin, E.Zimmerman, H.Rozenberg, A.Bashan, M.Fridman, A.Yonath. Structural Insights of Lincosamides Targeting the Ribosome of Staphylococcus Aureus. Nucleic Acids Res. V. 45 10284 2017.
ISSN: ESSN 1362-4962
PubMed: 28973455
DOI: 10.1093/NAR/GKX658