Calcium in PDB 7a0s: 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I, PDB code: 7a0s was solved by E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.67 / 3.22
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.995, 410.736, 697.778, 90, 90, 90
R / Rfree (%)	22.4 / 25.3

The structure of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I also contains other interesting chemical elements:

Sodium	(Na)	1 atom
Magnesium	(Mg)	367 atoms
Potassium	(K)	1 atom

The binding sites of Calcium atom in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I (pdb code 7a0s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I, PDB code: 7a0s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca3251 b:78.6 occ:1.00 OP2 X:A1278 2.5 78.0 1.0 OP1 X:U2594 2.6 77.9 1.0 P X:A1278 3.4 77.9 1.0 OP1 X:A1278 3.5 77.6 1.0 P X:U2594 3.9 78.2 1.0 O5' X:U2594 4.1 78.4 1.0 O2' X:U1280 4.1 77.2 1.0 OP1 X:A2593 4.2 76.5 1.0 O5' X:A1278 4.5 78.1 1.0 O3' X:G1277 4.5 78.3 1.0 C5' X:A1278 4.5 78.1 1.0 C3' X:A2593 4.5 77.7 1.0 O3' X:A2593 4.7 78.1 1.0 C5' X:A2593 4.7 77.1 1.0 C5' X:U2594 4.8 78.8 1.0 C4' X:A2593 5.0 77.5 1.0

Calcium binding site 2 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca3252 b:100.2 occ:1.00 OP2 X:U2594 2.7 78.6 1.0 OP2 X:C2595 2.8 79.7 1.0 P X:U2594 3.9 78.2 1.0 OP1 X:U2594 4.1 77.9 1.0 P X:C2595 4.2 80.1 1.0 O2' X:A2593 4.6 78.1 1.0 O3' X:A2593 4.7 78.1 1.0 OP1 X:C2595 4.9 80.5 1.0

Calcium binding site 3 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca3253 b:72.6 occ:1.00 O6 X:G1993 3.9 76.5 1.0 O6 X:G1992 4.1 76.3 1.0 N7 X:G1992 4.1 77.0 1.0 N7 X:G1993 4.3 77.2 1.0 OP2 X:U1280 4.6 77.6 1.0 C6 X:G1992 4.7 76.6 1.0 C5 X:G1992 4.7 76.9 1.0 O4 X:U1994 4.7 77.0 1.0 OP1 X:U1280 4.8 77.8 1.0 C6 X:G1993 4.8 76.7 1.0 N4 X:C1991 4.8 76.0 1.0 C5 X:G1993 5.0 77.0 1.0

Calcium binding site 4 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca3254 b:82.5 occ:1.00 OP1 X:U1280 2.2 77.8 1.0 P X:U1280 3.5 77.7 1.0 C3' X:G1279 4.1 78.1 1.0 O5' X:U1280 4.2 77.5 1.0 O3' X:G1279 4.2 77.7 1.0 C5' X:U1280 4.3 77.6 1.0 OP2 X:C1991 4.4 77.3 1.0 OP2 X:U1280 4.8 77.6 1.0

Calcium binding site 5 out of 5 in the 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I within 5.0Å range: probe atom residue distance (Å) B Occ X:Ca3255 b:78.1 occ:1.00 OP2 X:A1682 2.3 81.8 1.0 OP1 X:A1681 2.9 80.2 1.0 O5' X:A1681 3.6 80.7 1.0 P X:A1682 3.6 82.3 1.0 P X:A1681 3.7 80.1 1.0 OP1 X:A1682 4.0 82.8 1.0 C5' X:A1681 4.4 80.6 1.0 O5' X:A1682 4.5 82.8 1.0 OP2 X:A1681 4.5 80.0 1.0 O3' X:A1681 4.7 82.1 1.0 OP2 X:G1683 5.0 83.4 1.0 O3' X:U1680 5.0 79.7 1.0

E.Breiner, Z.Eyal, D.Matzov, Y.Halfon, G.Cimicata, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. 50S Deinococcus Radiodurans Ribosome Bounded with Mycinamicin I To Be Published.