Magnesium in PDB 5nrg: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02, PDB code: 5nrg 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)	49.37 / 3.44
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	279.797, 279.797, 873.274, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 26.1

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 also contains other interesting chemical elements:

Manganese

(Mn)

210 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 84;

Binding sites:

The binding sites of Magnesium atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 (pdb code 5nrg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 84 binding sites of Magnesium where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02, PDB code: 5nrg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3032 b:31.7 occ:1.00 OP1 X:A1019 2.2 51.4 1.0 P X:A1019 3.6 51.7 1.0 OP2 X:A1019 4.1 53.0 1.0 O2' X:A1027 4.2 56.3 1.0 OP1 X:G1016 4.2 51.6 1.0 O5' X:A1019 4.6 51.7 1.0 O3' X:A1018 4.7 52.0 1.0 C3' X:A1018 4.8 52.0 1.0 C5' X:A1019 4.8 51.4 1.0 C4' X:A1027 4.8 53.5 1.0 O4' X:A1027 5.0 52.5 1.0

Magnesium binding site 2 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3036 b:55.6 occ:1.00 OP2 X:G990 2.2 61.4 1.0 OP2 X:A989 2.6 69.4 1.0 O5' X:G990 3.2 59.6 1.0 P X:G990 3.3 58.6 1.0 O5' X:A989 3.6 63.6 1.0 P X:A989 3.7 67.2 1.0 OP2 X:U867 3.8 56.6 1.0 O3' X:A866 4.0 57.7 1.0 O3' X:C988 4.1 60.4 1.0 O2' X:A866 4.3 55.8 1.0 OP1 X:G990 4.3 58.1 1.0 C5' X:G990 4.4 58.5 1.0 O3' X:A989 4.4 57.7 1.0 C4' X:A989 4.5 58.8 1.0 C3' X:A989 4.6 57.5 1.0 P X:U867 4.6 56.4 1.0 C5' X:A989 4.6 60.5 1.0 C5' X:U867 4.9 57.3 1.0

Magnesium binding site 3 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3058 b:64.0 occ:1.00 OP1 X:U1683 2.4 77.8 1.0 OP2 X:C1334 3.5 84.8 1.0 O2' X:G2736 3.6 76.1 1.0 P X:U1683 3.8 77.4 1.0 O5' X:A1333 3.9 83.3 1.0 OP2 X:A1333 4.1 89.2 1.0 OP1 X:A1333 4.3 87.1 1.0 P X:A1333 4.3 86.3 1.0 OP2 X:U1683 4.3 74.1 1.0 N3 X:G2736 4.6 78.4 1.0 C5' X:U1683 4.7 82.5 1.0 C2' X:G2736 4.7 77.7 1.0 O5' X:U1683 4.8 80.6 1.0 O3' X:C1682 4.8 80.0 1.0 C1' X:G2736 4.9 80.7 1.0 P X:C1334 4.9 81.2 1.0 O4' X:C2737 4.9 78.6 1.0 C3' X:A1333 5.0 77.9 1.0 C5' X:A1333 5.0 80.0 1.0 N2 X:G2736 5.0 82.8 1.0

Magnesium binding site 4 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3069 b:52.4 occ:1.00 OP1 X:G2645 3.6 47.8 1.0 OP2 X:A2050 3.8 50.9 1.0 C2 X:A574 4.1 54.9 1.0 OP2 X:G2645 4.1 47.5 1.0 N1 X:A574 4.2 54.4 1.0 P X:G2645 4.3 47.5 1.0 C5' X:C2644 4.4 49.4 1.0 OP1 X:C2644 4.6 47.6 1.0 O3' X:C2644 4.7 53.4 1.0 O4' X:A2050 4.8 55.1 1.0

Magnesium binding site 5 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3072 b:41.5 occ:1.00 OP1 X:A2032 2.3 59.7 1.0 OP2 X:G1307 2.7 61.9 1.0 OP2 X:A1306 3.7 62.5 1.0 P X:A2032 3.8 61.7 1.0 P X:G1307 4.1 61.6 1.0 N7 X:G1307 4.3 60.0 1.0 N4 X:C1308 4.5 57.8 1.0 P X:A1306 4.6 61.0 1.0 O3' X:G2031 4.6 62.8 1.0 OP2 X:C2033 4.6 54.6 1.0 OP1 X:A1306 4.6 60.9 1.0 C5' X:A2032 4.6 60.0 1.0 O5' X:G1307 4.7 62.9 1.0 O5' X:A2032 4.7 61.2 1.0 C8 X:G1307 4.7 59.7 1.0 OP2 X:A2032 4.8 62.9 1.0 OP1 X:G1307 5.0 61.9 1.0

Magnesium binding site 6 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3112 b:84.4 occ:1.00 OP2 X:A725 2.8 81.5 1.0 OP1 X:C821 3.1 91.8 1.0 P X:A725 4.1 84.5 1.0 P X:C821 4.1 89.2 1.0 OP2 X:C821 4.2 85.6 1.0 O5' X:A725 4.4 84.3 1.0 C5 X:C821 4.5 0.2 1.0 N7 X:A725 4.6 82.8 1.0 C8 X:A725 4.7 86.4 1.0 OP1 X:A725 4.9 89.1 1.0 N7 X:G726 4.9 85.4 1.0

Magnesium binding site 7 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3126 b:58.1 occ:1.00 OP2 X:U830 2.2 69.8 1.0 P X:U830 3.4 72.0 1.0 OP1 X:U830 4.0 69.8 1.0 O3' X:U829 4.0 71.7 1.0 OP2 X:C831 4.1 71.1 1.0 OP1 X:C836 4.1 78.0 1.0 OP2 X:G837 4.4 73.6 1.0 O5' X:U830 4.7 75.0 1.0 O2' X:U829 4.7 72.1 1.0 C3' X:U829 5.0 72.4 1.0 C5' X:U830 5.0 73.9 1.0

Magnesium binding site 8 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3152 b:57.8 occ:1.00 OP2 X:U964 4.3 76.2 1.0 OP2 X:G965 4.3 68.8 1.0 OP1 X:U964 4.7 71.9 1.0 C5' X:U964 4.8 67.2 1.0 P X:U964 4.9 73.0 1.0 OP1 X:A897 5.0 74.6 1.0

Magnesium binding site 9 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3158 b:48.7 occ:1.00 O6 X:G2522 3.5 55.6 1.0 O6 X:G2521 3.9 58.4 1.0 N7 X:G2521 4.1 64.0 1.0 N4 X:C2483 4.3 59.8 1.0 C6 X:G2522 4.6 56.6 1.0 O4 X:U2484 4.6 58.8 1.0 C6 X:G2521 4.7 61.1 1.0 O6 X:G2482 4.8 62.7 1.0 C5 X:G2521 4.8 63.8 1.0

Magnesium binding site 10 out of 84 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3160 b:69.3 occ:1.00 OP1 X:C2479 2.7 71.4 1.0 P X:C2479 4.1 67.8 1.0 OP2 X:A2480 4.3 65.4 1.0 OP2 X:G2521 4.5 72.5 1.0 C5' X:C2479 4.6 67.4 1.0 OP1 X:G2521 4.7 76.2 1.0 OP1 X:U2520 4.8 70.7 1.0 O5' X:C2479 4.9 65.4 1.0 O3' X:A2478 4.9 69.5 1.0 OP1 X:A2480 4.9 68.8 1.0 OP2 X:C2479 5.0 65.2 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