Magnesium in PDB 4wfb: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205, PDB code: 4wfb was solved by Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, E.Zimmerman, H.Rozenberg, A.Bashan, A.E.Yonath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.54 / 3.43
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	280.918, 280.918, 875.585, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 24.2

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 also contains other interesting chemical elements:

Manganese

(Mn)

311 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 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110; Page 12, Binding sites: 111 - 111;

Binding sites:

The binding sites of Magnesium atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205 (pdb code 4wfb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 111 binding sites of Magnesium where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205, PDB code: 4wfb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3017 b:53.3 occ:1.00 OP1 X:A868 2.4 40.1 1.0 P X:A868 3.4 40.0 1.0 OP2 X:G869 3.5 45.7 1.0 OP2 X:A868 3.6 39.6 1.0 O5' X:A868 3.9 41.0 1.0 C5' X:A868 4.3 41.6 1.0 P X:G869 4.5 47.2 1.0 C5' X:A2300 4.7 42.2 1.0 O3' X:U867 4.7 39.0 1.0 C4' X:A2300 4.8 41.7 1.0 O3' X:A868 4.9 43.5 1.0 OP1 X:G869 4.9 48.0 1.0

Magnesium binding site 2 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3026 b:50.2 occ:1.00 OP1 X:U2636 3.2 58.8 1.0 OP1 X:G2609 3.3 44.5 1.0 OP1 X:G2635 4.5 55.8 1.0 O5' X:G2635 4.5 54.9 1.0 P X:U2636 4.5 58.4 1.0 P X:G2609 4.6 45.0 1.0 OP2 X:G2635 4.7 56.9 1.0 P X:G2635 4.7 56.4 1.0 C3' X:G2608 5.0 51.9 1.0 OP2 X:U2636 5.0 58.1 1.0

Magnesium binding site 3 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3027 b:38.6 occ:1.00 OP2 X:G875 4.2 46.1 1.0 O2' X:A2475 4.5 45.2 1.0 OP1 X:G875 4.7 46.4 1.0 P X:G875 4.9 46.8 1.0 O3' X:A2475 5.0 45.3 1.0

Magnesium binding site 4 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3028 b:66.2 occ:1.00 OP2 X:A713 3.6 60.1 1.0 OP1 X:U712 4.4 55.9 1.0 OP1 X:A713 4.4 62.9 1.0 P X:A713 4.5 61.8 1.0

Magnesium binding site 5 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3029 b:55.1 occ:1.00 OP2 X:C2468 4.1 51.8 1.0 OP1 X:C2468 4.2 50.8 1.0 OP1 X:C2469 4.3 47.5 1.0 P X:C2468 4.7 52.0 1.0 C8 X:A2089 4.8 53.0 1.0

Magnesium binding site 6 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3030 b:59.1 occ:1.00 N1 X:A2387 4.3 58.0 1.0 O6 X:G2455 4.4 46.0 1.0 OP1 X:C2287 4.6 48.3 1.0 N7 X:G2455 4.6 48.7 1.0 C2 X:A2387 4.7 58.9 1.0 C6 X:G2455 4.9 46.4 1.0

Magnesium binding site 7 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3031 b:64.8 occ:1.00 OP1 X:C2100 2.8 49.5 1.0 OP2 X:C2100 3.5 48.5 1.0 P X:C2100 3.5 48.8 1.0 N7 X:A838 3.6 64.9 1.0 O3' X:G2099 4.0 47.7 1.0 OP1 X:A2268 4.1 60.4 1.0 N6 X:A838 4.4 65.3 1.0 C8 X:A838 4.5 64.6 1.0 C5' X:G2099 4.5 45.6 1.0 C5 X:A838 4.6 64.6 1.0 OP2 X:A2268 4.7 63.4 1.0 C3' X:G2099 4.9 46.7 1.0 P X:A2268 4.9 62.3 1.0 O5' X:G2099 4.9 45.7 1.0 MG X:MG3167 4.9 0.0 1.0 C6 X:A838 4.9 64.8 1.0 O5' X:C2100 5.0 49.3 1.0

Magnesium binding site 8 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3042 b:75.0 occ:1.00 OP2 X:G2630 2.3 82.6 1.0 OP2 X:A2629 2.5 0.8 1.0 P X:A2629 3.8 0.3 1.0 P X:G2630 3.8 85.6 1.0 O5' X:A2629 3.9 0.5 1.0 O3' X:C2628 4.5 78.9 1.0 O3' X:A2629 4.5 0.7 1.0 OP1 X:G2630 4.6 86.1 1.0 O5' X:G2630 4.7 87.1 1.0 C5' X:G2630 4.9 85.9 1.0 OP1 X:A2629 5.0 0.2 1.0

Magnesium binding site 9 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3043 b:75.7 occ:1.00 OP1 X:C777 2.5 80.6 1.0 OP1 X:G805 3.0 65.8 1.0 P X:C777 3.3 81.9 1.0 OP2 X:C777 3.4 82.3 1.0 OP2 X:G805 3.9 64.4 1.0 P X:G805 4.0 65.0 1.0 O3' X:C776 4.0 65.8 1.0 OP1 X:G2007 4.5 66.0 1.0 O5' X:C777 4.7 81.9 1.0 O3' X:G804 4.9 69.5 1.0

Magnesium binding site 10 out of 111 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Bc-3205


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 Bc-3205 within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3044 b:27.8 occ:1.00 O6 X:G2851 2.8 45.6 1.0 O6 X:G2850 3.0 45.2 1.0 N7 X:G2851 3.1 47.2 1.0 N7 X:G2850 3.4 46.4 1.0 C6 X:G2851 3.5 46.1 1.0 C6 X:G2850 3.5 45.8 1.0 C5 X:G2851 3.6 46.9 1.0 C5 X:G2850 3.7 46.4 1.0 N B:SER65 3.7 40.3 1.0 CA B:SER65 3.9 40.2 1.0 CB B:LYS64 4.1 69.6 1.0 CB B:SER65 4.2 40.5 1.0 C8 X:G2851 4.3 47.9 1.0 C8 X:G2850 4.4 47.1 1.0 CG B:LYS64 4.6 70.3 1.0 C B:LYS64 4.6 69.2 1.0 N1 X:G2850 4.7 46.1 1.0 N1 X:G2851 4.8 46.0 1.0 C4 X:G2850 4.9 47.1 1.0 CA B:LYS64 4.9 69.5 1.0 C4 X:G2851 5.0 47.4 1.0

Z.Eyal, D.Matzov, M.Krupkin, I.Wekselman, S.Paukner, E.Zimmerman, H.Rozenberg, A.Bashan, A.Yonath. Structural Insights Into Species-Specific Features of the Ribosome From the Pathogen Staphylococcus Aureus. Proc.Natl.Acad.Sci.Usa V. 112 E5805 2015.
ISSN: ESSN 1091-6490
PubMed: 26464510
DOI: 10.1073/PNAS.1517952112