Magnesium in PDB 3cf5: Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans

The structure of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans, PDB code: 3cf5 was solved by J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.T.Spahn, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.900, 408.900, 694.500, 90.00, 90.00, 90.00
R / Rfree (%)	27.6 / 31.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Magnesium atom in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans (pdb code 3cf5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 36 binding sites of Magnesium where determined in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans, PDB code: 3cf5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg167 b:3.4 occ:1.00 ND2 M:ASN58 2.4 25.0 1.0 CG M:ASN58 3.8 23.9 1.0 OP1 X:U2700 4.3 12.8 1.0 OP1 X:G2699 4.4 3.4 1.0 OP2 X:G2664 4.4 8.7 1.0 OD1 M:ASN58 4.6 26.5 1.0 CB M:ASN58 4.6 20.3 1.0 C5' X:G2664 4.7 9.4 1.0

Magnesium binding site 2 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2881 b:59.5 occ:1.00 OP1 X:G2466 3.9 43.8 1.0 O2' X:A1039 4.3 63.9 1.0 O3' X:G2465 4.7 43.1 1.0 C2 Z:A91 4.7 25.3 1.0 N1 Z:A91 4.7 26.2 1.0 P X:G2466 4.9 43.6 1.0

Magnesium binding site 3 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2882 b:12.9 occ:1.00 O4 X:U2222 3.9 15.9 1.0 N7 X:A2220 4.0 20.0 1.0 O6 X:G2221 4.1 19.0 1.0 N7 X:G2221 4.2 18.7 1.0 O4 X:U2057 4.5 15.4 1.0 C5 X:A2220 4.6 18.3 1.0 C8 X:A2220 4.6 18.9 1.0 C4 X:U2222 4.6 14.4 1.0 C5 X:U2222 4.7 13.8 1.0 N7 X:G2217 4.7 29.3 1.0 N6 X:A2220 4.7 18.9 1.0 C8 X:G2217 4.8 30.1 1.0 C6 X:G2221 4.9 18.3 1.0 C6 X:A2220 4.9 18.0 1.0 C5 X:G2221 4.9 17.8 1.0

Magnesium binding site 4 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2883 b:49.1 occ:1.00 OP1 X:G2415 2.3 26.2 1.0 P X:G2415 3.2 26.0 1.0 OP2 X:G2415 3.3 25.9 1.0 O5' X:G2415 4.1 24.2 1.0 C5' X:G2415 4.3 21.4 1.0 O3' X:A2414 4.5 26.2 1.0 O2' X:U2224 4.9 15.8 1.0

Magnesium binding site 5 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2884 b:55.4 occ:1.00 O4 X:U1370 3.1 46.9 1.0 OP2 X:C1385 4.1 58.3 1.0 O6 X:G1369 4.1 52.8 1.0 C4 X:U1370 4.3 46.7 1.0 OP1 X:C1385 4.6 58.3 1.0 N2 X:G1371 4.7 52.2 1.0 N1 X:G1371 4.8 50.9 1.0 P X:C1385 4.8 58.2 1.0 N7 X:G1369 4.9 50.5 1.0 C6 X:G1369 5.0 51.8 1.0

Magnesium binding site 6 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2885 b:56.2 occ:1.00 OP1 X:G746 3.4 18.6 1.0 OP2 X:A747 3.4 16.4 1.0 OP2 X:G772 3.9 26.8 1.0 OP1 X:A747 3.9 14.9 1.0 O5' X:G746 4.0 16.9 1.0 P X:A747 4.1 16.1 1.0 P X:G746 4.1 18.3 1.0 C5' X:G746 4.3 14.8 1.0 O3' X:G746 4.5 14.2 1.0 OP2 X:C771 4.6 24.7 1.0 OP2 X:G746 4.6 17.9 1.0 C3' X:G746 4.8 13.6 1.0

Magnesium binding site 7 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2886 b:41.6 occ:1.00 OP1 X:G772 2.6 27.8 1.0 OP2 X:G773 3.5 22.3 1.0 OP1 X:C745 3.7 21.5 1.0 P X:G772 3.9 27.0 1.0 OP1 X:G773 4.2 23.0 1.0 P X:G773 4.3 22.8 1.0 OP2 X:G746 4.4 17.9 1.0 OP2 X:G772 4.4 26.8 1.0 O5' X:G772 4.5 24.1 1.0 C5' X:G772 4.7 23.9 1.0 O3' X:G772 4.8 21.8 1.0 P X:C745 4.9 22.1 1.0

Magnesium binding site 8 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2887 b:3.4 occ:1.00 OP2 X:G1767 1.8 20.8 1.0 P X:G1767 3.1 20.9 1.0 O5' X:G1767 3.7 21.2 1.0 OP1 X:G1767 4.0 20.7 1.0 N7 X:G1767 4.0 19.3 1.0 C8 X:G1767 4.2 19.4 1.0 O3' X:U1766 4.3 17.5 1.0 OP2 X:U1766 4.7 19.0 1.0 C3' X:U1766 4.7 15.9 1.0 O5' X:U1766 4.8 16.3 1.0 OP1 X:A1964 4.8 22.6 1.0 OP1 X:U1766 4.9 18.2 1.0 P X:U1766 5.0 18.3 1.0

Magnesium binding site 9 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2888 b:3.4 occ:1.00 OP1 X:C1765 2.6 22.5 1.0 OP1 X:A1777 3.1 11.9 1.0 OP2 X:A1777 3.6 14.5 1.0 P X:A1777 3.8 13.3 1.0 O2' X:G1763 4.0 21.1 1.0 N3 X:G1763 4.0 24.9 1.0 P X:C1765 4.1 22.0 1.0 N2 X:G1763 4.2 26.0 1.0 C5' X:A1777 4.3 10.0 1.0 O5' X:A1777 4.6 11.3 1.0 C2 X:G1763 4.6 25.8 1.0 OP2 X:C1765 4.7 21.8 1.0 C1' X:G1763 4.8 21.2 1.0 O3' X:A1764 4.8 22.6 1.0 O6 X:G1767 4.8 22.2 1.0 C2' X:G1763 4.9 21.1 1.0 OP2 X:U1766 5.0 19.0 1.0

Magnesium binding site 10 out of 36 in the Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Thiopeptide Antibiotic Thiostrepton Bound to the Large Ribosomal Subunit of Deinococcus Radiodurans within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2889 b:3.4 occ:1.00 OP2 X:A2034 4.0 6.5 1.0 N7 X:A2034 4.1 8.0 1.0 OP1 X:G2557 4.1 3.8 1.0 C8 X:A2034 4.2 7.9 1.0 OP1 X:U2592 4.3 8.9 1.0 OP2 X:G2557 4.4 3.4 1.0 N7 X:A2593 4.6 7.5 1.0 OP2 X:C2033 4.7 7.8 1.0 P X:G2557 4.8 5.5 1.0 OP2 X:A2593 4.8 6.4 1.0 C8 X:A2593 4.9 8.4 1.0

J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, P.Fucini. Translational Regulation Via L11: Molecular Switches on the Ribosome Turned on and Off By Thiostrepton and Micrococcin. Mol.Cell V. 30 26 2008.
ISSN: ISSN 1097-2765
PubMed: 18406324
DOI: 10.1016/J.MOLCEL.2008.01.009