Manganese 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:

Magnesium

(Mg)

84 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 - 120; Page 13, Binding sites: 121 - 130; Page 14, Binding sites: 131 - 140; Page 15, Binding sites: 141 - 150; Page 16, Binding sites: 151 - 160; Page 17, Binding sites: 161 - 170; Page 18, Binding sites: 171 - 180; Page 19, Binding sites: 181 - 190; Page 20, Binding sites: 191 - 200; Page 21, Binding sites: 201 - 210;

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 210 binding sites of Manganese where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with RB02, PDB code: 5nrg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 210 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 Manganese with other atoms in the Mn 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:Mn3004 b:60.8 occ:1.00 OP2 X:A621 2.4 53.0 1.0 OP2 X:A2045 3.3 50.6 1.0 OP1 X:C2044 3.6 50.4 1.0 P X:A621 3.8 53.3 1.0 O5' X:A621 4.1 53.3 1.0 OP2 X:C2044 4.2 50.8 1.0 N7 X:A621 4.2 52.5 1.0 C8 X:A621 4.3 52.7 1.0 P X:C2044 4.4 50.5 1.0 P X:A2045 4.4 49.5 1.0 OP2 X:A622 4.5 53.2 1.0 OP1 X:A2045 4.7 49.8 1.0 OP1 X:A621 4.7 53.6 1.0 C3' X:G620 4.8 53.1 1.0 OP2 X:G620 4.8 52.7 1.0 O3' X:G620 4.9 53.7 1.0 O5' X:G620 4.9 53.0 1.0

Manganese binding site 2 out of 210 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 Manganese with other atoms in the Mn 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:Mn3005 b:53.7 occ:1.00 OP2 X:A1017 2.9 51.6 1.0 P X:A1017 3.9 51.8 1.0 OP2 X:G613 3.9 55.4 1.0 N6 X:A865 3.9 53.8 1.0 OP1 X:A1017 4.0 52.2 1.0 O2' X:G1016 4.0 52.3 1.0 OP1 X:G613 4.0 57.1 1.0 N1 X:A866 4.1 53.8 1.0 C5 X:U611 4.2 56.8 1.0 O3' X:G1016 4.4 51.8 1.0 P X:G613 4.4 55.6 1.0 OP2 X:U612 4.5 54.7 1.0 C6 X:U611 4.6 55.6 1.0 C2 X:A866 4.7 54.1 1.0 C2' X:G1016 4.8 52.4 1.0 C4 X:U611 4.9 56.5 1.0 C6 X:A866 4.9 53.9 1.0 N6 X:A866 4.9 53.6 1.0 C6 X:A865 5.0 54.2 1.0 N1 X:A865 5.0 54.4 1.0

Manganese binding site 3 out of 210 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 Manganese with other atoms in the Mn 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:Mn3006 b:49.6 occ:1.00 N7 X:G2059 1.6 56.6 1.0 C5 X:G2059 2.2 58.5 1.0 C8 X:G2059 2.8 55.3 1.0 C6 X:G2059 3.0 61.0 1.0 O6 X:G2059 3.1 62.1 1.0 C4 X:G2059 3.5 58.3 1.0 O2 X:C2526 3.6 57.7 1.0 N3 X:C2082 3.8 54.1 1.0 N9 X:G2059 3.8 56.2 1.0 O2 X:C2082 3.9 56.0 1.0 C2 X:A2480 4.2 53.2 1.0 N3 X:A2480 4.2 54.9 1.0 C2 X:C2082 4.2 54.2 1.0 N1 X:G2059 4.3 62.4 1.0 C2 X:C2526 4.5 58.5 1.0 C1' X:G2481 4.5 52.0 1.0 N3 X:C2526 4.5 60.8 1.0 O2 X:U2527 4.7 57.6 1.0 C4 X:C2082 4.7 52.4 1.0 O4' X:G2481 4.8 53.7 1.0 N3 X:G2059 4.8 59.7 1.0 N4 X:C2082 4.8 52.4 1.0

Manganese binding site 4 out of 210 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 Manganese with other atoms in the Mn 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:Mn3007 b:61.1 occ:1.00 OP2 X:C627 2.2 60.3 1.0 P X:C627 3.5 62.5 1.0 OP2 X:A1289 3.7 59.4 1.0 O5' X:C627 4.0 60.3 1.0 C5 X:C627 4.3 57.4 1.0 OP1 X:C627 4.3 65.4 1.0 N7 X:A1289 4.4 57.9 1.0 C8 X:A1289 4.4 55.8 1.0 C6 X:C627 4.6 59.4 1.0 CA N:GLY6 4.6 68.0 1.0 N7 X:G628 4.7 57.4 1.0 OG1 N:THR10 4.7 61.2 1.0 O3' X:G626 4.7 61.2 1.0 O5' X:G626 4.7 57.3 1.0 C3' X:G626 4.9 59.1 1.0 OP2 X:G628 4.9 59.5 1.0

Manganese binding site 5 out of 210 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 Manganese with other atoms in the Mn 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:Mn3008 b:50.6 occ:1.00 OP1 X:C1702 1.3 64.7 1.0 P X:C1702 2.3 64.1 1.0 NE2 B:HIS148 2.4 62.8 1.0 CD2 B:HIS148 3.0 60.7 1.0 OP2 X:C1702 3.1 64.7 1.0 O5' X:C1702 3.2 64.8 1.0 CE1 B:HIS148 3.6 63.7 1.0 O3' X:U1701 3.6 58.5 1.0 C5' X:C1702 3.9 64.2 1.0 OP1 X:C789 4.2 60.4 1.0 CG B:HIS148 4.2 60.4 1.0 OP2 X:U1703 4.3 62.4 1.0 ND1 B:HIS148 4.5 62.3 1.0 O B:SER145 4.7 61.4 1.0 C3' X:U1701 4.9 57.7 1.0 O3' X:A788 4.9 61.0 1.0

Manganese binding site 6 out of 210 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 Manganese with other atoms in the Mn 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:Mn3009 b:59.1 occ:1.00 OP1 X:U856 3.6 55.8 1.0 OP1 X:U855 3.8 52.3 1.0 OP2 X:U855 3.8 52.5 1.0 N7 X:A1291 4.2 53.2 1.0 P X:U855 4.3 52.6 1.0 O3' X:C608 4.4 53.4 1.0 OP1 X:U609 4.8 54.6 1.0 O5' X:U855 4.9 53.0 1.0 O2' X:C608 4.9 53.3 1.0 C8 X:A1291 4.9 53.4 1.0 OD1 O:ASN81 5.0 57.2 1.0

Manganese binding site 7 out of 210 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 Manganese with other atoms in the Mn 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:Mn3010 b:59.3 occ:1.00 O4 X:U2061 3.8 48.2 1.0 OP1 X:A617 3.9 54.5 1.0 OP2 X:C2082 3.9 45.1 1.0 C8 X:A617 4.1 51.5 1.0 O3' X:A2081 4.1 45.3 1.0 N7 X:A617 4.2 51.4 1.0 O6 X:G2062 4.2 48.4 1.0 O2' X:A2081 4.3 45.3 1.0 C5 X:U2061 4.5 50.4 1.0 C4 X:U2061 4.5 48.8 1.0 O5' X:A617 4.6 51.6 1.0 N7 X:G2062 4.6 50.8 1.0 P X:C2082 4.7 45.2 1.0

Manganese binding site 8 out of 210 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 Manganese with other atoms in the Mn 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:Mn3011 b:40.4 occ:1.00 N7 X:G1229 2.2 53.9 1.0 OP2 X:A1228 2.2 52.9 1.0 C5 X:G1229 3.1 54.3 1.0 O6 X:G1229 3.2 54.0 1.0 C8 X:G1229 3.2 54.1 1.0 P X:A1228 3.4 52.6 1.0 C6 X:G1229 3.5 54.3 1.0 OP1 X:A1228 3.8 52.5 1.0 O5' X:A1228 4.0 52.9 1.0 OP2 X:G1229 4.1 53.5 1.0 N9 X:G1229 4.3 54.5 1.0 C4 X:G1229 4.4 54.7 1.0 CG2 I:THR25 4.4 58.2 1.0 N2 X:G863 4.7 53.5 1.0 O3' X:U1227 4.7 52.2 1.0 N1 X:G1229 4.9 54.8 1.0 OP2 X:U1227 4.9 53.1 1.0

Manganese binding site 9 out of 210 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 Manganese with other atoms in the Mn 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:Mn3012 b:72.8 occ:1.00 OP2 X:A1200 2.1 58.4 1.0 P X:A1200 3.6 55.6 1.0 C5' X:A1200 4.2 57.4 1.0 O6 X:G1041 4.3 58.0 1.0 O6 X:G1201 4.3 57.2 1.0 C3' X:A1199 4.3 55.4 1.0 OP1 X:A1200 4.4 54.5 1.0 O5' X:A1200 4.4 55.3 1.0 O3' X:A1199 4.4 54.6 1.0 N4 X:C1202 4.6 57.3 1.0 N4 X:C1042 4.7 58.0 1.0 O5' X:A1199 4.7 57.4 1.0 OP2 X:A1199 5.0 61.1 1.0

Manganese binding site 10 out of 210 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 Manganese with other atoms in the Mn 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:Mn3013 b:67.3 occ:1.00 OP1 X:A1291 3.7 55.6 1.0 O6 X:G625 3.9 55.9 1.0 O6 X:G626 4.0 56.1 1.0 N7 X:G625 4.2 55.8 1.0 N4 X:C624 4.4 55.1 1.0 O6 X:G1294 4.5 53.8 1.0 C6 X:G625 4.7 56.1 1.0 C5 X:C624 4.8 54.8 1.0 C4 X:C624 4.8 55.1 1.0 C5 X:G625 4.8 56.1 1.0 N4 X:C1295 4.9 53.6 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