Manganese in PDB 5hl7: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin, PDB code: 5hl7 was solved by Z.Eyal, D.Matzov, M.Krupkin, 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)	49.93 / 3.55
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	282.112, 282.112, 875.343, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 22.7

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

Magnesium

(Mg)

240 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; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 274;

Binding sites:

The binding sites of Manganese atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin (pdb code 5hl7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 274 binding sites of Manganese where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin, PDB code: 5hl7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:0.4 occ:1.00 CD2 A:TYR6 3.4 0.5 1.0 CE2 A:TYR6 3.6 0.2 1.0 O2' X:A772 3.9 0.8 1.0 CG A:TYR6 4.1 0.6 1.0 CD1 A:ILE9 4.1 0.5 1.0 CB A:ARG13 4.1 0.8 1.0 C5' X:G773 4.2 0.6 1.0 C4' X:G773 4.2 0.6 1.0 CZ A:TYR6 4.3 0.0 1.0 SD A:MET16 4.5 0.1 1.0 CD1 A:TYR6 4.7 0.5 1.0 CB A:TYR6 4.7 0.9 1.0 CE A:MET16 4.8 0.4 1.0 CE1 A:TYR6 4.8 0.2 1.0 OP2 X:G774 4.9 0.2 1.0 O4' X:G773 4.9 0.9 1.0 OH A:TYR6 5.0 0.6 1.0

Manganese binding site 2 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3001 b:97.0 occ:1.00 OP1 X:A2625 2.2 92.9 1.0 O A:ILE241 3.4 0.7 1.0 O A:HIS232 3.5 1.0 1.0 P X:A2625 3.7 92.8 1.0 O A:GLY233 4.0 96.5 1.0 O A:PRO240 4.1 0.5 1.0 C A:HIS232 4.1 0.7 1.0 O A:GLY234 4.2 98.2 1.0 O3' X:G2624 4.3 93.0 1.0 C A:ILE241 4.3 0.4 1.0 CA A:HIS232 4.5 0.2 1.0 CB A:ALA239 4.5 0.8 1.0 OP2 X:A2625 4.6 93.7 1.0 O A:PRO231 4.6 0.7 1.0 O5' X:A2625 4.7 90.8 1.0 CA A:GLY242 4.7 0.9 1.0 C A:GLY233 4.8 96.2 1.0 C5' X:A2625 4.9 89.7 1.0 N A:GLY242 4.9 0.1 1.0 C A:GLY234 4.9 97.6 1.0 N A:GLY233 4.9 96.8 1.0

Manganese binding site 3 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3012 b:79.9 occ:1.00 OP1 X:A2089 2.6 68.1 1.0 P X:A2089 3.5 68.6 1.0 OP2 X:A2089 3.7 69.3 1.0 OP2 X:C2470 4.0 67.3 1.0 OP2 X:G2471 4.2 61.6 1.0 C5' X:A2089 4.2 69.9 1.0 O5' X:A2089 4.3 69.2 1.0 OP1 X:G2088 4.5 60.4 1.0 N7 X:G2471 4.7 64.2 1.0 C6 X:C2470 4.8 68.9 1.0 C5 X:C2470 4.8 69.8 1.0 O3' X:G2088 4.8 62.0 1.0 O5' X:C2470 4.9 67.2 1.0

Manganese binding site 4 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3013 b:70.4 occ:1.00 OP2 X:G2529 2.1 60.3 1.0 OP2 X:G2088 2.3 60.2 1.0 P X:G2529 3.5 60.0 1.0 P X:G2088 3.7 60.1 1.0 O2' X:C2528 4.0 60.5 1.0 O3' X:C2528 4.1 59.2 1.0 O3' X:A2087 4.3 61.1 1.0 N7 X:G2473 4.3 60.8 1.0 OP1 X:G2529 4.4 59.9 1.0 OP1 X:G2088 4.4 60.4 1.0 OP2 X:G2473 4.5 59.6 1.0 O2' X:A2087 4.5 61.5 1.0 O5' X:G2529 4.6 59.6 1.0 C5' X:G2529 4.6 59.6 1.0 O5' X:G2088 4.8 60.1 1.0 C2' X:C2528 4.8 60.2 1.0 N7 X:G2472 4.8 61.4 1.0 C2' X:G2088 4.8 61.5 1.0 C3' X:G2088 4.8 61.3 1.0 C5' X:G2088 4.9 60.1 1.0 C3' X:C2528 4.9 59.5 1.0 N3 X:A2087 5.0 61.2 1.0 C8 X:G2472 5.0 61.2 1.0

Manganese binding site 5 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3014 b:53.5 occ:1.00 N7 X:G2529 2.4 59.6 1.0 O6 X:G2529 2.8 60.2 1.0 OP1 X:G2473 3.1 59.3 1.0 C5 X:G2529 3.3 59.7 1.0 C6 X:G2529 3.4 60.0 1.0 C8 X:G2529 3.5 59.4 1.0 P X:G2473 4.2 59.7 1.0 OP2 X:G2474 4.2 59.7 1.0 OP2 X:G2473 4.5 59.6 1.0 C4 X:G2529 4.5 59.6 1.0 C2 X:A2087 4.5 61.4 1.0 N9 X:G2529 4.6 59.4 1.0 OP1 X:G2529 4.6 59.9 1.0 O5' X:G2473 4.7 59.9 1.0 O4' X:U619 4.7 56.9 1.0 C4' X:U619 4.7 56.9 1.0 N1 X:G2529 4.8 60.2 1.0 N1 X:A2087 5.0 61.5 1.0

Manganese binding site 6 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3015 b:80.2 occ:1.00 OP1 X:A2475 1.9 60.2 1.0 OP1 X:C2526 2.0 58.9 1.0 O6 X:G613 2.1 59.8 1.0 C6 X:G613 3.2 59.5 1.0 P X:A2475 3.3 60.8 1.0 P X:C2526 3.4 58.8 1.0 OP2 X:A2475 3.8 61.4 1.0 N1 X:G613 3.8 59.3 1.0 OP2 X:U2527 4.0 58.4 1.0 O5' X:C2526 4.1 58.2 1.0 O4 X:U612 4.2 59.1 1.0 O3' X:C2525 4.2 58.6 1.0 O5' X:A2475 4.2 61.4 1.0 O3' X:G2474 4.3 60.8 1.0 N1 X:A2057 4.3 59.4 1.0 C2 X:A2057 4.4 59.2 1.0 C5 X:G613 4.4 59.4 1.0 OP2 X:C2526 4.5 59.4 1.0 C3' X:G2474 4.7 60.2 1.0 O2' X:U611 4.9 60.7 1.0 C4 X:U612 4.9 59.2 1.0 C5' X:C2526 4.9 57.9 1.0 N7 X:G613 4.9 59.6 1.0

Manganese binding site 7 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3016 b:75.2 occ:1.00 OP2 X:A2475 2.3 61.4 1.0 OP2 X:C2525 2.3 60.7 1.0 OP2 X:C2526 2.5 59.4 1.0 O3' X:A2524 3.2 61.5 1.0 P X:C2525 3.3 61.2 1.0 O2' X:A2524 3.5 62.6 1.0 P X:C2526 3.6 58.8 1.0 P X:A2475 3.7 60.8 1.0 OP1 X:C2526 3.7 58.9 1.0 O3' X:G2474 4.0 60.8 1.0 O5' X:C2525 4.0 60.5 1.0 C3' X:A2524 4.3 62.7 1.0 OP2 X:U2476 4.4 63.6 1.0 C2' X:A2524 4.5 63.3 1.0 C3' X:C2525 4.5 59.1 1.0 O3' X:C2525 4.6 58.6 1.0 OP1 X:A2475 4.6 60.2 1.0 OP1 X:C2525 4.7 61.9 1.0 C5' X:C2525 4.7 60.0 1.0 O5' X:C2526 4.8 58.2 1.0 O5' X:A2475 4.8 61.4 1.0 C5' X:A2475 4.9 62.4 1.0

Manganese binding site 8 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3017 b:92.3 occ:1.00 OP1 X:U1007 2.4 63.7 1.0 P X:U1007 3.8 64.8 1.0 OP1 X:C2525 3.8 61.9 1.0 C5' X:U1007 4.0 68.5 1.0 O5' X:U1007 4.1 67.4 1.0 C5' X:A2524 4.2 64.5 1.0 O3' X:G1006 4.6 66.4 1.0 OP1 X:A2524 4.7 67.6 1.0 OP1 X:A991 4.7 63.0 1.0 OP2 X:U1007 4.8 64.4 1.0 C4' X:A2524 5.0 63.2 1.0

Manganese binding site 9 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3018 b:86.8 occ:1.00 OP2 X:U1007 2.1 64.4 1.0 OP1 X:G1006 2.1 64.3 1.0 OP1 X:A992 2.3 60.0 1.0 P X:U1007 3.2 64.8 1.0 P X:A992 3.3 60.1 1.0 OP1 X:U1007 3.5 63.7 1.0 P X:G1006 3.6 64.1 1.0 OP2 X:A992 3.6 61.3 1.0 O3' X:G1006 4.2 66.4 1.0 O3' X:A991 4.2 59.1 1.0 O5' X:U1007 4.4 67.4 1.0 O5' X:G1006 4.4 64.9 1.0 OP2 X:G1006 4.4 64.4 1.0 O5' X:A992 4.5 59.8 1.0 O3' X:G1005 4.6 72.1 1.0 C3' X:G1006 4.6 66.8 1.0 C5' X:G1006 4.8 64.6 1.0 OP1 X:A991 4.8 63.0 1.0

Manganese binding site 10 out of 274 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lefamulin


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 Lefamulin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mn3019 b:0.5 occ:1.00 OP2 X:G1005 3.4 73.8 1.0 N7 X:G1006 3.8 69.5 1.0 OP2 X:G1006 3.9 64.4 1.0 C8 X:G1006 4.0 68.5 1.0 OP2 X:A1004 4.3 71.5 1.0 O4 X:U1007 4.4 69.4 1.0 O5' X:A1004 4.4 68.2 1.0 P X:G1005 4.6 72.1 1.0 O5' X:G1005 4.6 71.7 1.0 P X:A1004 4.7 69.5 1.0 C3' X:A1004 4.8 65.9 1.0 OP1 X:A1004 4.9 68.3 1.0 O3' X:A1004 4.9 64.6 1.0 O5' X:G1006 4.9 64.9 1.0

Z.Eyal, D.Matzov, M.Krupkin, S.Paukner, R.Riedl, H.Rozenberg, E.Zimmerman, A.Bashan, A.Yonath. A Novel Pleuromutilin Antibacterial Compound, Its Binding Mode and Selectivity Mechanism. Sci Rep V. 6 39004 2016.
ISSN: ESSN 2045-2322
PubMed: 27958389
DOI: 10.1038/SREP39004