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

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin, PDB code: 5hkv 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)	50.00 / 3.66
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	280.885, 280.885, 873.522, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 23.4

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

Manganese	(Mn)	338 atoms
Calcium	(Ca)	1 atom

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 - 162;

Binding sites:

The binding sites of Magnesium atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin (pdb code 5hkv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 162 binding sites of Magnesium where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin, PDB code: 5hkv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range:

Magnesium binding site 2 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3034 b:92.3 occ:1.00 OP2 X:A2588 3.0 90.4 1.0 O5' X:A2588 3.4 89.4 1.0 C8 X:A2588 3.6 86.0 1.0 OP2 X:U2589 3.8 92.7 1.0 P X:A2588 3.9 90.5 1.0 N7 X:A2588 3.9 86.2 1.0 C3' X:A2588 4.4 87.9 1.0 N9 X:A2588 4.6 84.6 1.0 C5' X:A2588 4.7 89.5 1.0 C4' X:A2588 4.9 88.1 1.0 O4' X:A2588 5.0 86.6 1.0 C5 X:A2588 5.0 84.9 1.0 OP1 X:A2588 5.0 92.3 1.0 C3' X:C2587 5.0 88.4 1.0

Magnesium binding site 3 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3035 b:89.4 occ:1.00 O4 X:U2590 4.0 92.5 1.0 O4 X:U2589 4.8 92.0 1.0

Magnesium binding site 4 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3036 b:71.0 occ:1.00 O6 X:G7 4.2 90.8 1.0 N7 X:G7 4.3 88.8 1.0 N7 X:A6 4.3 95.5 1.0 N6 X:A6 4.7 97.5 1.0 C6 X:G7 5.0 90.3 1.0

Magnesium binding site 5 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3037 b:58.3 occ:1.00 O2' X:C736 3.4 98.0 1.0 O4' X:C736 3.6 94.2 1.0 C1' X:C736 3.6 95.1 1.0 CB A:ARG43 3.7 0.3 1.0 CD1 A:LEU49 3.8 82.4 1.0 N A:ARG43 3.8 0.7 1.0 C4' X:C736 4.1 95.2 1.0 C2' X:C736 4.2 96.7 1.0 CG A:LEU49 4.2 83.7 1.0 CA A:ARG43 4.3 0.8 1.0 C A:GLY42 4.5 87.1 1.0 O2 X:C735 4.6 90.9 1.0 CB A:LEU49 4.6 83.2 1.0 CA A:GLY42 4.7 87.0 1.0 C3' X:C736 4.9 96.3 1.0 OP1 X:A824 4.9 93.5 1.0 N1 X:C736 4.9 94.2 1.0 N2 X:G817 4.9 93.0 1.0

Magnesium binding site 6 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3038 b:0.4 occ:1.00 OP2 X:A229 3.9 0.6 1.0 MG X:MG3040 4.3 0.2 1.0 OP1 X:A229 4.4 0.0 1.0 O2' X:A259 4.4 0.2 1.0 P X:A229 4.5 0.6 1.0 O3' X:A228 4.6 0.9 1.0 C5' X:A228 4.8 0.9 1.0

Magnesium binding site 7 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3039 b:0.2 occ:1.00 OP1 X:A430 4.7 0.6 1.0 O2' X:C429 4.7 0.2 1.0

Magnesium binding site 8 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3040 b:0.2 occ:1.00 OP2 X:A229 2.2 0.6 1.0 P X:A229 3.5 0.6 1.0 O3' X:G456 3.8 0.9 1.0 OP1 X:A229 4.0 0.0 1.0 OP2 X:G457 4.0 0.3 1.0 O5' X:A229 4.2 0.5 1.0 MG X:MG3038 4.3 0.4 1.0 P X:G457 4.6 0.3 1.0 O3' X:A228 4.7 0.9 1.0 O2' X:G456 4.7 0.4 1.0 C4' X:G456 4.8 0.6 1.0 C3' X:G456 4.9 0.7 1.0

Magnesium binding site 9 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3041 b:76.8 occ:1.00 O2 X:U11 4.1 0.6 1.0 OP1 X:G2658 4.6 78.7 1.0 N1 X:A10 4.8 0.1 1.0 O3' X:G2657 4.9 79.1 1.0

Magnesium binding site 10 out of 162 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Lincomycin


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 Lincomycin within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3042 b:98.2 occ:1.00 OP2 X:C378 2.2 0.5 1.0 OP2 X:C345 2.9 0.4 1.0 O R:EOH203 3.4 48.4 1.0 C3' X:U344 3.4 0.8 1.0 P X:C378 3.5 0.5 1.0 P X:C345 3.7 0.9 1.0 OP2 X:U344 3.9 0.2 1.0 C5' X:C378 3.9 0.9 1.0 OP1 X:C345 3.9 0.9 1.0 C5' X:U344 4.0 0.7 1.0 O3' X:U344 4.0 0.1 1.0 OP1 X:C378 4.1 0.8 1.0 C4' X:U344 4.2 0.6 1.0 O5' X:C378 4.2 0.7 1.0 O2' X:U377 4.2 0.3 1.0 O5' X:U344 4.4 0.6 1.0 C2' X:U344 4.4 1.0 1.0 CD R:PRO78 4.6 0.6 1.0 C1 R:EOH203 4.7 48.4 1.0 CG R:PRO78 4.7 0.1 1.0 O3' X:U377 4.7 0.7 1.0 P X:U344 4.7 0.4 1.0 O2' X:U344 4.9 0.5 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