Magnesium in PDB 4wfa: The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid

The structure of The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid, PDB code: 4wfa 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)	64.88 / 3.39
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	279.922, 279.922, 870.586, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 24.3

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

Fluorine	(F)	1 atom
Manganese	(Mn)	195 atoms
Sodium	(Na)	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 - 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 - 246;

Binding sites:

The binding sites of Magnesium atom in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid (pdb code 4wfa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 246 binding sites of Magnesium where determined in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid, PDB code: 4wfa:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3011 b:85.0 occ:1.00 OP1 X:G1340 3.6 82.5 1.0 O2' X:G1687 4.2 81.3 1.0 O3' X:G1687 4.4 86.1 1.0 C5' X:U1688 4.4 75.8 1.0 OP1 X:U1688 4.6 84.9 1.0

Magnesium binding site 2 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3012 b:13.6 occ:0.50 C5' X:A1052 4.4 53.7 1.0 C4' X:G602 4.7 52.6 1.0 C4' X:A1052 4.8 55.4 1.0 OP1 X:A1053 4.9 52.6 1.0 C5' X:G602 5.0 51.1 1.0

Magnesium binding site 3 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3013 b:61.2 occ:1.00 OP1 X:A1052 2.3 49.9 1.0 P X:A1052 3.8 50.5 1.0 O3' X:C1051 4.4 50.9 1.0 OP2 X:A1052 4.5 50.6 1.0 N7 X:A1052 4.5 50.1 1.0 C8 X:A1052 4.5 50.4 1.0 C2' X:C1051 4.7 50.8 1.0 O5' X:A1052 4.8 52.5 1.0 O2' X:C1051 4.9 50.6 1.0 OP1 X:C603 4.9 47.6 1.0

Magnesium binding site 4 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3014 b:85.6 occ:1.00 OP2 X:A713 3.5 77.8 1.0 OP1 X:A713 3.8 85.7 1.0 OP1 X:U712 4.1 70.0 1.0 P X:A713 4.2 83.3 1.0 O2' X:G197 4.9 77.5 1.0 OP1 X:G255 4.9 73.6 1.0

Magnesium binding site 5 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3015 b:36.0 occ:0.50 OP2 X:G257 4.3 65.7 1.0 OP1 X:G257 4.7 70.6 1.0 OP1 X:C256 4.7 76.1 1.0

Magnesium binding site 6 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3016 b:81.3 occ:1.00 OP2 X:G745 2.4 0.2 1.0 P X:G745 3.7 0.4 1.0 N7 X:G745 3.9 0.8 1.0 O5' X:G745 4.0 0.6 1.0 C8 X:G745 4.2 0.8 1.0 O5' X:A744 4.2 91.6 1.0 OP1 X:A744 4.3 96.7 1.0 OP2 X:A744 4.3 89.9 1.0 P X:A744 4.5 92.1 1.0 OP1 X:G745 4.6 0.1 1.0 O3' X:A744 4.8 94.0 1.0 OP2 X:G746 5.0 0.9 1.0

Magnesium binding site 7 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3017 b:75.1 occ:1.00 O6 X:G1211 4.2 97.2 1.0 O4 X:U1210 4.7 78.9 1.0

Magnesium binding site 8 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3018 b:76.4 occ:1.00 OP1 X:U2519 3.0 54.6 1.0 O4' X:C2600 3.6 70.5 1.0 O5' X:U2519 3.8 63.2 1.0 OP1 X:A2480 3.8 61.1 1.0 P X:U2519 3.8 59.3 1.0 C1' X:C2600 4.0 74.8 1.0 O3' X:U2518 4.0 71.4 1.0 N1 X:C2600 4.1 75.4 1.0 C6 X:C2600 4.2 71.9 1.0 OP2 X:U2520 4.6 62.0 1.0 C5' X:U2519 4.7 67.8 1.0 C2 X:C2600 4.8 80.0 1.0 C4' X:C2600 4.9 68.5 1.0 C5 X:C2600 5.0 72.7 1.0

Magnesium binding site 9 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3019 b:69.3 occ:1.00 O2 X:U2384 3.6 68.0 1.0 N6 X:A2388 4.0 69.2 1.0 N3 X:C2383 4.3 64.4 1.0 C2 X:U2384 4.4 67.8 1.0 N7 X:A2388 4.5 71.5 1.0 O6 X:G2389 4.5 58.9 1.0 N4 X:C2383 4.7 61.6 1.0 N3 X:U2384 4.9 66.8 1.0 C6 X:A2388 5.0 71.2 1.0

Magnesium binding site 10 out of 246 in the The Crystal Structure of the Large Ribosomal Subunit of Staphylococcus Aureus in Complex with Linezolid


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 Linezolid within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg3020 b:53.4 occ:1.00 N7 X:G1320 3.1 86.6 1.0 C8 X:G1320 4.0 88.0 1.0 C5 X:G1320 4.1 81.0 1.0 O6 X:G1320 4.1 78.5 1.0 OP2 X:U1319 4.1 98.3 1.0 OP2 X:G1320 4.4 0.3 1.0 C6 X:G1320 4.4 77.4 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