Magnesium in PDB 3dll: The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning

The structure of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning, PDB code: 3dll was solved by D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.98 / 3.50
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	169.700, 410.000, 695.000, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 28

The structure of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 35;

Binding sites:

The binding sites of Magnesium atom in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning (pdb code 3dll). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 35 binding sites of Magnesium where determined in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning, PDB code: 3dll:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg124 b:11.4 occ:1.00 O6 Z:G99 2.8 50.0 1.0 N4 Z:C98 3.1 68.6 1.0 N7 Z:G99 3.2 50.1 1.0 C6 Z:G99 3.5 50.1 1.0 O6 Z:G100 3.6 47.6 1.0 C5 Z:G99 3.7 50.3 1.0 C4 Z:C98 3.7 67.0 1.0 N3 Z:C98 4.2 66.5 1.0 O4 Z:U82 4.2 40.9 1.0 N7 Z:G100 4.3 49.0 1.0 C8 Z:G99 4.4 50.1 1.0 C6 Z:G100 4.4 48.4 1.0 C5 Z:C98 4.4 66.7 1.0 C5 Z:G100 4.7 49.0 1.0 N3 Z:U82 4.7 40.5 1.0 N1 Z:G99 4.8 49.8 1.0 C4 Z:U82 4.9 39.9 1.0 C4 Z:G99 5.0 50.4 1.0

Magnesium binding site 2 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg125 b:1.1 occ:1.00 O6 Z:G85 3.7 24.4 1.0 N7 Z:G85 3.8 27.7 1.0 OP2 Z:C83 4.3 38.2 1.0 O6 Z:G84 4.4 26.8 1.0 N7 Z:G84 4.4 29.1 1.0 N6 Z:A86 4.5 44.8 1.0 C6 Z:G85 4.5 25.6 1.0 C5 Z:G85 4.5 25.9 1.0 C6 Z:G84 4.8 27.0 1.0 C5 Z:G84 4.8 28.0 1.0 C8 Z:G85 4.9 27.1 1.0

Magnesium binding site 3 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg126 b:12.7 occ:1.00 O2' Z:C98 4.1 62.9 1.0 C1' Z:G84 4.8 31.9 1.0 N3 Z:G84 4.8 26.6 1.0 O2 Z:C98 4.9 66.1 1.0 O2 Z:C83 4.9 29.4 1.0 C1' Z:G99 5.0 52.3 1.0

Magnesium binding site 4 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg127 b:3.9 occ:1.00 OP2 Z:G105 3.7 57.2 1.0 N6 Z:A74 4.2 68.5 1.0 OP1 Z:A104 4.2 59.8 1.0 OP2 Z:C73 4.3 68.7 1.0 N7 Z:A74 4.4 67.7 1.0 P Z:G105 4.9 56.6 1.0 C6 Z:A74 4.9 67.7 1.0 C5 Z:A74 4.9 67.7 1.0

Magnesium binding site 5 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2881 b:10.7 occ:1.00 OP1 X:G961 3.0 39.6 1.0 OP1 Z:A91 3.7 52.3 1.0 O6 Z:G89 4.1 64.8 1.0 C5' X:G961 4.2 39.3 1.0 P X:G961 4.3 39.5 1.0 O5' X:G961 4.5 39.3 1.0

Magnesium binding site 6 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2882 b:49.4 occ:1.00 OP1 X:G2466 3.3 34.4 1.0 N1 Z:A91 3.8 40.7 1.0 C2 Z:A91 3.9 40.2 1.0 P X:G2466 4.5 33.5 1.0 O3' X:G2465 4.7 34.2 1.0 O2' X:A1039 4.8 55.3 1.0 N4 Z:C90 4.8 47.3 1.0 C6 Z:A91 4.8 40.4 1.0 N3 Z:A91 5.0 39.5 1.0

Magnesium binding site 7 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2883 b:1.1 occ:1.00 O4 X:U2222 3.3 22.4 1.0 O4 X:U2057 3.4 6.7 1.0 O4 X:U2058 4.0 11.7 1.0 O6 X:G2221 4.1 9.9 1.0 N6 X:A2060 4.3 23.1 1.0 C4 X:U2222 4.3 21.0 1.0 C4 X:U2057 4.3 6.2 1.0 N7 X:G2217 4.4 29.6 1.0 C5 X:U2057 4.7 6.5 1.0 C8 X:G2217 4.8 29.7 1.0 C5 X:U2222 4.9 20.4 1.0 N7 X:G2221 5.0 12.0 1.0

Magnesium binding site 8 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2884 b:19.4 occ:1.00 OP1 X:G2415 2.7 8.2 1.0 OP2 X:G2415 3.2 7.9 1.0 P X:G2415 3.3 8.3 1.0 O2' X:U2224 4.2 18.0 1.0 C5' X:G2415 4.2 8.2 1.0 O5' X:G2415 4.2 8.2 1.0 OP2 X:G2225 4.5 21.1 1.0 O3' X:A2414 4.7 7.3 1.0

Magnesium binding site 9 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2885 b:45.2 occ:1.00 OP2 X:C1385 3.1 39.7 1.0 OP2 X:A1386 3.2 55.0 1.0 O4 X:U1370 3.6 42.0 1.0 N2 X:G1371 3.6 60.9 1.0 OP1 X:C1385 3.6 39.3 1.0 P X:C1385 3.8 39.5 1.0 N1 X:G1371 3.9 60.1 1.0 C2 X:G1371 4.3 60.7 1.0 O5' X:C1385 4.4 41.6 1.0 P X:A1386 4.7 54.7 1.0 C4 X:U1370 4.8 41.9 1.0 O6 X:G1387 4.9 36.0 1.0 O6 X:G1369 4.9 41.2 1.0 C6 X:G1371 5.0 59.3 1.0

Magnesium binding site 10 out of 35 in the The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl- Transferase Center and Effect Trna Positioning within 5.0Å range: probe atom residue distance (Å) B Occ X:Mg2886 b:15.4 occ:1.00 OP1 X:A747 2.9 9.0 1.0 O3' X:G746 3.4 8.6 1.0 P X:A747 3.6 9.8 1.0 OP2 X:A747 4.0 8.9 1.0 C5' X:G746 4.1 10.2 1.0 C3' X:G746 4.4 8.4 1.0 C4' X:G746 4.4 9.3 1.0 C5' X:A1753 4.6 16.2 1.0 OP1 X:A1753 4.7 7.6 1.0 OP2 X:G1754 4.7 15.0 1.0 OP1 X:G746 4.9 10.0 1.0

D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, P.Fucini. The Oxazolidinone Antibiotics Perturb the Ribosomal Peptidyl-Transferase Center and Effect Trna Positioning Proc.Natl.Acad.Sci.Usa V. 105 13339 2008.
ISSN: ISSN 0027-8424
PubMed: 18757750
DOI: 10.1073/PNAS.0804276105