Magnesium in PDB 4b3t: Crystal Structure of the 30S Ribosome in Complex with Compound 39

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 39, PDB code: 4b3t was solved by C.L.Ng, K.Lang, D.Shcherbakov, T.Matt, D.Perez-Fernandez, R.Patak, M.Meyer, S.Duscha, R.Akbergenov, H.Boukari, P.Freihofer, I.Kudyba, M.S.K.Reddy, R.S.Nandurikar, V.Ramakrishnan, A.Vasella, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.730, 401.730, 173.910, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.3

The structure of Crystal Structure of the 30S Ribosome in Complex with Compound 39 also contains other interesting chemical elements:

Potassium	(K)	17 atoms
Chlorine	(Cl)	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 - 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 - 219;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 30S Ribosome in Complex with Compound 39 (pdb code 4b3t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 219 binding sites of Magnesium where determined in the Crystal Structure of the 30S Ribosome in Complex with Compound 39, PDB code: 4b3t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2545 b:78.7 occ:1.00 O6 A:G703 2.6 81.2 1.0 O2 A:C701 2.7 81.5 1.0 O2' A:C701 3.4 72.2 1.0 C6 A:G703 3.4 79.5 1.0 C1' A:C701 3.8 70.6 1.0 C2 A:C701 3.8 81.2 1.0 N1 A:G703 4.0 79.1 1.0 O3' A:C701 4.1 70.6 1.0 C2' A:C701 4.1 70.3 1.0 OP2 A:A702 4.2 77.4 1.0 C5 A:G703 4.3 78.0 1.0 N1 A:C701 4.3 80.0 1.0 N7 A:G703 4.7 78.3 1.0 C3' A:C701 4.8 70.0 1.0 P A:A702 4.8 76.6 1.0 O4' A:C701 4.9 69.7 1.0 N3 A:C701 4.9 82.5 1.0

Magnesium binding site 2 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2546 b:94.5 occ:1.00 O6 A:G77 3.2 67.2 1.0 O6 A:G78 3.6 67.2 1.0 N7 A:G77 3.9 64.2 1.0 C6 A:G77 4.0 64.7 1.0 N7 A:G78 4.1 64.3 1.0 C5 A:G77 4.2 63.6 1.0 C6 A:G78 4.5 65.4 1.0 C5 A:G78 4.7 64.2 1.0 C8 A:G77 5.0 64.7 1.0

Magnesium binding site 3 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2547 b:81.3 occ:1.00 OP2 A:G731 3.5 58.0 1.0 OP1 A:G730 4.0 61.3 1.0 OP1 A:C1527 4.1 54.8 1.0 N7 A:G731 4.1 50.6 1.0 C8 A:G731 4.5 50.9 1.0 C5' A:G730 4.7 63.4 1.0 P A:G730 4.8 58.8 1.0 O5' A:G730 4.8 61.8 1.0 P A:G731 4.9 58.0 1.0

Magnesium binding site 4 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2548 b:48.5 occ:1.00 MG A:MG2707 1.6 48.3 1.0 N7 A:G581 2.1 49.8 1.0 C8 A:G581 2.8 53.1 1.0 N7 A:G758 2.9 60.8 1.0 O6 A:G758 3.3 62.1 1.0 C5 A:G581 3.3 51.4 1.0 C5 A:G758 3.6 61.5 1.0 OP2 A:G581 3.8 65.1 1.0 C6 A:G758 3.8 61.2 1.0 O6 A:G581 3.9 54.8 1.0 C8 A:G758 4.0 60.1 1.0 C6 A:G581 4.0 51.0 1.0 N9 A:G581 4.0 55.1 1.0 C4 A:G581 4.3 52.1 1.0 OP2 A:U580 4.5 65.8 1.0 O5' A:G581 4.5 62.4 1.0 P A:G581 4.8 65.7 1.0 C4 A:G758 4.9 61.1 1.0 C5 A:U580 5.0 52.4 1.0

Magnesium binding site 5 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2549 b:61.1 occ:1.00 O6 A:G260 2.6 72.2 1.0 OP1 A:U264 2.8 58.4 1.0 O4 A:U261 2.9 69.0 1.0 NH2 T:ARG76 3.2 89.1 1.0 C6 A:G260 3.6 71.7 1.0 OP2 A:U264 3.6 60.3 1.0 P A:U264 3.7 60.1 1.0 C4 A:U261 3.9 69.3 1.0 N1 A:G260 4.2 70.6 1.0 N3 A:U261 4.4 69.1 1.0 CZ T:ARG76 4.5 89.8 1.0 C5 A:G260 4.7 72.1 1.0 O5' A:U264 4.7 60.2 1.0 O3' A:A263 4.9 60.2 1.0 N1 A:G189G 4.9 65.9 1.0 OP2 A:G265 4.9 73.3 1.0

Magnesium binding site 6 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2550 b:63.6 occ:1.00 OP1 A:U387 2.5 62.1 1.0 O2' A:C58 2.9 67.0 1.0 OP1 A:G388 3.5 56.1 1.0 O3' A:C58 3.6 66.8 1.0 C5' A:A59 3.6 67.2 1.0 P A:U387 3.6 61.8 1.0 C5' A:U387 4.1 76.8 1.0 O5' A:U387 4.1 75.9 1.0 OP2 A:U387 4.1 60.4 1.0 C2' A:C58 4.1 67.4 1.0 MG A:MG2633 4.1 72.3 1.0 OP1 A:A59 4.2 74.5 1.0 C3' A:C58 4.3 66.9 1.0 P A:A59 4.4 75.1 1.0 O5' A:A59 4.5 67.4 1.0 C8 A:G388 4.5 68.3 1.0 C4' A:C58 4.6 67.8 1.0 P A:G388 4.6 60.2 1.0 C4' A:A59 4.7 66.5 1.0 N7 A:G388 4.8 68.7 1.0 OP2 A:G388 4.8 61.1 1.0 O3' A:C386 5.0 63.5 1.0

Magnesium binding site 7 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2551 b:39.0 occ:1.00 O4 A:U12 2.7 57.7 1.0 O6 A:G22 2.7 59.8 1.0 O6 A:G21 3.1 68.3 1.0 O6 A:G11 3.1 56.4 1.0 N4 A:C23 3.6 56.1 1.0 C4 A:U12 3.6 54.8 1.0 C6 A:G21 3.6 65.1 1.0 N3 A:U12 3.8 55.7 1.0 C6 A:G22 3.9 58.7 1.0 N1 A:G21 4.1 65.2 1.0 C6 A:G11 4.1 56.7 1.0 C5 A:G21 4.4 63.7 1.0 N7 A:G22 4.6 57.2 1.0 C5 A:G22 4.6 57.8 1.0 C4 A:C23 4.7 54.1 1.0 N7 A:G21 4.9 64.2 1.0 N1 A:G22 4.9 59.0 1.0 C5 A:U12 5.0 54.6 1.0 N1 A:G11 5.0 56.0 1.0

Magnesium binding site 8 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2552 b:75.5 occ:1.00 OP2 A:G667 2.8 66.4 1.0 O3' A:A665 2.8 63.4 1.0 O2' A:A665 2.9 57.6 1.0 O5' A:G666 2.9 57.3 1.0 P A:G666 3.4 70.0 1.0 OP1 A:G666 3.7 69.3 1.0 C3' A:A665 3.9 61.3 1.0 C2' A:A665 3.9 59.2 1.0 C5' A:G666 4.0 56.7 1.0 P A:G667 4.2 67.3 1.0 C3' A:G666 4.3 57.9 1.0 C4' A:A665 4.4 62.4 1.0 O2' A:C732 4.6 67.7 1.0 O3' A:G666 4.6 58.6 1.0 C8 A:G666 4.7 64.8 1.0 C4' A:G666 4.7 57.4 1.0 OP2 A:G666 4.8 70.3 1.0 N7 A:G667 4.9 58.3 1.0 N7 A:G666 4.9 64.9 1.0

Magnesium binding site 9 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2553 b:0.3 occ:1.00 OP1 A:C883 3.0 54.6 1.0 O3' A:C882 3.5 43.6 1.0 P A:C883 3.8 52.3 1.0 O6 A:G890 4.5 68.7 1.0 OP2 A:G906 4.6 56.0 1.0 C3' A:C882 4.6 43.6 1.0 C4' A:C882 4.6 43.5 1.0 C5' A:C883 4.8 47.0 1.0 O5' A:C883 4.8 45.1 1.0 C5' A:C882 4.9 44.5 1.0 OP2 A:C883 5.0 52.5 1.0

Magnesium binding site 10 out of 219 in the Crystal Structure of the 30S Ribosome in Complex with Compound 39


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the 30S Ribosome in Complex with Compound 39 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2554 b:67.2 occ:1.00 O6 A:G584 3.5 57.8 1.0 N2 A:G758 3.6 61.4 1.0 OP2 A:A583 3.7 64.5 1.0 O4 A:U757 3.8 66.0 1.0 N7 A:G584 3.9 52.3 1.0 N4 A:C756 3.9 56.4 1.0 O6 A:G585 4.0 57.1 1.0 C2 A:G758 4.2 62.3 1.0 C6 A:G584 4.3 55.4 1.0 N1 A:G758 4.5 61.8 1.0 C5 A:G584 4.5 54.5 1.0 C4 A:U757 4.7 63.1 1.0 N3 A:U757 4.9 62.1 1.0 OP2 A:U582 4.9 73.3 1.0

D.Perez-Fernandez, D.Shcherbakov, T.Matt, N.C.Leong, I.Kudyba, S.Duscha, H.Boukari, R.Patak, S.R.Dubakka, K.Lang, M.Meyer, R.Akbergenov, P.Freihofer, S.Vaddi, P.Thommes, V.Ramakrishnan, A.Vasella, E.C.Bottger. 4'-O-Substitutions Determine Selectivity of Aminoglycoside Antibiotics Nat.Commun. V. 5 3112 2014.
ISSN: ESSN 2041-1723
PubMed: 24473108
DOI: 10.1038/NCOMMS4112