Magnesium in PDB 4aqy: Structure of Ribosome-Apramycin Complexes

The structure of Structure of Ribosome-Apramycin Complexes, PDB code: 4aqy was solved by T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.50
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.180, 402.180, 175.000, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.5

The structure of Structure of Ribosome-Apramycin Complexes also contains other interesting chemical elements:

Potassium	(K)	15 atoms
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 - 203;

Binding sites:

The binding sites of Magnesium atom in the Structure of Ribosome-Apramycin Complexes (pdb code 4aqy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 203 binding sites of Magnesium where determined in the Structure of Ribosome-Apramycin Complexes, PDB code: 4aqy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2545 b:0.0 occ:1.00 O6 A:G1482 2.4 0.7 1.0 O6 A:G1417 2.9 0.7 1.0 N7 A:G1482 3.1 0.3 1.0 C6 A:G1482 3.2 0.6 1.0 C5 A:G1482 3.5 0.2 1.0 C6 A:G1417 3.6 0.0 1.0 C5 A:G1417 4.3 0.1 1.0 C8 A:G1482 4.4 0.9 1.0 N1 A:G1417 4.5 0.2 1.0 N7 A:G1417 4.5 0.4 1.0 NC4 A:AM23005 4.5 0.8 1.0 N1 A:G1482 4.5 0.2 1.0 C4 A:G1482 4.9 0.9 1.0 C5 A:U1481 4.9 0.8 1.0

Magnesium binding site 2 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2546 b:0.7 occ:1.00 OP2 A:G1120 1.9 0.5 1.0 N7 A:G1120 3.1 0.6 1.0 P A:G1120 3.2 0.2 1.0 C8 A:G1120 3.2 0.7 1.0 O5' A:G1120 3.5 0.1 1.0 MG A:MG2743 3.6 0.5 1.0 C5' A:C1119 3.6 0.9 1.0 C3' A:C1119 3.6 0.1 1.0 O3' A:C1119 3.9 0.4 1.0 C4' A:C1119 4.2 0.1 1.0 OP1 A:G1120 4.4 0.4 1.0 C5 A:G1120 4.4 0.6 1.0 N9 A:G1120 4.6 1.0 1.0 C6 A:C1119 4.7 0.7 1.0 C2' A:C1119 4.8 0.7 1.0 O5' A:C1119 4.8 0.0 1.0 C5' A:G1120 4.9 0.6 1.0 O4' A:C1119 5.0 0.7 1.0

Magnesium binding site 3 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2547 b:0.3 occ:1.00 OP1 A:G758 1.8 0.2 1.0 C5' A:G758 2.1 87.9 1.0 P A:G758 2.2 0.7 1.0 O5' A:G758 2.3 90.7 1.0 O3' A:U757 2.4 87.3 1.0 N2 A:G821 3.1 99.2 1.0 C4' A:G758 3.6 87.3 1.0 C3' A:U757 3.6 83.7 1.0 OP2 A:G758 3.7 0.5 1.0 O2 A:C880 3.7 94.2 1.0 O2' A:U757 3.9 80.2 1.0 O6 A:G576 3.9 94.6 1.0 C2 A:G821 4.1 98.1 1.0 C2' A:U757 4.1 81.4 1.0 C1' A:C880 4.1 86.6 1.0 N3 A:G821 4.1 98.1 1.0 O4' A:G758 4.3 86.3 1.0 C3' A:G758 4.5 88.1 1.0 C2 A:C880 4.5 92.0 1.0 O4' A:C880 4.6 84.7 1.0 O2 A:C879 4.7 87.4 1.0 C4' A:U757 4.7 82.4 1.0 N1 A:C880 4.7 91.4 1.0 O2' A:C880 4.8 88.0 1.0 O3' A:G758 4.9 90.4 1.0

Magnesium binding site 4 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2548 b:0.0 occ:1.00 OP2 A:C307 3.1 0.5 1.0 O6 A:G309 3.3 92.0 1.0 OP2 A:G306 3.6 0.5 1.0 C6 A:G309 4.2 92.3 1.0 N4 A:C308 4.3 0.8 1.0 N7 A:G309 4.4 95.0 1.0 C5 A:C308 4.5 0.6 1.0 O6 A:G310 4.5 82.9 1.0 P A:C307 4.5 0.9 1.0 C5 A:G309 4.6 94.3 1.0 C4 A:C308 4.8 0.3 1.0 P A:G306 4.8 0.6 1.0 N4 A:C291 5.0 0.7 1.0

Magnesium binding site 5 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2549 b:0.9 occ:1.00 O6 A:G592 2.4 0.6 1.0 O4 A:U646 2.9 0.1 1.0 O6 A:G593 3.1 0.2 1.0 C6 A:G592 3.5 1.0 1.0 N4 A:C647 3.9 0.2 1.0 C4 A:U646 4.1 0.8 1.0 C6 A:G593 4.1 0.9 1.0 N4 A:C645 4.2 0.7 1.0 C5 A:G592 4.3 0.8 1.0 N7 A:G592 4.4 0.2 1.0 N1 A:G592 4.4 0.1 1.0 N7 A:G593 4.5 0.9 1.0 N3 A:U646 4.5 0.9 1.0 O6 A:G594 4.6 0.7 1.0 C5 A:G593 4.7 0.8 1.0 C4 A:C647 5.0 0.9 1.0

Magnesium binding site 6 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2550 b:0.7 occ:1.00 O N:ALA2 2.9 0.0 1.0 OP1 A:U1049 3.2 0.4 1.0 OP1 A:G1048 3.4 0.7 1.0 MG A:MG2693 3.8 89.3 1.0 C N:ALA2 4.1 0.0 1.0 P A:G1048 4.2 0.0 1.0 OP1 A:C1203 4.3 0.2 1.0 OP2 A:G1048 4.3 0.4 1.0 P A:U1049 4.5 0.7 1.0 OP2 A:A1204 4.5 0.2 1.0 CA N:ARG3 4.5 0.3 1.0 O5' A:G1048 4.5 0.5 1.0 OP1 A:A1204 4.6 0.8 1.0 OP2 A:U1049 4.8 0.4 1.0 N N:ARG3 4.8 0.3 1.0

Magnesium binding site 7 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2551 b:0.1 occ:1.00 O4 A:U261 2.6 94.1 1.0 O6 A:G260 2.6 0.2 1.0 OP1 A:U264 3.0 92.6 1.0 OP2 A:U264 3.5 93.8 1.0 C6 A:G260 3.5 0.8 1.0 C4 A:U261 3.7 93.4 1.0 P A:U264 3.7 92.4 1.0 NH2 T:ARG83 4.0 1.0 1.0 N3 A:U261 4.1 93.8 1.0 N1 A:G260 4.1 1.0 1.0 C5 A:G260 4.6 0.8 1.0 OP2 A:G265 4.7 0.7 1.0 O5' A:U264 4.8 91.5 1.0 O3' A:A263 4.9 87.9 1.0 C5 A:U261 4.9 93.9 1.0

Magnesium binding site 8 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2552 b:84.8 occ:1.00 OP1 A:U387 2.8 99.1 1.0 OP1 A:G388 3.0 0.6 1.0 O2' A:C58 3.3 0.3 1.0 O3' A:C58 3.8 0.7 1.0 MG A:MG2736 3.8 0.1 0.9 P A:U387 3.9 0.3 1.0 O5' A:A59 4.1 0.8 1.0 OP2 A:U387 4.2 0.6 1.0 P A:G388 4.3 0.1 1.0 C2' A:C58 4.4 0.6 1.0 C3' A:C58 4.5 0.2 1.0 P A:A59 4.5 1.0 1.0 C4' A:C58 4.6 0.3 1.0 O5' A:U387 4.7 0.2 1.0 OP2 A:G388 4.7 0.5 1.0 OP1 A:A59 4.8 0.4 1.0 N7 A:G388 4.8 0.4 1.0

Magnesium binding site 9 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2553 b:69.3 occ:1.00 O6 A:G22 2.8 95.3 1.0 O6 A:G11 3.2 0.8 1.0 O6 A:G21 3.2 98.6 1.0 O4 A:U12 3.3 0.1 1.0 N4 A:C23 3.3 83.0 1.0 C6 A:G21 3.7 98.4 1.0 C6 A:G22 3.9 95.0 1.0 N3 A:U12 4.0 0.1 1.0 C4 A:U12 4.1 0.6 1.0 N1 A:G21 4.1 97.3 1.0 N7 A:G22 4.2 95.7 1.0 C6 A:G11 4.3 0.3 1.0 C5 A:G22 4.4 95.1 1.0 C5 A:G21 4.5 98.7 1.0 C4 A:C23 4.5 84.8 1.0 N7 A:G21 5.0 0.4 1.0

Magnesium binding site 10 out of 203 in the Structure of Ribosome-Apramycin Complexes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Ribosome-Apramycin Complexes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2554 b:0.2 occ:1.00 O6 A:G474 3.7 0.6 1.0 N7 A:G474 4.0 0.8 1.0 O6 A:G475 4.3 0.2 1.0 C6 A:G474 4.4 0.1 1.0 C5 A:G474 4.5 0.5 1.0 O6 A:G473 4.8 0.6 1.0

T.Matt, C.L.Ng, K.Lang, S.H.Sha, R.Akbergenov, D.Shcherbakov, M.Meyer, S.Duscha, J.Xie, S.R.Dubbaka, D.Perez-Fernandez, A.Vasella, V.Ramakrishnan, J.Schacht, E.C.Bottger. Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin. Proc.Natl.Acad.Sci.Usa V. 109 10984 2012.
ISSN: ISSN 0027-8424
PubMed: 22699498
DOI: 10.1073/PNAS.1204073109