Magnesium in PDB 8cgr: Apramycin Bound to the 30S Body

The structure of Apramycin Bound to the 30S Body also contains other interesting chemical elements:

Potassium

(K)

28 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 - 57;

Binding sites:

The binding sites of Magnesium atom in the Apramycin Bound to the 30S Body (pdb code 8cgr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 57 binding sites of Magnesium where determined in the Apramycin Bound to the 30S Body, PDB code: 8cgr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:20.1 occ:1.00 OP1 A:C578 1.9 21.3 1.0 O A:HOH2188 2.0 19.1 1.0 O A:HOH2196 2.1 21.4 1.0 O A:HOH2158 2.1 19.2 1.0 O A:HOH3179 2.1 21.5 1.0 O A:HOH1882 2.1 18.7 1.0 P A:C578 3.2 19.1 1.0 O3' A:G577 3.6 21.2 1.0 OP2 A:C576 3.7 24.8 1.0 O A:HOH3274 3.9 51.8 1.0 OP1 A:U820 4.1 24.4 1.0 OP2 A:C817 4.2 23.2 1.0 O A:HOH2107 4.3 28.4 1.0 O5' A:C578 4.3 21.0 1.0 OP2 A:C578 4.3 20.9 1.0 C5' A:G821 4.3 22.9 1.0 C5' A:C578 4.4 21.7 1.0 O A:HOH2414 4.4 28.4 1.0 C4' A:G821 4.6 21.9 1.0 O2' A:G575 4.6 22.9 1.0 O3' A:G575 4.6 25.2 1.0 P A:C576 4.8 22.6 1.0 O A:HOH2182 4.9 22.9 1.0 O A:HOH3107 4.9 36.6 1.0 C3' A:G577 4.9 19.2 1.0

Magnesium binding site 2 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:19.5 occ:1.00 OP2 A:C352 1.9 24.2 1.0 O A:HOH2978 2.0 20.2 1.0 O A:HOH2921 2.1 19.1 1.0 O A:HOH2112 2.1 17.8 1.0 O A:HOH2798 2.1 20.7 1.0 O A:HOH1733 2.1 17.5 1.0 P A:C352 3.3 24.0 1.0 O2 A:C330 3.5 32.1 1.0 O A:HOH2042 3.8 34.0 1.0 O5' A:C352 3.9 25.8 1.0 O A:HOH2467 4.0 32.8 1.0 O4' A:G331 4.1 22.5 1.0 N7 A:G354 4.1 18.7 1.0 O4' A:C352 4.1 25.0 1.0 OP1 A:C352 4.1 24.5 1.0 N1 A:A59 4.2 19.1 1.0 OP1 A:G354 4.4 22.6 1.0 O3' A:G351 4.4 27.4 1.0 O A:HOH2379 4.4 35.1 1.0 N6 A:A59 4.6 20.6 1.0 C8 A:G354 4.6 18.7 1.0 C3' A:G351 4.6 29.5 1.0 C1' A:G331 4.7 21.2 1.0 C4' A:C352 4.7 25.1 1.0 C2 A:C330 4.7 29.9 1.0 C6 A:A59 4.9 19.9 1.0 C5' A:C352 4.9 25.3 1.0

Magnesium binding site 3 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:38.5 occ:1.00 OP2 A:G111 2.1 28.0 1.0 O A:HOH2663 2.1 36.6 1.0 O A:HOH2827 2.3 41.7 1.0 O A:HOH3293 2.4 39.2 1.0 O A:HOH2127 2.4 33.1 1.0 P A:G111 3.4 21.6 1.0 N7 A:G112 3.4 23.4 1.0 O5' A:G111 3.6 22.5 1.0 N7 A:G111 3.8 20.9 1.0 C8 A:G111 3.9 20.9 1.0 O A:HOH2140 4.2 46.4 1.0 O6 A:G112 4.3 23.2 1.0 C8 A:G112 4.3 21.8 1.0 OP1 A:G111 4.4 25.5 1.0 C5 A:G112 4.4 22.7 1.0 OP1 A:C110 4.4 25.4 1.0 OP2 A:G112 4.4 27.9 1.0 OP2 A:C110 4.5 26.8 1.0 O3' A:C110 4.5 22.2 1.0 O5' A:C110 4.5 23.7 1.0 C3' A:C110 4.7 21.9 1.0 P A:C110 4.7 21.6 1.0 C6 A:G112 4.7 21.1 1.0 K A:K1683 4.9 49.3 1.0

Magnesium binding site 4 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:23.4 occ:1.00 OP1 A:A547 2.0 28.6 1.0 O A:HOH3079 2.0 22.9 1.0 O A:HOH3080 2.1 27.1 1.0 O A:HOH3100 2.1 23.3 1.0 O A:HOH3111 2.1 22.6 1.0 O A:HOH2554 2.1 23.3 1.0 P A:A547 3.4 25.6 1.0 OP1 A:G548 3.9 31.4 1.0 OP2 A:A547 4.0 30.4 1.0 O A:HOH2833 4.0 30.9 1.0 N7 A:G402 4.2 25.0 1.0 O5' A:G548 4.3 27.8 1.0 C5' A:A547 4.3 27.3 1.0 O A:HOH2593 4.3 41.1 1.0 O5' A:A547 4.3 27.2 1.0 O A:HOH1891 4.3 42.6 1.0 O3' A:A546 4.4 27.9 1.0 N4 A:C403 4.4 27.3 1.0 O A:HOH2816 4.4 34.8 1.0 O A:HOH3241 4.4 49.9 1.0 O6 A:G402 4.5 25.9 1.0 N4 A:C401 4.8 21.8 1.0 O A:HOH3142 4.8 50.6 1.0 C4' A:A547 4.8 27.0 1.0 P A:G548 4.8 27.8 1.0 C5 A:C401 4.8 21.4 1.0 C4 A:C401 5.0 22.0 1.0 C5 A:G402 5.0 23.9 1.0

Magnesium binding site 5 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:33.8 occ:1.00 O6 A:G895 2.6 25.5 1.0 O4 A:U904 2.7 19.9 1.0 O A:HOH2116 2.8 28.2 1.0 O6 A:G894 2.8 27.4 1.0 O A:HOH1876 2.8 40.8 1.0 O A:HOH3171 3.0 32.5 1.0 O A:HOH2408 3.0 42.3 1.0 O A:HOH3374 3.2 45.2 1.0 O4 A:U905 3.5 27.8 1.0 C4 A:U904 3.6 21.1 1.0 C6 A:G895 3.6 25.1 1.0 N3 A:U904 3.7 20.3 1.0 C6 A:G894 3.8 27.4 1.0 O6 A:G903 4.0 21.8 1.0 N3 A:U905 4.0 26.3 1.0 O A:HOH1735 4.0 25.5 1.0 C4 A:U905 4.1 26.0 1.0 N7 A:G895 4.2 29.5 1.0 C5 A:G895 4.3 28.7 1.0 N7 A:G894 4.3 29.5 1.0 C5 A:G894 4.4 28.8 1.0 N4 A:C893 4.4 27.8 1.0 N4 A:C896 4.5 26.1 1.0 O A:HOH2576 4.7 33.6 1.0 N1 A:G895 4.7 26.3 1.0 C6 A:G903 4.8 19.9 1.0 N1 A:G894 4.9 26.6 1.0 C2 A:U904 4.9 22.6 1.0 C5 A:U904 5.0 21.9 1.0

Magnesium binding site 6 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:52.2 occ:1.00 O A:HOH2895 2.1 47.0 1.0 O A:HOH1912 2.3 32.3 1.0 O A:HOH1814 2.5 39.4 1.0 OP1 A:C797 3.9 30.2 1.0 O A:HOH3128 4.1 70.5 1.0 CE1 U:PHE37 4.1 56.7 1.0 O K:HOH304 4.2 33.7 1.0 OP1 A:U692 4.2 41.9 1.0 OP1 A:U798 4.6 34.0 1.0 CZ U:PHE37 4.7 59.4 1.0 OP2 A:U798 4.7 36.6 1.0 CB K:PRO124 4.8 27.4 1.0 CG K:PRO124 4.9 28.6 1.0 CD K:ARG127 5.0 35.2 1.0 P A:U798 5.0 32.9 1.0

Magnesium binding site 7 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1612 b:28.3 occ:1.00 O A:HOH3262 2.0 28.9 1.0 O A:HOH2404 2.0 27.4 1.0 O A:HOH3357 2.1 31.0 1.0 O A:HOH2939 2.1 27.3 1.0 O A:HOH2502 2.1 28.9 1.0 N7 A:G362 2.2 22.7 1.0 C8 A:G362 3.0 21.7 1.0 C5 A:G362 3.3 21.1 1.0 O6 A:G362 3.7 24.3 1.0 C6 A:G362 3.9 23.3 1.0 N7 A:G361 4.0 26.4 1.0 O A:HOH2654 4.2 40.8 1.0 N9 A:G362 4.3 22.2 1.0 C8 A:G361 4.3 25.9 1.0 OP2 A:G361 4.3 34.7 1.0 OP2 A:G362 4.3 28.0 1.0 C4 A:G362 4.4 22.0 1.0 NH2 L:ARG31 4.8 38.5 1.0 O A:HOH1861 5.0 39.0 1.0

Magnesium binding site 8 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1613 b:24.9 occ:1.00 O A:HOH1824 1.9 26.6 1.0 O A:HOH3351 1.9 28.0 1.0 O A:HOH1830 2.0 27.6 1.0 O A:HOH1922 2.1 22.7 1.0 O A:HOH3167 2.1 24.5 1.0 O A:HOH1863 2.1 19.6 1.0 O A:HOH2893 3.6 47.8 1.0 O A:HOH2220 3.9 43.6 1.0 OP2 A:G731 3.9 23.3 1.0 OP1 A:G730 4.0 22.5 1.0 OP1 A:G731 4.1 23.2 1.0 O A:HOH3377 4.1 56.7 1.0 O3' A:G1526 4.2 22.5 1.0 OP1 A:U1527 4.2 25.9 1.0 OP2 A:A816 4.2 21.0 1.0 N1 A:A814 4.3 19.4 1.0 O A:HOH2820 4.4 57.3 1.0 P A:G731 4.4 20.2 1.0 O2' A:G1526 4.5 19.9 1.0 O3' A:G730 4.6 19.6 1.0 C5' A:G730 4.6 19.0 1.0 C2 A:A814 4.6 18.9 1.0 O2' A:A816 4.7 18.4 1.0 C5' A:U1527 4.8 23.4 1.0 P A:U1527 4.9 21.7 1.0

Magnesium binding site 9 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1614 b:33.5 occ:1.00 O A:HOH3362 2.0 35.6 1.0 O A:HOH2111 2.0 32.8 1.0 O A:HOH2423 2.1 31.4 1.0 O A:HOH2230 2.1 38.3 1.0 O K:HOH316 2.1 28.9 1.0 O A:HOH3074 2.1 35.6 1.0 O4 A:U798 4.0 31.2 1.0 O6 A:G800 4.0 24.8 1.0 O A:HOH3121 4.0 33.2 1.0 O6 A:G799 4.2 32.5 1.0 OP2 A:A781 4.2 25.1 1.0 O A:HOH2964 4.2 48.9 1.0 O A:HOH2104 4.3 47.7 1.0 O A:HOH2278 4.3 30.1 1.0 O A:HOH2400 4.5 27.0 1.0 C6 A:G800 4.5 22.5 1.0 CE K:LYS125 4.5 35.3 1.0 N7 A:G799 4.6 31.1 1.0 N1 A:G800 4.6 21.2 1.0 C4 A:U798 4.7 28.2 1.0 C5 A:U798 4.8 26.7 1.0 NZ K:LYS125 4.9 34.4 1.0 OP1 A:A781 4.9 24.8 1.0 P A:A781 5.0 23.4 1.0

Magnesium binding site 10 out of 57 in the Apramycin Bound to the 30S Body


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Apramycin Bound to the 30S Body within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1615 b:27.2 occ:1.00 O A:HOH3281 2.0 30.1 1.0 O A:HOH2345 2.0 24.2 1.0 O A:HOH3376 2.1 28.9 1.0 O A:HOH3191 2.1 28.2 1.0 N7 A:G324 2.2 19.7 1.0 O A:HOH2546 2.3 18.6 1.0 C8 A:G324 3.2 18.4 1.0 C5 A:G324 3.3 19.2 1.0 O6 A:G324 3.6 21.7 1.0 C6 A:G324 3.8 19.5 1.0 O A:HOH3133 4.0 47.3 1.0 O A:HOH2617 4.2 27.6 1.0 OP2 A:U323 4.2 21.3 1.0 O T:HOH116 4.2 32.0 1.0 N9 A:G324 4.4 20.2 1.0 O A:HOH2732 4.4 38.4 1.0 OP2 A:G324 4.4 25.7 1.0 C4 A:G324 4.5 20.0 1.0 C5 A:U323 4.6 17.0 1.0 OP2 A:G326 4.6 26.6 1.0 C6 A:U323 5.0 17.6 1.0 O A:HOH3307 5.0 42.8 1.0

H.Paternoga, C.Crowe-Mcauliffe, L.V.Bock, T.O.Koller, M.Morici, B.Beckert, A.G.Myasnikov, H.Grubmueller, J.Novacek, D.N.Wilson. Structural Conservation of Antibiotic Interaction with Ribosomes To Be Published.