Magnesium in PDB 8ca7: Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head

The structure of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head also contains other interesting chemical elements:

Potassium

(K)

14 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 26;

Binding sites:

The binding sites of Magnesium atom in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head (pdb code 8ca7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 26 binding sites of Magnesium where determined in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head, PDB code: 8ca7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:31.4 occ:1.00 O A:HOH2001 1.9 30.9 1.0 OP2 A:A1110 1.9 31.1 1.0 O A:HOH1843 2.0 29.7 1.0 O A:HOH1936 2.1 29.2 1.0 O A:HOH2131 2.3 30.2 1.0 O A:HOH2014 2.4 27.7 1.0 P A:A1110 3.3 33.9 1.0 O5' A:A1110 3.7 34.0 1.0 O2 A:U1189 3.8 38.2 1.0 OP1 A:C1109 3.8 32.4 1.0 OP2 A:C1109 4.1 31.8 1.0 N7 A:A1110 4.1 33.7 1.0 OP1 A:A1110 4.2 40.5 1.0 C8 A:A1110 4.2 33.8 1.0 N7 A:A1111 4.3 38.2 1.0 P A:C1109 4.3 29.1 1.0 O A:HOH1901 4.3 28.8 1.0 O3' A:C1109 4.4 33.5 1.0 O A:HOH1878 4.5 60.8 1.0 N6 A:A1111 4.6 39.0 1.0 C3' A:C1109 4.6 32.1 1.0 O5' A:C1109 4.7 32.4 1.0 ND1 C:HIS176 4.8 39.9 1.0 OP2 A:A1111 4.8 39.9 1.0 C2 A:U1189 4.8 33.6 1.0

Magnesium binding site 2 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:33.5 occ:1.00 O N:HOH211 2.1 31.8 1.0 O A:HOH1866 2.1 30.9 1.0 O A:HOH2126 2.1 35.7 1.0 O A:HOH2052 2.1 33.1 1.0 O A:HOH1790 2.1 31.4 1.0 O N:ALA2 3.8 36.9 1.0 OP2 A:A1204 3.9 36.0 1.0 OP1 A:A1204 4.0 36.0 1.0 O N:HOH217 4.0 32.9 1.0 O A:HOH1729 4.0 40.7 1.0 OP1 A:G1048 4.2 33.9 1.0 OP1 A:U1049 4.4 32.9 1.0 NE2 N:GLN4 4.4 36.4 1.0 P A:A1204 4.4 34.2 1.0 OP2 A:G1048 4.4 34.6 1.0 OP1 A:C1203 4.5 32.8 1.0 O A:HOH1950 4.6 54.5 1.0 C N:ALA2 4.7 33.5 1.0 O A:HOH2098 4.8 40.7 1.0 P A:G1048 4.8 30.1 1.0

Magnesium binding site 3 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:21.2 occ:1.00 O4 A:U981 1.9 23.8 1.0 OP2 A:C980 2.1 22.2 1.0 O6 A:G1222 2.1 26.1 1.0 O A:HOH1804 2.1 21.3 1.0 O A:HOH1884 2.1 22.6 1.0 OP1 A:C979 2.1 24.2 1.0 C4 A:U981 2.9 22.7 1.0 P A:C979 3.2 23.3 1.0 C6 A:G1222 3.3 25.5 1.0 P A:C980 3.4 22.9 1.0 C5 A:U981 3.5 24.8 1.0 OP2 A:C979 3.7 23.4 1.0 O5' A:C979 3.8 24.5 1.0 O2 A:U982 3.8 21.8 1.0 N4 A:C1223 3.9 22.6 1.0 O6 A:G1221 4.0 27.0 1.0 OP1 A:C980 4.0 24.7 1.0 K A:K1629 4.0 27.7 1.0 N3 A:U981 4.2 23.8 1.0 C5 A:G1222 4.2 25.7 1.0 N1 A:G1222 4.2 24.0 1.0 C5' A:C979 4.2 26.8 1.0 C2 A:U982 4.3 23.0 1.0 O5' A:C980 4.4 23.4 1.0 O3' A:C979 4.4 25.9 1.0 N7 A:G1222 4.4 25.5 1.0 O A:HOH2091 4.5 33.2 1.0 O A:HOH1824 4.5 29.5 1.0 N3 A:U982 4.5 23.3 1.0 C4 A:C1223 4.7 22.6 1.0 O3' A:A978 4.7 26.7 1.0 C6 A:U981 4.8 24.3 1.0 O2' A:U982 4.8 27.7 1.0 O2' A:A977 4.9 28.0 1.0 C3' A:C979 4.9 27.1 1.0 C6 A:G1221 5.0 24.2 1.0

Magnesium binding site 4 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:28.4 occ:1.00 O6 A:G1370 1.8 36.8 1.0 O A:HOH1702 1.9 27.2 1.0 O A:HOH1792 2.0 28.7 1.0 O A:HOH1961 2.0 31.1 1.0 O A:HOH2146 2.1 23.1 1.0 O A:HOH2137 2.5 29.8 1.0 C6 A:G1370 2.9 40.4 1.0 N7 A:G1370 3.4 38.5 1.0 C5 A:G1370 3.5 38.9 1.0 O A:HOH1768 3.9 35.9 1.0 N4 A:C1352 4.1 36.8 1.0 N1 A:G1370 4.1 37.5 1.0 O6 A:G1371 4.1 47.7 1.0 O I:HOH212 4.2 30.5 1.0 O A:HOH1731 4.2 35.7 1.0 O4 A:U1351 4.3 34.8 1.0 N4 A:C1369 4.3 34.0 1.0 O I:HOH202 4.5 31.2 1.0 N7 A:G1371 4.5 47.7 1.0 O A:HOH2090 4.5 49.1 1.0 C8 A:G1370 4.7 37.9 1.0 CG1 I:VAL111 4.8 30.0 1.0 C4 A:G1370 4.9 36.0 1.0 C4 A:C1369 4.9 35.9 1.0 C6 A:G1371 4.9 45.5 1.0 N6 A:A1350 4.9 24.9 1.0

Magnesium binding site 5 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:27.7 occ:1.00 OP1 A:G944 2.0 27.8 1.0 O A:HOH1758 2.1 31.3 1.0 O A:HOH1904 2.1 28.8 1.0 O A:HOH1746 2.1 29.4 1.0 OP2 A:G945 2.1 31.2 1.0 O A:HOH1796 2.3 24.3 1.0 P A:G944 3.1 29.3 1.0 OP2 A:G944 3.5 28.7 1.0 P A:G945 3.5 31.9 1.0 O5' A:G944 3.8 32.2 1.0 O5' A:G945 4.2 34.1 1.0 C5' A:G944 4.2 34.2 1.0 N7 A:A946 4.3 29.2 1.0 OP1 A:G945 4.3 32.5 1.0 K A:K1636 4.3 38.1 1.0 OP2 A:A946 4.4 40.3 1.0 O3' A:U943 4.5 30.1 1.0 O3' A:G944 4.6 30.1 1.0 O A:HOH1706 4.8 34.4 1.0 O A:HOH1736 4.8 29.5 1.0 O A:HOH1994 4.8 50.0 1.0 O6 A:G947 4.8 27.4 1.0 C3' A:G944 4.9 32.4 1.0 C8 A:A946 4.9 31.3 1.0 O6 A:G1233 4.9 26.7 1.0

Magnesium binding site 6 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:23.6 occ:1.00 O A:HOH1722 1.9 24.3 1.0 O N:HOH207 1.9 28.1 1.0 O A:HOH2066 2.0 22.8 1.0 O A:HOH1812 2.1 24.8 1.0 O A:HOH1737 2.3 35.5 1.0 O N:HOH224 2.3 23.7 1.0 O6 A:G1361 3.8 39.0 1.0 O A:HOH2026 3.9 31.9 1.0 O N:SER58 3.9 38.3 1.0 O2 A:C980 4.1 28.9 1.0 N3 A:C980 4.1 26.6 1.0 O N:GLN60 4.2 35.2 1.0 O A:HOH2047 4.2 26.7 1.0 O A:HOH1998 4.2 23.6 1.0 OP1 A:A1360 4.3 28.6 1.0 N7 A:A1360 4.3 44.9 1.0 O A:HOH1817 4.4 32.7 1.0 O3' A:C1359 4.4 32.4 1.0 N4 A:C979 4.5 28.9 1.0 C2 A:C980 4.6 25.3 1.0 NH1 N:ARG61 4.7 31.6 1.0 C6 A:G1361 4.8 37.4 1.0 C8 A:A1360 4.8 43.3 1.0 CD N:ARG61 4.9 31.6 1.0

Magnesium binding site 7 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:53.0 occ:1.00 O A:HOH1798 2.1 45.7 1.0 OP2 A:C1069 2.4 30.7 1.0 O A:HOH1793 2.5 31.9 1.0 O A:HOH2099 2.7 45.0 1.0 O2 A:U1085 3.5 38.0 1.0 P A:C1069 3.7 31.9 1.0 O6 A:G1094 4.2 34.9 1.0 O A:HOH1741 4.2 34.5 1.0 OP1 A:C1069 4.3 35.4 1.0 O5' A:C1069 4.5 30.2 1.0 N7 A:G1094 4.6 36.4 1.0 C2 A:U1085 4.6 34.7 1.0 O3' A:G1068 4.9 33.1 1.0 OP1 A:C1389 4.9 45.4 1.0 C1' A:U1085 5.0 39.5 1.0

Magnesium binding site 8 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:42.9 occ:1.00 O A:HOH1947 1.9 45.0 1.0 O A:HOH1960 2.0 38.8 1.0 O A:HOH1810 2.1 45.8 1.0 O A:HOH1995 2.1 46.3 1.0 O A:HOH2145 2.1 42.8 1.0 O A:HOH2030 3.6 41.1 1.0 N7 A:G1279 3.7 46.0 1.0 C8 A:G1279 4.1 43.4 1.0 O A:HOH1764 4.2 45.1 1.0 N7 A:A1254 4.2 45.7 1.0 OP2 A:A1254 4.3 39.9 1.0 N7 A:G1255 4.5 44.2 1.0 O6 A:G1255 4.7 36.6 1.0 CD J:ARG45 4.7 49.0 1.0 C5 A:G1279 4.7 44.3 1.0 C8 A:A1254 4.8 45.8 1.0 CG J:ARG45 4.9 45.7 1.0 NE J:ARG45 4.9 49.0 1.0 C5 A:A1254 4.9 46.6 1.0 N6 A:A1254 5.0 40.8 1.0

Magnesium binding site 9 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1612 b:57.8 occ:1.00 O A:HOH1826 2.1 61.6 1.0 O A:HOH2149 2.6 47.1 1.0 OP1 A:C1200 3.0 30.4 1.0 O A:HOH1856 3.1 49.4 1.0 O A:HOH1898 3.1 35.4 1.0 O5' A:C1200 3.7 29.2 1.0 P A:C1200 3.7 28.6 1.0 O A:HOH2004 3.8 51.1 1.0 OP2 A:C1200 4.0 32.3 1.0 O A:HOH1784 4.1 47.7 1.0 O A:HOH1907 4.1 26.5 1.0 OP2 A:C1051 4.2 37.8 1.0 O2' A:A1201 4.4 35.8 1.0 O A:HOH2046 4.5 38.6 1.0 O2' A:C962 4.5 29.7 1.0 C2' A:A1201 4.5 34.2 1.0 C5' A:C1200 4.7 28.4 1.0 C8 A:A1201 4.8 31.6 1.0 OP1 A:A1201 4.8 34.4 1.0 C3' A:C1200 4.9 28.6 1.0 OP1 A:C1051 4.9 39.2 1.0 C5' A:G963 4.9 28.3 1.0 OP2 A:U1052 5.0 34.0 1.0

Magnesium binding site 10 out of 26 in the Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Omadacycline and Spectinomycin Bound to the 30S Ribosomal Subunit Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1613 b:31.2 occ:1.00 O A:HOH1939 2.0 33.1 1.0 OP2 A:A937 2.0 35.5 1.0 O A:HOH2002 2.1 33.5 1.0 O A:HOH2080 2.1 32.2 1.0 O A:HOH2037 2.1 25.8 1.0 O A:HOH1820 2.1 31.6 1.0 P A:A937 3.3 33.0 1.0 O5' A:A937 3.6 34.7 1.0 N7 A:A938 4.0 29.5 1.0 OP1 A:A937 4.1 38.6 1.0 C8 A:A937 4.2 29.8 1.0 N7 A:A937 4.3 28.6 1.0 O A:HOH1808 4.3 34.0 1.0 O A:HOH1771 4.3 24.8 1.0 N6 A:A938 4.4 24.9 1.0 O3' A:C936 4.5 35.6 1.0 O6 A:G939 4.5 32.9 1.0 OP2 A:A938 4.6 34.5 1.0 N7 A:G939 4.8 31.1 1.0 C3' A:C936 4.8 34.1 1.0 C5' A:A937 4.9 33.6 1.0 C5 A:A938 4.9 27.1 1.0 C8 A:A938 4.9 32.0 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.