Magnesium in PDB 8cgi: Pentacycline TP038 Bound to the 30S Head

The structure of Pentacycline TP038 Bound to the 30S Head also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Potassium	(K)	10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Magnesium atom in the Pentacycline TP038 Bound to the 30S Head (pdb code 8cgi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 32 binding sites of Magnesium where determined in the Pentacycline TP038 Bound to the 30S Head, PDB code: 8cgi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:24.9 occ:1.00 O A:HOH1715 1.9 34.5 1.0 O A:HOH1831 2.1 29.6 1.0 OP1 A:G944 2.1 28.1 1.0 OP2 A:G945 2.1 30.6 1.0 O A:HOH2170 2.3 29.2 1.0 O A:HOH1804 2.3 40.5 1.0 O A:HOH1749 2.9 52.9 1.0 P A:G944 3.3 25.9 1.0 P A:G945 3.6 28.2 1.0 OP2 A:G944 3.9 28.6 1.0 O5' A:G944 3.9 27.1 1.0 C5' A:G944 4.2 28.3 1.0 O5' A:G945 4.2 30.1 1.0 N7 A:A946 4.3 22.7 1.0 O A:HOH2269 4.3 38.4 1.0 OP1 A:G945 4.3 35.5 1.0 O A:HOH2291 4.4 25.2 1.0 OP2 A:A946 4.5 33.1 1.0 O3' A:G944 4.7 29.9 1.0 O3' A:U943 4.7 27.1 1.0 O A:HOH2355 4.9 46.4 1.0 C8 A:A946 4.9 21.6 1.0 O6 A:G947 4.9 23.2 1.0 O6 A:G1233 5.0 23.3 1.0 C3' A:G944 5.0 28.9 1.0 O A:HOH1919 5.0 33.0 1.0

Magnesium binding site 2 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:25.0 occ:1.00 OP1 A:U1224 2.0 23.0 1.0 O A:HOH2327 2.0 30.0 1.0 O A:HOH1773 2.1 30.0 1.0 O A:HOH2276 2.1 25.3 1.0 O A:HOH2445 2.1 29.5 1.0 O A:HOH1813 2.1 29.5 1.0 P A:U1224 3.3 20.1 1.0 OP2 A:U1224 3.7 26.7 1.0 O A:HOH2079 3.9 46.9 1.0 O3' A:C1223 4.2 20.2 1.0 N6 A:A977 4.2 29.3 1.0 O2' A:C1223 4.3 23.6 1.0 O A:HOH2333 4.3 54.6 1.0 OP1 A:G951 4.3 31.2 1.0 O5' A:U1224 4.3 22.1 1.0 N7 A:A977 4.3 25.5 1.0 OP2 A:U952 4.4 26.1 1.0 C2' A:C1223 4.4 20.5 1.0 O A:HOH2366 4.6 32.5 1.0 O A:HOH2139 4.7 40.1 1.0 C3' A:C1223 4.7 20.3 1.0 O A:HOH2169 4.9 42.9 1.0 C5 A:A977 5.0 25.4 1.0 C6 A:A977 5.0 27.0 1.0 OP1 A:U952 5.0 29.7 1.0

Magnesium binding site 3 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:23.9 occ:1.00 OP1 A:C980 1.9 22.0 1.0 O A:HOH2350 1.9 29.3 1.0 O A:HOH2263 2.0 30.6 1.0 O A:HOH2281 2.1 23.2 1.0 O A:HOH1977 2.1 23.8 1.0 O A:HOH2287 2.1 31.2 1.0 P A:C980 3.4 18.4 1.0 O A:HOH1980 3.9 30.2 1.0 O3' A:C979 3.9 20.3 1.0 O6 A:G1220 4.0 22.9 1.0 O A:HOH2317 4.0 24.6 1.0 O A:HOH2435 4.1 42.6 1.0 O A:HOH2310 4.2 56.3 1.0 O A:HOH1844 4.2 31.5 1.0 O A:HOH2016 4.2 42.3 1.0 O5' A:C980 4.3 20.2 1.0 N7 A:G1220 4.3 20.6 1.0 C5' A:C980 4.4 21.4 1.0 OP2 A:C980 4.5 19.8 1.0 N7 A:A1219 4.5 25.6 1.0 O A:HOH2042 4.6 17.6 1.0 OP2 A:A1219 4.6 32.9 1.0 O A:HOH2245 4.6 20.7 1.0 O6 A:G1221 4.7 21.0 1.0 C6 A:G1220 4.9 20.4 1.0 O A:HOH2258 4.9 41.9 1.0 C5 A:G1220 5.0 20.6 1.0

Magnesium binding site 4 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:30.7 occ:1.00 OP2 A:A1110 2.0 33.7 1.0 O A:HOH1744 2.1 31.2 1.0 O A:HOH2306 2.1 31.6 1.0 O A:HOH2431 2.1 29.9 1.0 O A:HOH1786 2.1 30.0 1.0 O A:HOH2164 2.1 29.6 1.0 P A:A1110 3.3 33.4 1.0 O5' A:A1110 3.7 32.7 1.0 O2 A:U1189 3.8 41.0 1.0 OP1 A:C1109 4.0 35.1 1.0 OP2 A:C1109 4.0 33.5 1.0 N7 A:A1110 4.1 34.7 1.0 OP1 A:A1110 4.1 38.9 1.0 N7 A:A1111 4.2 40.8 1.0 C8 A:A1110 4.2 33.1 1.0 O A:HOH2209 4.2 31.2 1.0 O A:HOH2408 4.3 47.5 1.0 P A:C1109 4.4 30.5 1.0 N6 A:A1111 4.5 41.1 1.0 O3' A:C1109 4.5 34.7 1.0 O A:HOH2083 4.5 38.4 1.0 OP2 A:A1111 4.6 45.3 1.0 O5' A:C1109 4.7 32.9 1.0 C3' A:C1109 4.8 35.0 1.0 CD2 C:HIS176 4.9 39.8 1.0 C2 A:U1189 4.9 36.4 1.0

Magnesium binding site 5 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:39.5 occ:1.00 OP2 A:U1095 1.9 38.5 1.0 O6 A:G1108 2.0 36.3 1.0 O A:HOH2068 2.0 45.5 1.0 O A:HOH2275 2.0 44.2 1.0 O A:HOH2091 2.1 40.3 1.0 O A:HOH1945 2.1 41.0 1.0 C6 A:G1108 3.0 30.5 1.0 N1 A:G1108 3.4 31.0 1.0 P A:U1095 3.4 33.6 1.0 O3' A:G1094 4.1 39.4 1.0 O5' A:U1095 4.2 39.4 1.0 C5 A:G1108 4.3 30.5 1.0 O A:HOH2023 4.3 56.5 1.0 O2' A:G1094 4.3 36.6 1.0 OP2 A:C1096 4.3 52.3 1.0 OP1 A:U1095 4.4 35.3 1.0 C5' A:U1095 4.4 41.8 1.0 N3 A:C1109 4.5 36.1 1.0 C2 A:G1108 4.7 31.6 1.0 C2 A:C1109 4.7 32.8 1.0 O A:HOH1929 4.7 56.3 1.0 C4 A:C1109 4.9 32.9 1.0 O2 A:C1109 4.9 35.3 1.0 O6 A:G1068 4.9 28.4 1.0 N7 A:G1108 5.0 30.6 1.0 N4 A:C1107 5.0 30.7 1.0

Magnesium binding site 6 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1612 b:35.5 occ:1.00 OP1 A:G1094 1.9 37.8 1.0 O A:HOH2388 2.0 33.4 1.0 OP1 A:G1068 2.0 35.6 1.0 O A:HOH2154 2.1 38.6 1.0 O A:HOH2272 2.1 43.3 1.0 O A:HOH2102 2.1 36.0 1.0 P A:G1068 3.3 32.2 1.0 P A:G1094 3.3 37.5 1.0 O2' A:G1387 3.7 49.0 1.0 OP2 A:G1094 3.9 39.2 1.0 OP2 A:G1068 3.9 35.8 1.0 C3' A:A1067 3.9 32.8 1.0 O3' A:A1067 3.9 31.8 1.0 O A:HOH2249 4.3 52.2 1.0 O3' A:A1093 4.3 42.5 1.0 O5' A:G1094 4.3 37.7 1.0 O A:HOH2252 4.3 48.2 1.0 C5' A:G1094 4.3 39.3 1.0 O5' A:G1068 4.5 33.4 1.0 O4' A:C1388 4.5 52.3 1.0 C4' A:A1067 4.6 34.4 1.0 C5' A:A1067 4.8 35.8 1.0 C2' A:G1387 4.9 47.4 1.0 C4' A:C1388 4.9 49.9 1.0

Magnesium binding site 7 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1613 b:46.7 occ:1.00 OP2 A:C1069 1.9 39.6 1.0 O A:HOH1935 2.1 39.0 1.0 O A:HOH1897 2.1 41.6 1.0 O A:HOH1845 2.1 44.8 1.0 O A:HOH1961 2.1 45.8 1.0 P A:C1069 3.3 37.8 1.0 O2 A:U1085 4.1 38.3 1.0 OP1 A:C1069 4.1 52.8 1.0 O5' A:C1069 4.2 37.9 1.0 O6 A:G1094 4.2 39.5 1.0 N7 A:G1094 4.2 40.0 1.0 O A:HOH2171 4.3 59.2 1.0 O A:HOH1876 4.3 45.9 1.0 O3' A:G1068 4.4 36.6 1.0 C3' A:G1068 4.7 35.1 1.0 C5' A:G1068 4.8 33.8 1.0 OP1 A:C1388 4.8 52.7 1.0 C6 A:G1094 5.0 39.3 1.0 C5 A:G1094 5.0 40.6 1.0

Magnesium binding site 8 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1614 b:41.8 occ:1.00 O A:HOH2267 2.0 41.1 1.0 OP1 A:C934 2.0 40.3 1.0 O A:HOH2114 2.1 44.8 1.0 O A:HOH1918 2.1 40.5 1.0 O A:HOH2295 2.1 40.5 1.0 O A:HOH1849 2.1 38.0 1.0 P A:C934 3.5 40.2 1.0 OP2 A:U1345 4.1 34.4 1.0 C5' A:C934 4.1 43.6 1.0 O A:HOH2201 4.2 39.5 1.0 O5' A:C934 4.2 41.4 1.0 OP1 A:U1345 4.3 34.1 1.0 O3' A:G933 4.4 40.7 1.0 OP2 A:C934 4.4 44.0 1.0 O2' A:U1345 4.5 31.5 1.0 P A:U1345 4.7 28.8 1.0 C2' A:U1345 4.7 29.6 1.0

Magnesium binding site 9 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1615 b:37.4 occ:1.00 O A:HOH2314 1.9 37.6 1.0 OP2 A:A937 2.0 44.0 1.0 O A:HOH2326 2.0 37.8 1.0 O A:HOH2251 2.1 41.1 1.0 O A:HOH2297 2.1 36.5 1.0 O A:HOH1785 2.1 37.7 1.0 P A:A937 3.3 44.1 1.0 O5' A:A937 3.7 41.7 1.0 OP1 A:A937 4.0 57.4 1.0 O A:HOH1920 4.1 42.3 1.0 N7 A:A938 4.2 35.0 1.0 O A:HOH1716 4.3 52.5 1.0 O A:HOH1783 4.4 32.7 1.0 N7 A:A937 4.4 36.5 1.0 N6 A:A938 4.4 27.9 1.0 C8 A:A937 4.4 35.8 1.0 O6 A:G939 4.4 30.6 1.0 O3' A:C936 4.4 48.5 1.0 C3' A:C936 4.7 43.8 1.0 N7 A:G939 4.7 30.9 1.0

Magnesium binding site 10 out of 32 in the Pentacycline TP038 Bound to the 30S Head


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Pentacycline TP038 Bound to the 30S Head within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1616 b:39.8 occ:1.00 O A:HOH2448 1.9 44.2 1.0 O A:HOH2450 2.0 43.1 1.0 O A:HOH2069 2.1 40.5 1.0 O A:HOH2265 2.1 37.3 1.0 O A:HOH2339 2.1 39.0 1.0 O A:HOH2030 2.1 37.3 1.0 O A:HOH1858 3.9 42.3 1.0 O A:HOH1756 4.0 44.2 1.0 N7 A:A1254 4.0 34.1 1.0 N7 A:G1279 4.1 36.1 1.0 OP2 A:A1254 4.2 37.9 1.0 C8 A:G1279 4.4 36.5 1.0 O A:HOH2424 4.6 46.2 1.0 CD J:ARG45 4.7 46.3 1.0 C8 A:A1254 4.7 33.2 1.0 N7 A:G1255 4.7 34.1 1.0 C5 A:A1254 4.8 32.4 1.0 N6 A:A1254 4.8 30.2 1.0 O6 A:G1255 4.9 33.9 1.0 O A:HOH2453 4.9 56.1 1.0 NE J:ARG45 5.0 46.0 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.