Magnesium in PDB 8cgd: Clindamycin Bound to the 50S Subunit

The structure of Clindamycin Bound to the 50S Subunit also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Potassium	(K)	85 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 - 210; Page 22, Binding sites: 211 - 220; Page 23, Binding sites: 221 - 230; Page 24, Binding sites: 231 - 240; Page 25, Binding sites: 241 - 250; Page 26, Binding sites: 251 - 254;

Binding sites:

The binding sites of Magnesium atom in the Clindamycin Bound to the 50S Subunit (pdb code 8cgd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 254 binding sites of Magnesium where determined in the Clindamycin Bound to the 50S Subunit, PDB code: 8cgd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3004 b:21.3 occ:1.00 O a:HOH7301 2.0 22.9 1.0 O4 a:U2593 2.0 22.6 1.0 O a:HOH5323 2.1 24.6 1.0 O a:HOH5899 2.1 21.8 1.0 O c:HOH430 2.1 19.9 1.0 O a:HOH8670 2.1 22.1 1.0 C4 a:U2593 3.1 22.1 1.0 C5 a:U2593 3.8 23.7 1.0 O c:GLU236 3.9 35.6 1.0 N6 a:A2600 3.9 24.9 1.0 N7 a:G2592 4.0 23.5 1.0 OD1 c:ASN239 4.1 33.2 1.0 O6 a:G2592 4.2 24.6 1.0 N4 a:C2594 4.2 27.1 1.0 N3 a:U2593 4.3 22.0 1.0 O a:HOH162 4.3 35.0 1.0 OP2 a:C2591 4.3 25.3 1.0 OP2 a:G2592 4.4 27.8 1.0 O c:ARG238 4.5 31.9 1.0 O a:HOH6013 4.6 39.3 1.0 O c:HOH520 4.7 55.0 1.0 C5 a:G2592 4.7 22.8 1.0 C5 a:C2591 4.7 23.0 1.0 C6 a:G2592 4.8 21.8 1.0 O6 a:G2599 4.9 24.5 1.0 O a:HOH9967 4.9 31.1 1.0 CA c:GLY237 4.9 31.9 1.0 C8 a:G2592 4.9 23.0 1.0

Magnesium binding site 2 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3005 b:29.9 occ:1.00 O a:HOH3439 2.0 27.1 1.0 O a:HOH3647 2.1 30.1 1.0 O a:HOH3615 2.1 32.0 1.0 O a:HOH4929 2.1 25.1 1.0 OP2 a:G1622 2.1 31.3 1.0 O a:HOH8600 2.1 31.6 1.0 P a:G1622 3.3 30.3 1.0 OP1 a:G1622 3.8 36.3 1.0 O a:HOH96 3.9 59.0 1.0 O a:HOH5287 3.9 49.5 1.0 OP2 a:U1621 4.0 27.6 1.0 OP1 a:U1621 4.0 32.6 1.0 O a:HOH8931 4.0 36.0 1.0 N4 a:C1607 4.1 37.4 1.0 N3 a:C1607 4.1 35.4 1.0 O5' a:G1622 4.2 30.3 1.0 O a:HOH6457 4.3 38.9 1.0 P a:U1621 4.3 26.2 1.0 OP1 a:C736 4.4 35.7 1.0 OP1 a:C737 4.4 29.8 1.0 O5' a:U1621 4.4 27.7 1.0 O a:HOH6846 4.5 42.3 1.0 C4 a:C1607 4.6 36.8 1.0 O3' a:U1621 4.6 29.7 1.0 C3' a:U1621 4.8 27.2 1.0 O3' a:C736 4.8 27.9 1.0 C5' a:C736 4.9 27.9 1.0 P a:C737 4.9 27.2 1.0

Magnesium binding site 3 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3006 b:28.0 occ:1.00 OP1 a:U1995 1.9 24.9 1.0 O a:HOH6346 2.1 32.7 1.0 O d:HOH430 2.1 27.7 1.0 O a:HOH8414 2.1 33.0 1.0 O a:HOH9690 2.1 26.1 1.0 O a:HOH4184 2.1 28.4 1.0 P a:U1995 3.2 21.0 1.0 O3' a:C1994 3.7 21.5 1.0 O d:THR129 3.9 27.9 1.0 OP2 a:U1995 4.1 22.3 1.0 O a:HOH9305 4.1 33.0 1.0 O a:HOH8384 4.1 45.6 1.0 OP1 a:U2511 4.2 27.9 1.0 OP1 a:C1997 4.3 29.1 1.0 O a:HOH7653 4.3 30.9 1.0 O a:HOH5603 4.3 28.5 1.0 O a:HOH9444 4.4 26.2 1.0 O5' a:U1995 4.4 22.5 1.0 CB d:ARG128 4.5 32.0 1.0 C5' a:U1995 4.7 24.1 1.0 C3' a:C1994 5.0 21.1 1.0

Magnesium binding site 4 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3007 b:25.5 occ:1.00 OP2 a:U1379 1.9 28.6 1.0 OP2 a:G1380 2.0 26.6 1.0 O a:HOH8941 2.1 28.8 1.0 O a:HOH9365 2.1 25.9 1.0 O a:HOH9600 2.1 24.6 1.0 O2' a:A1378 2.1 23.7 1.0 C2' a:A1378 3.1 24.1 1.0 P a:U1379 3.3 26.7 1.0 C3' a:A1378 3.5 25.9 1.0 P a:G1380 3.5 26.4 1.0 O3' a:A1378 3.6 28.6 1.0 N7 a:G1380 3.7 23.3 1.0 O a:HOH5981 3.9 63.6 1.0 O5' a:U1379 4.2 28.8 1.0 O a:HOH9689 4.2 36.0 1.0 O a:HOH5699 4.3 36.8 1.0 C5' a:U1379 4.3 28.8 1.0 C3' a:U1379 4.3 26.6 1.0 C8 a:G1380 4.4 23.3 1.0 O3' a:U1379 4.4 29.1 1.0 OP1 a:U1379 4.4 32.6 1.0 O5' a:G1380 4.4 25.4 1.0 OP1 a:G1380 4.4 31.3 1.0 C1' a:A1378 4.4 23.7 1.0 O a:HOH6053 4.5 36.6 1.0 C5 a:G1380 4.8 22.5 1.0 O6 a:G1380 4.9 25.5 1.0 C4' a:U1379 4.9 27.9 1.0 C4' a:A1378 5.0 26.7 1.0

Magnesium binding site 5 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3008 b:28.0 occ:1.00 OP2 a:G1024 1.9 28.7 1.0 O a:HOH7863 1.9 25.8 1.0 OP2 a:U1023 2.0 29.5 1.0 OP1 a:G1026 2.0 30.3 1.0 O a:HOH7039 2.1 28.5 1.0 O2' a:G1025 2.4 26.4 1.0 P a:U1023 3.3 27.0 1.0 P a:G1026 3.3 29.8 1.0 P a:G1024 3.4 27.0 1.0 C2' a:G1025 3.4 27.9 1.0 O a:HOH7459 3.6 43.5 1.0 O3' a:G1025 3.6 29.0 1.0 O a:HOH9249 3.7 57.3 1.0 C3' a:G1025 3.8 27.3 1.0 OP2 a:C1135 3.8 34.4 1.0 OP1 a:U1023 3.8 30.5 1.0 O5' a:U1023 4.0 28.2 1.0 K a:K3241 4.0 26.4 1.0 O3' a:U1023 4.1 28.5 1.0 C5' a:U1023 4.1 28.5 1.0 OP1 a:G1024 4.1 31.6 1.0 OP2 a:G1026 4.3 32.4 1.0 O5' a:G1024 4.3 26.9 1.0 O5' a:G1026 4.4 36.3 1.0 O3' a:G1022 4.5 27.8 1.0 C3' a:U1023 4.5 28.0 1.0 O a:HOH9532 4.6 35.5 1.0 C1' a:G1025 4.7 25.8 1.0 N7 a:G1024 4.8 23.4 1.0 C5' a:G1026 4.8 43.4 1.0 C4' a:U1023 4.9 28.0 1.0 C8 a:G1024 4.9 23.6 1.0

Magnesium binding site 6 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3009 b:49.4 occ:1.00 O a:HOH3401 2.1 51.1 1.0 OP1 a:A1328 2.1 33.9 1.0 O a:HOH4267 2.1 49.4 1.0 O a:HOH5204 2.1 40.8 1.0 P a:A1328 3.4 28.2 1.0 O6 a:G489 3.9 36.8 1.0 OP2 a:A1328 4.1 30.2 1.0 O3' a:A1327 4.1 28.2 1.0 OP2 a:A1321 4.2 48.8 1.0 O a:HOH7503 4.4 54.0 1.0 O a:HOH3589 4.4 42.1 1.0 O a:HOH5597 4.5 38.6 1.0 O5' a:A1328 4.6 29.6 1.0 N1 a:A1284 4.6 32.6 1.0 O a:HOH9691 4.7 49.1 1.0 C2 a:A1285 4.8 29.5 1.0 C6 a:G489 4.8 32.7 1.0 C5' a:A1328 4.9 29.4 1.0

Magnesium binding site 7 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3010 b:20.0 occ:1.00 OP1 a:G2576 2.0 20.7 1.0 OP1 a:A2577 2.0 20.9 1.0 O a:HOH4311 2.1 19.2 1.0 O a:HOH3461 2.1 21.5 1.0 O a:HOH9180 2.1 21.6 1.0 O a:HOH4539 2.1 21.8 1.0 P a:G2576 3.2 18.6 1.0 P a:A2577 3.3 18.9 1.0 O3' a:C2575 3.5 21.0 1.0 O a:HOH9969 3.6 58.1 1.0 OP2 a:A2577 3.8 20.8 1.0 O a:HOH4477 3.9 20.6 1.0 OP2 a:G2053 4.1 21.9 1.0 O3' a:G2576 4.1 20.7 1.0 K a:K3228 4.1 27.5 1.0 OP1 a:G2053 4.2 23.0 1.0 OP2 a:A2052 4.2 20.0 1.0 O a:HOH5305 4.3 43.1 1.0 O5' a:G2576 4.3 19.9 1.0 C3' a:G2576 4.3 20.7 1.0 OP2 a:G2576 4.3 23.0 1.0 O a:HOH445 4.3 36.4 1.0 N2 a:G2576 4.3 20.4 1.0 C5' a:G2576 4.4 20.1 1.0 O5' a:A2577 4.5 20.1 1.0 O a:HOH6957 4.6 45.0 1.0 P a:G2053 4.6 18.7 1.0 O a:HOH5127 4.8 29.4 1.0 C3' a:C2575 4.8 20.0 1.0 C4' a:G2576 4.9 20.2 1.0

Magnesium binding site 8 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3011 b:26.7 occ:1.00 OP1 a:A2406 2.0 31.7 1.0 O a:HOH5468 2.0 25.5 1.0 O a:HOH6116 2.1 27.8 1.0 O a:HOH5006 2.1 26.4 1.0 O a:HOH7332 2.1 27.4 1.0 O a:HOH8360 2.1 27.3 1.0 P a:A2406 3.2 30.3 1.0 OP2 a:A2406 3.6 31.3 1.0 OP2 a:U2408 3.8 33.4 1.0 O a:HOH9215 4.0 23.5 1.0 O2' a:G2405 4.0 32.2 1.0 C5 a:U2408 4.1 27.7 1.0 N7 a:G2410 4.2 26.6 1.0 N7 a:G2409 4.2 29.1 1.0 O3' a:G2405 4.2 34.7 1.0 O5' a:A2406 4.3 34.0 1.0 O6 a:G2410 4.4 26.9 1.0 C5' a:A2406 4.4 34.1 1.0 N6 a:A2411 4.5 24.3 1.0 O6 a:G2409 4.5 28.3 1.0 C4 a:U2408 4.6 27.3 1.0 OP2 a:G2409 4.6 40.7 1.0 C6 a:U2408 4.6 28.2 1.0 O4 a:U2408 4.7 27.5 1.0 C3' a:G2405 4.7 34.8 1.0 OP1 a:A2407 4.8 25.8 1.0 O a:HOH9491 4.9 25.7 1.0 O a:HOH7376 4.9 55.2 1.0 C2' a:G2405 4.9 33.3 1.0 C3' a:A2406 4.9 32.9 1.0 C5 a:G2410 5.0 26.6 1.0

Magnesium binding site 9 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3012 b:38.3 occ:1.00 O a:HOH7726 2.1 36.9 1.0 O a:HOH7716 2.1 38.0 1.0 O a:HOH4665 2.1 37.1 1.0 O a:HOH184 2.1 31.9 1.0 O a:HOH8540 2.1 34.7 1.0 O a:HOH39 2.3 43.8 1.0 OP2 a:C1990 3.8 31.8 1.0 O2' a:G1667 4.1 19.6 1.0 O a:HOH3559 4.2 27.9 1.0 O a:HOH7111 4.3 38.8 1.0 C2' a:G1667 4.3 20.0 1.0 OP2 a:G1989 4.4 40.5 1.0 OP2 a:G1667 4.6 23.4 1.0 OP1 a:G1989 4.8 45.0 1.0 C5 a:C1990 5.0 21.9 1.0

Magnesium binding site 10 out of 254 in the Clindamycin Bound to the 50S Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Clindamycin Bound to the 50S Subunit within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3013 b:35.5 occ:1.00 OP2 a:A2682 1.8 32.1 1.0 O a:HOH5111 2.0 31.6 1.0 O a:HOH5384 2.1 36.4 1.0 O a:HOH7497 2.1 36.1 1.0 O a:HOH9486 2.1 37.5 1.0 O a:HOH4376 2.1 35.8 1.0 P a:A2682 3.1 27.3 1.0 OP2 a:G2722 3.6 26.0 1.0 O3' a:C2681 3.7 28.4 1.0 OP1 a:A2682 3.9 30.4 1.0 O a:HOH7500 4.0 54.0 1.0 OP1 a:A2721 4.1 28.7 1.0 O a:HOH138 4.1 37.0 1.0 O a:HOH5069 4.2 48.5 1.0 O a:HOH4829 4.3 49.5 1.0 O5' a:A2682 4.3 27.9 1.0 O a:HOH8032 4.5 36.0 1.0 OP2 a:C2683 4.5 26.9 1.0 O a:HOH5560 4.5 38.7 1.0 O a:HOH7744 4.5 24.3 1.0 C3' a:C2681 4.5 26.4 1.0 O2' a:C2681 4.6 24.0 1.0 P a:G2722 4.6 23.7 1.0 OP1 a:G2722 4.7 27.4 1.0 C5' a:A2682 4.8 26.3 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.