Magnesium in PDB 9c4g: Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound

The structure of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Zinc	(Zn)	4 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 - 247;

Binding sites:

The binding sites of Magnesium atom in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound (pdb code 9c4g). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 247 binding sites of Magnesium where determined in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound, PDB code: 9c4g:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg301 b:25.2 occ:1.00 OE1 c:GLN60 3.9 26.0 1.0 O c:PRO86 4.0 28.2 1.0 O c:ASN87 4.3 26.5 1.0 NE2 c:GLN60 4.4 27.2 1.0 CA c:ASN87 4.5 24.7 1.0 C c:ASN87 4.6 26.7 1.0 CD c:GLN60 4.6 25.0 1.0 C c:PRO86 5.0 25.8 1.0

Magnesium binding site 2 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ d:Mg301 b:42.0 occ:1.00 NE2 d:HIS146 1.9 36.7 1.0 OP1 a:G1842 2.1 26.5 1.0 CD2 d:HIS146 2.7 30.8 1.0 CE1 d:HIS146 3.1 28.6 1.0 P a:G1842 3.4 23.3 1.0 OP2 a:G1842 3.9 22.8 1.0 CG d:HIS146 4.0 27.5 1.0 O5' a:G1842 4.0 22.8 1.0 ND1 d:HIS146 4.1 27.9 1.0 O d:VAL142 4.5 32.8 1.0 C5' a:G1842 4.6 21.5 1.0 O3' a:C1841 4.7 23.2 1.0 OP1 a:A829 4.7 22.1 1.0 OP2 a:U1843 4.7 20.6 1.0 O3' a:C828 4.7 22.9 1.0 N d:ARG144 4.9 27.6 1.0 O d:ALA138 4.9 32.3 1.0

Magnesium binding site 3 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ k:Mg201 b:39.4 occ:1.00 OE1 k:GLU25 2.0 28.5 1.0 OE2 k:GLU25 2.2 32.2 1.0 CD k:GLU25 2.3 27.8 1.0 OP1 a:A1266 3.0 26.2 1.0 CG k:GLU25 3.6 22.5 1.0 O q:THR80 3.7 23.9 1.0 CB k:GLU25 4.0 20.6 1.0 CA q:GLY81 4.2 16.4 1.0 P a:A1266 4.3 23.4 1.0 CD k:LYS30 4.4 11.6 1.0 CB k:LYS30 4.4 15.7 1.0 O3' a:U1265 4.5 19.4 1.0 C q:THR80 4.6 18.5 1.0 N q:GLY81 4.8 18.7 1.0 O k:GLY29 4.9 22.1 1.0 C q:GLY81 4.9 18.0 1.0

Magnesium binding site 4 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3101 b:50.5 occ:1.00 OP2 a:C2124 2.4 46.5 1.0 P a:C2124 3.5 48.3 1.0 OP1 a:C2124 3.9 47.0 1.0 O3' a:U2123 4.1 43.8 1.0 O2' a:U2126 4.2 45.6 1.0 OP2 a:C2125 4.4 49.6 1.0 O2' a:U2123 4.8 37.7 1.0 O5' a:C2124 4.9 44.8 1.0 O3' a:U2126 4.9 47.3 1.0 OP2 a:U2127 4.9 46.4 1.0 C3' a:U2123 5.0 40.7 1.0

Magnesium binding site 5 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3102 b:35.6 occ:1.00 OP2 a:U1831 2.3 35.7 1.0 OP2 a:G1348 2.5 36.2 1.0 OP1 a:U1349 3.0 39.3 1.0 P a:U1831 3.7 34.4 1.0 P a:G1348 3.8 35.2 1.0 P a:U1349 4.3 39.3 1.0 OP1 a:G1348 4.4 29.8 1.0 O3' a:A1830 4.4 35.5 1.0 OP1 a:U1831 4.4 36.4 1.0 OP1 a:C1832 4.5 30.8 1.0 OP2 a:U1349 4.6 34.5 1.0 C5' a:U1831 4.7 27.4 1.0 O5' a:G1348 4.7 33.4 1.0 O5' a:U1831 4.7 30.7 1.0 O3' a:C1347 4.9 31.9 1.0 OP2 a:G1833 4.9 21.1 1.0

Magnesium binding site 6 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3103 b:35.9 occ:1.00 O a:HOH3425 2.7 30.0 1.0 N3 a:A1607 4.0 22.2 1.0 C5 a:C1608 4.2 24.0 1.0 O a:HOH3449 4.4 25.1 1.0 C2 a:A1607 4.4 22.1 1.0 C6 a:C1608 4.5 26.4 1.0 CD1 c:LEU34 4.5 34.2 1.0 OP2 a:A1753 4.6 23.9 1.0 OP1 a:A1752 4.7 31.4 1.0 OP2 a:A1752 4.8 27.8 1.0 CG c:LYS31 4.9 27.6 1.0 C4 a:A1607 4.9 21.1 1.0 O a:HOH3446 4.9 30.0 1.0 C1' a:A1607 5.0 26.6 1.0

Magnesium binding site 7 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3104 b:19.9 occ:1.00 OP1 a:C763 2.1 20.6 1.0 O6 a:G861 2.2 21.9 1.0 OP1 a:C2254 2.2 18.7 1.0 C6 a:G861 3.0 16.6 1.0 P a:C763 3.3 19.6 1.0 N1 a:G861 3.5 14.1 1.0 P a:C2254 3.5 13.8 1.0 OP2 a:C763 3.9 16.5 1.0 O5' a:C763 4.0 20.9 1.0 O3' a:A2253 4.0 15.9 1.0 OP2 a:G764 4.0 18.7 1.0 C5 a:G861 4.1 17.0 1.0 C5' a:C763 4.2 18.2 1.0 OP2 a:C2254 4.2 17.4 1.0 O3' a:G762 4.6 16.6 1.0 O5' a:C2254 4.7 14.9 1.0 P a:G764 4.7 21.1 1.0 C2 a:G861 4.7 16.4 1.0 N7 a:G861 4.8 18.4 1.0 O2' a:A878 4.8 20.7 1.0 O3' a:C763 4.8 22.1 1.0 OP1 a:G764 4.8 18.4 1.0 C5' a:C2254 5.0 15.6 1.0

Magnesium binding site 8 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3105 b:31.2 occ:1.00 OP1 a:A2153 2.2 31.1 1.0 O5' a:U2154 3.1 27.9 1.0 OP1 a:U2154 3.6 26.5 1.0 P a:A2153 3.7 33.0 1.0 C5' a:U2154 3.9 25.7 1.0 OP1 a:A2152 3.9 35.2 1.0 P a:U2154 4.0 28.0 1.0 C4' a:A2153 4.2 27.4 1.0 C5' a:A2153 4.4 28.1 1.0 O3' a:A2152 4.4 33.1 1.0 OP2 a:A2153 4.5 33.4 1.0 O5' a:A2153 4.5 27.4 1.0 O3' a:A2153 4.5 26.6 1.0 C6 a:U2154 4.6 31.8 1.0 C3' a:A2153 4.8 25.7 1.0 O4' a:U2154 4.8 30.4 1.0 C4' a:U2154 5.0 26.4 1.0 C5 a:U2154 5.0 29.6 1.0

Magnesium binding site 9 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3106 b:18.0 occ:1.00 N7 a:G2222 3.9 15.0 1.0 O6 a:G2222 4.0 18.4 1.0 O4 a:U2223 4.3 18.8 1.0 O2' a:A617 4.6 23.1 1.0 C5 a:G2222 4.6 14.7 1.0 C6 a:G2222 4.7 15.9 1.0 N4 a:C2221 4.8 10.0 1.0 C8 a:G2222 4.9 15.5 1.0 N6 a:A2206 5.0 18.0 1.0 C5 a:C2221 5.0 11.9 1.0

Magnesium binding site 10 out of 247 in the Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Cutibacterium Acnes 50S Ribosomal Subunit with Clindamycin Bound within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3107 b:28.9 occ:1.00 N7 a:G26 1.9 17.7 1.0 C8 a:G26 2.9 14.9 1.0 C5 a:G26 2.9 14.3 1.0 O6 a:G26 3.3 13.8 1.0 C6 a:G26 3.5 13.6 1.0 N9 a:G26 4.1 14.7 1.0 C4 a:G26 4.1 15.2 1.0 OP2 a:G26 4.4 19.9 1.0 OP1 a:C597 4.6 56.9 1.0 N1 a:G600 4.8 15.6 1.0 N1 a:G26 4.8 14.2 1.0 N7 a:G25 4.8 15.2 1.0 O6 a:G600 4.9 26.3 1.0 C8 a:G25 4.9 16.2 1.0 OP2 a:G25 4.9 24.1 1.0 C6 a:G600 4.9 18.7 1.0

I.B.Lomakin, S.C.Devarkar, A.Grada, C.G.Bunick. Mechanistic Basis For the Translation Inhibition of Cutibacterium Acnes By Clindamycin. J Invest Dermatol. 2024.
ISSN: ESSN 1523-1747
PubMed: 39122144
DOI: 10.1016/J.JID.2024.07.013