Magnesium in PDB 8cvm: Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map

The structure of Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map also contains other interesting chemical elements:

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 - 250; Page 26, Binding sites: 251 - 260; Page 27, Binding sites: 261 - 270; Page 28, Binding sites: 271 - 280; Page 29, Binding sites: 281 - 290; Page 30, Binding sites: 291 - 300; Page 31, Binding sites: 301 - 305;

Binding sites:

The binding sites of Magnesium atom in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map (pdb code 8cvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 305 binding sites of Magnesium where determined in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map, PDB code: 8cvm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg301 b:34.1 occ:1.00 OE1 c:GLN60 4.2 43.0 1.0 O c:PRO86 4.3 44.0 1.0 O c:ASN87 4.4 45.0 1.0 CA c:ASN87 4.6 45.0 1.0 NE2 c:GLN60 4.6 43.0 1.0 C c:ASN87 4.7 45.0 1.0 CD c:GLN60 4.9 43.0 1.0

Magnesium binding site 2 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg302 b:54.6 occ:1.00 CD2 c:HIS53 2.1 44.5 1.0 OP2 a:G2007 2.3 46.6 1.0 CG c:HIS53 2.6 44.5 1.0 NE2 c:HIS53 3.0 44.5 1.0 CB c:HIS53 3.1 44.5 1.0 P a:G2007 3.3 46.6 1.0 OP1 a:G2007 3.4 46.6 1.0 ND1 c:HIS53 3.6 44.5 1.0 CE1 c:HIS53 3.8 44.5 1.0 O c:ARG52 4.1 46.8 1.0 OG1 c:THR220 4.2 42.3 1.0 O5' a:G2007 4.4 46.6 1.0 C c:ARG52 4.4 46.8 1.0 O3' a:G2006 4.4 46.7 1.0 CA c:HIS53 4.4 44.5 1.0 NH2 c:ARG52 4.6 46.8 1.0 N c:HIS53 4.7 44.5 1.0 CG2 c:THR220 4.7 42.3 1.0 CB c:ARG52 4.7 46.8 1.0 NE c:ARG52 5.0 46.8 1.0

Magnesium binding site 3 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ c:Mg303 b:61.7 occ:1.00 O c:GLY242 2.4 62.5 1.0 O c:GLY234 2.4 51.9 1.0 O c:HIS233 3.1 52.8 1.0 O c:PRO232 3.1 50.9 1.0 C c:HIS233 3.2 52.8 1.0 C c:GLY242 3.4 62.5 1.0 C c:GLY234 3.5 51.9 1.0 CA c:HIS233 3.7 52.8 1.0 N c:GLY234 3.7 51.9 1.0 OP1 a:A2780 3.8 45.4 1.0 C c:PRO232 4.1 50.9 1.0 N c:GLY243 4.1 62.1 1.0 CA c:GLY243 4.2 62.1 1.0 CA c:GLY234 4.2 51.9 1.0 O3' a:G2779 4.3 45.7 1.0 CA c:GLY242 4.3 62.5 1.0 N c:HIS233 4.3 52.8 1.0 N c:GLY235 4.5 54.3 1.0 O c:SER241 4.7 65.3 1.0 C5' a:A2780 4.7 45.4 1.0 P a:A2780 4.7 45.4 1.0 CA c:GLY235 4.8 54.3 1.0 O c:GLY235 4.8 54.3 1.0 C c:GLY243 4.9 62.1 1.0 CB c:HIS233 4.9 52.8 1.0 C c:GLY235 4.9 54.3 1.0

Magnesium binding site 4 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ d:Mg301 b:46.6 occ:1.00 OP1 a:G1842 2.3 43.0 1.0 NE2 d:HIS146 2.5 44.2 1.0 CE1 d:HIS146 3.4 44.2 1.0 CD2 d:HIS146 3.5 44.2 1.0 P a:G1842 3.5 43.0 1.0 OP2 a:U1843 3.9 43.0 1.0 O5' a:G1842 3.9 43.0 1.0 O3' a:C828 4.1 44.2 1.0 OP2 a:G1842 4.2 43.0 1.0 OP1 a:A829 4.3 45.6 1.0 C5' a:G1842 4.3 43.0 1.0 ND1 d:HIS146 4.5 44.2 1.0 CG d:HIS146 4.6 44.2 1.0 O d:VAL142 4.7 48.9 1.0 O3' a:C1841 4.8 42.1 1.0 O2' a:C828 4.9 44.2 1.0 P a:A829 4.9 45.6 1.0

Magnesium binding site 5 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ k:Mg201 b:51.1 occ:1.00 O k:GLY35 2.1 40.4 1.0 C k:GLY35 3.1 40.4 1.0 CA k:THR36 3.3 42.4 1.0 N k:THR36 3.6 42.4 1.0 N k:LYS37 3.6 41.2 1.0 CB k:ALA41 3.7 40.4 1.0 CG2 k:THR31 3.8 40.0 1.0 C k:THR36 3.9 42.4 1.0 CB k:THR31 4.1 40.0 1.0 O4 a:U895 4.2 39.1 1.0 CB k:THR36 4.4 42.4 1.0 CA k:GLY35 4.5 40.4 1.0 CA k:ALA41 4.5 40.4 1.0 OG1 k:THR36 4.6 42.4 1.0 N k:GLY35 4.6 40.4 1.0 MG a:MG3383 4.6 38.7 1.0 CA k:THR31 4.7 40.0 1.0 C k:ARG34 4.8 39.8 1.0 CA k:LYS37 4.8 41.2 1.0 O k:ARG34 4.8 39.8 1.0 CG2 k:THR36 4.9 42.4 1.0 CB k:ARG34 4.9 39.8 1.0 O k:ALA41 4.9 40.4 1.0 O k:THR31 4.9 40.0 1.0 O k:THR36 5.0 42.4 1.0

Magnesium binding site 6 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ k:Mg202 b:42.5 occ:1.00 OP1 a:A1266 2.3 37.2 1.0 OE1 k:GLU25 2.8 44.4 1.0 OE2 k:GLU25 2.9 44.4 1.0 CD k:GLU25 3.0 44.4 1.0 P a:A1266 3.7 37.2 1.0 O k:GLY29 4.0 40.0 1.0 CG k:GLU25 4.2 44.4 1.0 CB k:GLU25 4.3 44.4 1.0 O3' a:U1265 4.4 38.2 1.0 OP2 a:G1267 4.4 37.2 1.0 CA k:GLU25 4.6 44.4 1.0 OP2 a:A1266 4.6 37.2 1.0 C k:GLY29 4.6 40.0 1.0 CB k:LYS30 4.7 39.3 1.0 O5' a:A1266 4.7 37.2 1.0 O q:THR80 4.7 41.6 1.0 O k:GLU25 4.8 44.4 1.0 C5' a:A1266 4.9 37.2 1.0

Magnesium binding site 7 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg101 b:52.0 occ:1.00 N3 a:A873 1.9 40.9 1.0 OG1 1:THR4 2.1 46.5 1.0 C2 a:A873 2.5 40.9 1.0 CB 1:THR4 2.7 46.5 1.0 C 1:THR4 3.0 46.5 1.0 OP1 a:U553 3.1 39.6 1.0 C4 a:A873 3.1 40.9 1.0 O 1:THR4 3.2 46.5 1.0 N 1:PHE5 3.3 45.2 1.0 CA 1:THR4 3.5 46.5 1.0 C1' a:A873 3.7 40.9 1.0 N1 a:A873 3.8 40.9 1.0 CA 1:PHE5 3.8 45.2 1.0 N9 a:A873 3.8 40.9 1.0 CG2 1:THR4 4.0 46.5 1.0 C6 a:U553 4.1 39.6 1.0 CB 1:PHE5 4.2 45.2 1.0 C5 a:U553 4.2 39.6 1.0 C5 a:A873 4.3 40.9 1.0 O2' a:A873 4.3 40.9 1.0 P a:U553 4.5 39.6 1.0 C6 a:A873 4.6 40.9 1.0 N 1:THR4 4.6 46.5 1.0 O4' a:U553 4.6 39.6 1.0 C2' a:A873 4.7 40.9 1.0 O4' a:A873 4.7 40.9 1.0 O2' a:U771 4.8 41.5 1.0 N1 a:U553 5.0 39.6 1.0

Magnesium binding site 8 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3102 b:80.2 occ:1.00 OP2 a:C2124 2.1 74.8 1.0 OP2 a:C2125 3.5 77.1 1.0 P a:C2124 3.6 74.8 1.0 O2' a:U2126 3.6 78.9 1.0 OP2 a:U2127 4.2 73.6 1.0 O3' a:U2126 4.3 78.9 1.0 OP1 a:C2124 4.3 74.8 1.0 O5' a:C2124 4.3 74.8 1.0 O3' a:U2123 4.5 71.1 1.0 C5' a:C2124 4.7 74.8 1.0 C2' a:U2126 4.8 78.9 1.0 P a:C2125 4.9 77.1 1.0 P a:U2127 4.9 73.6 1.0

Magnesium binding site 9 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3103 b:57.5 occ:1.00 O6 a:G1039 2.2 43.8 1.0 C6 a:G1039 3.4 43.8 1.0 OP2 a:G1037 3.6 40.9 1.0 C5 a:G1039 4.2 43.8 1.0 N1 a:PSU1038 4.2 41.7 1.0 N7 a:G1039 4.2 43.8 1.0 N7 a:G1037 4.2 40.9 1.0 N1 a:G1039 4.4 43.8 1.0 O2 a:PSU1038 4.6 41.7 1.0 C8 a:G1037 4.7 40.9 1.0 P a:G1037 4.8 40.9 1.0 C2 a:PSU1038 4.9 41.7 1.0 O5' a:G1037 5.0 40.9 1.0

Magnesium binding site 10 out of 305 in the Cutibacterium Acnes 50S Ribosomal Subunit with P-Site Trna and Sarecycline Bound in the Local Refined Map


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 P-Site Trna and Sarecycline Bound in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ a:Mg3104 b:52.9 occ:1.00 OP1 a:A1838 2.3 42.9 1.0 O2 a:U1836 2.3 44.0 1.0 O2 a:C2189 3.1 41.5 1.0 O2' a:A3003 3.5 42.3 1.0 C2 a:U1836 3.5 44.0 1.0 O2' a:U1836 3.6 44.0 1.0 P a:A1838 3.7 42.9 1.0 C2' a:U1836 4.0 44.0 1.0 C2 a:C2189 4.0 41.5 1.0 C1' a:U1836 4.0 44.0 1.0 N1 a:U1836 4.3 44.0 1.0 O5' a:A1838 4.3 42.9 1.0 N2 a:G1835 4.4 43.3 1.0 O3' a:A3003 4.4 42.3 1.0 OP2 a:A1838 4.5 42.9 1.0 N3 a:U1836 4.5 44.0 1.0 N3 a:C2189 4.7 41.5 1.0 C8 a:A1838 4.7 42.9 1.0 C2' a:A3003 4.7 42.3 1.0 N6 a:A2188 4.7 42.4 1.0 C4' a:A3003 4.7 42.3 1.0 O3' a:G1837 4.8 44.1 1.0 N7 a:A1838 4.8 42.9 1.0 N1 a:C2189 4.9 41.5 1.0 C3' a:A3003 4.9 42.3 1.0 C1' a:C2189 4.9 41.5 1.0 N1 a:G1835 4.9 43.3 1.0 N1 a:A2188 4.9 42.4 1.0 C2 a:G1835 4.9 43.3 1.0

I.B.Lomakin, S.C.Devarkar, S.Patel, A.Grada, C.G.Bunick. Sarecycline Inhibits Protein Translation in Cutibacterium Acnes 70S Ribosome Using A Two-Site Mechanism. Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962
PubMed: 36864821
DOI: 10.1093/NAR/GKAD103