Magnesium in PDB 8cvo: Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map

The structure of Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map (pdb code 8cvo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map, PDB code: 8cvo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:48.7 occ:1.00 O S:ALA20 3.9 60.9 1.0 O2 A:C964 4.0 58.7 1.0 OP1 A:A1346 4.2 58.6 1.0 O6 A:G1347 4.3 58.0 1.0 N7 A:A1346 4.3 58.6 1.0 N4 A:C963 4.3 58.2 1.0 N3 A:C964 4.4 58.7 1.0 O S:VAL18 4.4 61.3 1.0 O3' A:C1345 4.4 61.1 1.0 C2 A:C964 4.6 58.7 1.0 C8 A:A1346 4.8 58.6 1.0

Magnesium binding site 2 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:57.2 occ:1.00 N7 A:G1035 4.0 70.9 1.0 OP2 A:A1187 4.1 63.4 1.0 OP2 A:U1034 4.1 67.1 1.0 O6 A:G1035 4.1 70.9 1.0 O4 A:U1191 4.3 65.6 1.0 O2' A:C1186 4.5 65.3 1.0 C5 A:G1035 4.5 70.9 1.0 N7 A:G1036 4.5 71.1 1.0 O6 A:G1036 4.5 71.1 1.0 C6 A:G1035 4.5 70.9 1.0 O3' A:C1186 4.6 65.3 1.0 P A:A1187 4.7 63.4 1.0 OP1 A:A1187 4.8 63.4 1.0 O4 A:U1037 4.8 69.7 1.0 C8 A:G1035 4.9 70.9 1.0

Magnesium binding site 3 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:76.0 occ:1.00 OP2 A:G1184 2.1 66.8 1.0 OP1 A:C1039 2.4 76.2 1.0 OAY A:V7A1601 2.4 80.2 1.0 OAZ A:V7A1601 2.6 80.2 1.0 OP1 A:A1183 2.6 70.1 1.0 OP1 A:G1184 2.7 66.8 1.0 P A:G1184 2.8 66.8 1.0 CAH A:V7A1601 3.1 80.2 1.0 CAL A:V7A1601 3.3 80.2 1.0 P A:C1039 3.5 76.2 1.0 CAI A:V7A1601 3.6 80.2 1.0 OP2 A:C1039 3.7 76.2 1.0 O3' A:A1183 3.8 70.1 1.0 P A:A1183 3.9 70.1 1.0 OAX A:V7A1601 4.0 80.2 1.0 O5' A:G1184 4.1 66.8 1.0 OP2 A:A1183 4.2 70.1 1.0 C5' A:A1183 4.2 70.1 1.0 CAE A:V7A1601 4.2 80.2 1.0 C3' A:A1183 4.2 70.1 1.0 O2' A:G1038 4.3 67.4 1.0 OBA A:V7A1601 4.3 80.2 1.0 O2' A:A1182 4.4 77.6 1.0 O3' A:G1038 4.5 67.4 1.0 CAM A:V7A1601 4.5 80.2 1.0 CAD A:V7A1601 4.5 80.2 1.0 C3' A:G1038 4.5 67.4 1.0 O5' A:A1183 4.6 70.1 1.0 MG A:MG1605 4.7 58.8 1.0 O5' A:C1039 4.7 76.2 1.0 C4' A:A1183 4.7 70.1 1.0 OP2 A:U1185 4.9 65.8 1.0 C2' A:G1038 4.9 67.4 1.0

Magnesium binding site 4 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:58.8 occ:1.00 OP1 A:A948 2.9 64.0 1.0 OP1 A:U1185 3.1 65.8 1.0 OP1 A:G1184 3.6 66.8 1.0 P A:U1185 4.1 65.8 1.0 OAY A:V7A1601 4.1 80.2 1.0 OP2 A:U1185 4.2 65.8 1.0 P A:A948 4.3 64.0 1.0 MG A:MG1604 4.7 76.0 1.0 P A:G1184 4.8 66.8 1.0 OP2 A:U949 4.8 71.0 1.0 O3' A:G1184 4.9 66.8 1.0 O3' A:G947 4.9 61.3 1.0

Magnesium binding site 5 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:65.7 occ:1.00 OP1 A:G1036 3.8 71.1 1.0 OP1 A:C1186 3.9 65.3 1.0 O2' A:C946 3.9 60.7 1.0 OP2 A:U1037 4.2 69.7 1.0 OP2 A:G1036 4.3 71.1 1.0 C5' A:G947 4.4 61.3 1.0 P A:G1036 4.5 71.1 1.0 C4' A:G947 4.9 61.3 1.0 P A:C1186 5.0 65.3 1.0

Magnesium binding site 6 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:66.8 occ:1.00 OP2 A:A1183 2.8 70.1 1.0 OP2 A:C1039 3.1 76.2 1.0 O4 A:U1185 3.4 65.8 1.0 N7 A:G1184 3.9 66.8 1.0 P A:A1183 4.2 70.1 1.0 P A:C1039 4.3 76.2 1.0 C4 A:U1185 4.4 65.8 1.0 O3' A:G1038 4.4 67.4 1.0 O6 A:G1184 4.5 66.8 1.0 O2' A:G1038 4.5 67.4 1.0 O3' A:A1182 4.7 77.6 1.0 C8 A:G1184 4.7 66.8 1.0 N7 A:A1183 4.8 70.1 1.0 C5 A:U1185 4.8 65.8 1.0 C5 A:G1184 4.8 66.8 1.0 C5 A:A1183 4.8 70.1 1.0 OP2 A:G1184 4.9 66.8 1.0 N6 A:A1183 4.9 70.1 1.0 C6 A:A1183 5.0 70.1 1.0

Magnesium binding site 7 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:62.7 occ:1.00 OP2 A:U1210 3.0 58.1 1.0 OP1 A:U1210 3.0 58.1 1.0 P A:U1210 3.4 58.1 1.0 OP1 A:G935 4.0 62.8 1.0 O3' A:C1209 4.3 57.2 1.0 OP2 A:C936 4.3 63.4 1.0 N7 A:A961 4.5 58.6 1.0 N6 A:A961 4.5 58.6 1.0 C2' A:C1209 4.7 57.2 1.0 O2' A:C1209 4.7 57.2 1.0 OP1 A:C936 4.7 63.4 1.0 O5' A:U1210 4.8 58.1 1.0 C3' A:C1209 4.9 57.2 1.0 P A:C936 4.9 63.4 1.0

Magnesium binding site 8 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:55.1 occ:1.00 OP2 A:A921 2.5 65.4 1.0 P A:A921 3.7 65.4 1.0 O6 A:G923 3.8 62.0 1.0 O5' A:A921 4.0 65.4 1.0 N7 A:G923 4.2 62.0 1.0 N7 A:A922 4.2 62.6 1.0 OP1 A:A921 4.5 65.4 1.0 C6 A:G923 4.6 62.0 1.0 N7 A:A921 4.6 65.4 1.0 N6 A:A922 4.6 62.6 1.0 C8 A:A921 4.7 65.4 1.0 C5 A:G923 4.7 62.0 1.0 O3' A:C920 5.0 69.1 1.0

Magnesium binding site 9 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:65.9 occ:1.00 OP2 A:G937 4.1 66.2 1.0 OP1 A:C936 4.2 63.4 1.0 OP1 A:G937 4.3 66.2 1.0 N4 A:C946 4.5 60.7 1.0 P A:G937 4.6 66.2 1.0 C5 A:C946 4.6 60.7 1.0 O6 A:G947 4.8 61.3 1.0 N6 A:A948 4.9 64.0 1.0 C4 A:C946 4.9 60.7 1.0 O3' A:C936 5.0 63.4 1.0

Magnesium binding site 10 out of 12 in the Cutibacterium Acnes 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only 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 30S Ribosomal Subunit with Sarecycline Bound, Head Domain Only in the Local Refined Map within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:59.2 occ:1.00 OP2 A:G929 2.4 62.0 1.0 OP1 A:G928 2.7 70.0 1.0 N7 A:A930 3.6 58.8 1.0 P A:G928 3.6 70.0 1.0 P A:G929 3.7 62.0 1.0 OP2 A:G928 3.8 70.0 1.0 O5' A:G928 4.2 70.0 1.0 O5' A:G929 4.2 62.0 1.0 OP2 A:A930 4.2 58.8 1.0 C8 A:A930 4.3 58.8 1.0 OP1 A:G929 4.4 62.0 1.0 C5 A:A930 4.5 58.8 1.0 N6 A:A930 4.5 58.8 1.0 C5' A:G928 4.7 70.0 1.0 O6 A:G931 4.9 56.0 1.0 C6 A:A930 4.9 58.8 1.0 O3' A:G928 4.9 70.0 1.0 N7 A:G929 5.0 62.0 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