Magnesium in PDB 7afk: Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)

The structure of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) 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 Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) (pdb code 7afk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain), PDB code: 7afk:
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 Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1601 b:144.9 occ:1.00 OP1 1:A1360 3.5 160.2 1.0 O6 1:G1361 3.7 165.2 1.0 O3' 1:C1359 4.0 196.1 1.0 O N:GLN60 4.1 162.5 1.0 N7 1:A1360 4.2 160.2 1.0 P 1:A1360 4.4 160.2 1.0 CD N:ARG61 4.4 164.8 1.0 O N:SER58 4.5 159.6 1.0 C8 1:A1360 4.6 160.2 1.0 C6 1:G1361 4.6 165.2 1.0 C5' 1:C1359 4.7 196.1 1.0 C4' 1:C1359 4.7 196.1 1.0 O2 1:C980 4.9 168.7 1.0 NE N:ARG61 4.9 164.8 1.0 C3' 1:C1359 4.9 196.1 1.0

Magnesium binding site 2 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1602 b:117.2 occ:1.00 OP2 1:A1204 3.5 214.2 1.0 OP1 1:U1049 3.8 190.4 1.0 OE1 N:GLN4 4.0 182.9 1.0 O N:ALA2 4.2 178.1 1.0 P 1:A1204 4.5 214.2 1.0 NE2 N:GLN4 4.5 182.9 1.0 OP1 1:A1204 4.6 214.2 1.0 OP2 1:U1049 4.7 190.4 1.0 CD N:GLN4 4.7 182.9 1.0 P 1:U1049 4.8 190.4 1.0 OP1 1:C1203 4.8 210.4 1.0 C N:ALA2 4.8 178.1 1.0

Magnesium binding site 3 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1603 b:131.7 occ:1.00 OP1 1:C980 2.6 168.7 1.0 N7 1:G1220 3.3 177.5 1.0 O6 1:G1220 3.8 177.5 1.0 P 1:C980 3.9 168.7 1.0 O3' 1:C979 4.0 166.8 1.0 C5 1:G1220 4.2 177.5 1.0 C8 1:G1220 4.3 177.5 1.0 C6 1:G1220 4.4 177.5 1.0 N7 1:A1219 4.4 176.5 1.0 OP2 1:A1219 4.4 176.5 1.0 C5' 1:C980 4.5 168.7 1.0 O5' 1:C980 4.6 168.7 1.0 OP2 1:G1220 4.7 177.5 1.0 C8 1:A1219 4.8 176.5 1.0 N7 1:G1221 4.8 172.3 1.0 C5 1:A1219 5.0 176.5 1.0

Magnesium binding site 4 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1604 b:186.3 occ:1.00 OP1 1:C1109 1.7 188.7 1.0 O2 1:U1065 2.5 236.3 1.0 N3 1:U1065 2.7 236.3 1.0 OP2 1:A1110 2.7 181.4 1.0 P 1:C1109 2.9 188.7 1.0 C2 1:U1065 3.0 236.3 1.0 O5' 1:C1109 3.2 188.7 1.0 C5' 1:C1109 3.5 188.7 1.0 P 1:A1110 3.5 181.4 1.0 OP1 1:A1110 3.7 181.4 1.0 OP2 1:C1109 3.7 188.7 1.0 CD2 C:HIS176 3.7 183.0 1.0 C4 1:U1065 3.9 236.3 1.0 O3' 1:C1109 3.9 188.7 1.0 NE2 C:HIS176 4.0 183.0 1.0 O2 1:U1189 4.0 245.6 1.0 O3' 1:G1108 4.1 188.7 1.0 O4 1:U1065 4.2 236.3 1.0 N1 1:U1065 4.3 236.3 1.0 C3' 1:C1109 4.4 188.7 1.0 C4' 1:C1109 4.4 188.7 1.0 C2 1:U1189 4.6 245.6 1.0 N3 1:U1189 4.7 245.6 1.0 CG C:HIS176 4.9 183.0 1.0 O5' 1:A1110 5.0 181.4 1.0

Magnesium binding site 5 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1605 b:221.1 occ:1.00 O5' 1:G1068 2.7 210.0 1.0 C5' 1:G1068 3.3 210.0 1.0 C4' 1:G1068 3.8 210.0 1.0 OP1 1:G1068 4.0 210.0 1.0 P 1:G1068 4.0 210.0 1.0 C4' 1:A1067 4.2 226.4 1.0 O4' 1:A1067 4.6 226.4 1.0 O4' 1:G1068 4.7 210.0 1.0 C5' 1:A1067 4.8 226.4 1.0 O3' 1:G1068 4.8 210.0 1.0 C3' 1:G1068 4.9 210.0 1.0 O3' 1:A1067 4.9 226.4 1.0 OP2 1:G1068 5.0 210.0 1.0

Magnesium binding site 6 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1606 b:122.2 occ:1.00 OP1 1:U1224 2.4 193.8 1.0 P 1:U1224 3.3 193.8 1.0 OP2 1:U1224 3.4 193.8 1.0 O3' 1:C1223 4.0 177.8 1.0 O2' 1:C1223 4.6 177.8 1.0 N7 1:A977 4.6 182.0 1.0 OP1 1:U952 4.7 200.3 1.0 O5' 1:U1224 4.7 193.8 1.0 OP2 1:U952 4.9 200.3 1.0 C2' 1:C1223 4.9 177.8 1.0 C3' 1:C1223 4.9 177.8 1.0

Magnesium binding site 7 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1607 b:188.1 occ:1.00 OP2 1:C972 1.7 220.5 1.0 P 1:C972 3.1 220.5 1.0 O3' 1:G971 3.7 242.8 1.0 OP1 1:C972 3.8 220.5 1.0 C5' 1:C1366 4.1 237.8 1.0 O5' 1:C972 4.2 220.5 1.0 C3' 1:G971 4.3 242.8 1.0 O2' 1:G971 4.4 242.8 1.0 OP1 1:C1366 4.6 237.8 1.0 CG J:LYS59 4.7 245.1 1.0 O5' 1:C1366 4.9 237.8 1.0 C2' 1:G971 4.9 242.8 1.0

Magnesium binding site 8 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1608 b:192.4 occ:1.00 O3' 1:U952 1.5 200.3 1.0 P 1:G953 2.4 195.6 1.0 OP1 1:G953 2.5 195.6 1.0 C5' 1:G953 2.6 195.6 1.0 C3' 1:U952 2.7 200.3 1.0 O2' 1:U952 2.7 200.3 1.0 N6 1:A964 2.8 204.5 1.0 O5' 1:G953 2.9 195.6 1.0 C2' 1:U952 3.2 200.3 1.0 C4' 1:U952 3.3 200.3 1.0 C6 1:A964 3.4 204.5 1.0 N1 1:A964 3.4 204.5 1.0 O4 1:U965 3.7 214.7 1.0 OP2 1:G953 3.7 195.6 1.0 N3 1:U965 3.7 214.7 1.0 C4' 1:G953 4.0 195.6 1.0 C2 1:A969 4.0 221.8 1.0 C4 1:U965 4.1 214.7 1.0 C5' 1:U952 4.2 200.3 1.0 O4' 1:G953 4.3 195.6 1.0 C1' 1:U952 4.4 200.3 1.0 O4' 1:U952 4.4 200.3 1.0 C2 1:A964 4.5 204.5 1.0 N3 1:A969 4.6 221.8 1.0 C5 1:A964 4.6 204.5 1.0 N1 1:A969 4.7 221.8 1.0 C2 1:U965 4.7 214.7 1.0 O2 1:U965 4.9 214.7 1.0

Magnesium binding site 9 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1609 b:170.4 occ:1.00 OP1 1:C1051 2.7 203.7 1.0 O2' 1:C962 3.3 189.1 1.0 P 1:C1051 4.0 203.7 1.0 O3' 1:C962 4.0 189.1 1.0 OP2 1:C1051 4.5 203.7 1.0 C2' 1:C962 4.5 189.1 1.0 C3' 1:C962 4.6 189.1 1.0 N7 1:A1201 4.6 190.8 1.0 C4' 1:C962 4.7 189.1 1.0 O5' 1:C1051 4.8 203.7 1.0 C8 1:A1201 4.8 190.8 1.0 C5' 1:G963 5.0 205.6 1.0

Magnesium binding site 10 out of 12 in the Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Bacterial 30S Ribosomal Subunit Assembly Complex State D (Head Domain) within 5.0Å range: probe atom residue distance (Å) B Occ 1:Mg1610 b:207.1 occ:1.00 OP1 1:A1197 1.6 225.2 1.0 C3' 1:A1196 2.9 224.7 1.0 OP1 1:G1198 2.9 208.9 1.0 P 1:A1197 3.0 225.2 1.0 O3' 1:A1196 3.3 224.7 1.0 O2' 1:A1196 3.4 224.7 1.0 C2' 1:A1196 3.4 224.7 1.0 OP1 1:C1054 3.6 233.7 1.0 C5' 1:A1197 3.6 225.2 1.0 O5' 1:C1054 3.7 233.7 1.0 O5' 1:A1197 3.7 225.2 1.0 P 1:G1198 3.9 208.9 1.0 P 1:C1054 4.0 233.7 1.0 O3' 1:A1197 4.1 225.2 1.0 OP2 1:A1197 4.2 225.2 1.0 C4' 1:A1196 4.3 224.7 1.0 OP2 1:G1198 4.3 208.9 1.0 OP2 1:C1054 4.3 233.7 1.0 C4' 1:A1197 4.5 225.2 1.0 C3' 1:A1197 4.6 225.2 1.0 O5' 1:A1196 4.6 224.7 1.0 C5' 1:A1196 4.6 224.7 1.0 C5' 1:C1054 4.9 233.7 1.0 C1' 1:A1196 4.9 224.7 1.0

A.Schedlbauer, I.Iturrioz, B.Ochoa-Lizarralde, T.Diercks, J.P.Lopez-Alonso, J.L.Lavin, T.Kaminishi, R.Capuni, N.Dhimole, E.De Astigarraga, D.Gil-Carton, P.Fucini, S.R.Connell. A Conserved Rrna Switch Is Central to Decoding Site Maturation on the Small Ribosomal Subunit. Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
PubMed: 34088665
DOI: 10.1126/SCIADV.ABF7547