Magnesium in PDB 4yy3: 30S Ribosomal Subunit- Higb Complex

The structure of 30S Ribosomal Subunit- Higb Complex, PDB code: 4yy3 was solved by M.A.Schureck, T.Maehigashi, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.16 / 3.60
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.594, 402.594, 176.035, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 23.9

The structure of 30S Ribosomal Subunit- Higb Complex also contains other interesting chemical elements:

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 - 194;

Binding sites:

The binding sites of Magnesium atom in the 30S Ribosomal Subunit- Higb Complex (pdb code 4yy3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 194 binding sites of Magnesium where determined in the 30S Ribosomal Subunit- Higb Complex, PDB code: 4yy3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:67.4 occ:1.00 O6 A:G703 2.6 0.2 1.0 O2 A:C701 3.4 98.0 1.0 C6 A:G703 3.6 0.1 1.0 N1 A:G703 4.2 0.1 1.0 O2' A:C701 4.4 97.5 1.0 C2 A:C701 4.6 97.8 1.0 OP2 A:A702 4.8 98.1 1.0 C5 A:G703 4.8 0.9 1.0

Magnesium binding site 2 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:74.6 occ:1.00 O6 A:G159 4.0 0.8 1.0 N7 A:G159 4.7 0.4 1.0 C6 A:G159 4.7 0.5 1.0

Magnesium binding site 3 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:68.5 occ:1.00 O6 A:G257 2.5 0.7 1.0 O6 A:G258 3.1 0.8 1.0 C6 A:G257 3.5 0.8 1.0 OP2 A:G266 3.5 96.8 1.0 N7 A:G257 3.9 0.3 1.0 C6 A:G258 3.9 0.1 1.0 O4 A:U256 4.0 1.0 1.0 C5 A:G257 4.0 0.6 1.0 N7 A:G258 4.0 1.0 1.0 OP1 A:G266 4.2 96.7 1.0 C5 A:G258 4.3 0.2 1.0 P A:G266 4.3 96.7 1.0 C4 A:U256 4.5 0.8 1.0 N4 A:C269 4.6 92.1 1.0 N1 A:G257 4.7 0.1 1.0 N4 A:C268 4.7 91.8 1.0 C5 A:U256 4.8 0.5 1.0

Magnesium binding site 4 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:69.9 occ:1.00 O6 A:G77 3.4 0.1 1.0 N7 A:G77 3.8 0.5 1.0 O6 A:G78 3.9 95.9 1.0 N7 A:G78 4.0 97.0 1.0 C6 A:G77 4.0 0.1 1.0 C5 A:G77 4.1 0.3 1.0 C6 A:G78 4.6 96.3 1.0 C5 A:G78 4.7 96.8 1.0 C8 A:G77 4.8 0.6 1.0

Magnesium binding site 5 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:80.0 occ:1.00 O6 A:G284 3.3 68.0 1.0 OP2 A:A282 3.7 71.1 1.0 N7 A:G284 3.7 70.1 1.0 C6 A:G284 4.1 68.0 1.0 C5 A:G284 4.2 68.9 1.0 OP2 A:C283 4.5 72.2 1.0 O6 A:G285 4.6 85.1 1.0 N4 A:C283 4.7 68.9 1.0 C8 A:G284 4.9 70.4 1.0 C5 A:C283 4.9 70.9 1.0

Magnesium binding site 6 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:49.4 occ:1.00 OP2 A:G731 3.9 63.2 1.0 N7 A:G731 3.9 65.4 1.0 OP1 A:C1527 4.1 78.3 1.0 OP1 A:G730 4.1 57.3 1.0 C8 A:G731 4.3 65.3 1.0

Magnesium binding site 7 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:68.5 occ:1.00 O2 A:C1336 3.2 96.3 1.0 O2' A:C1336 3.5 94.4 1.0 OP2 A:G942 4.1 79.9 1.0 C2 A:C1336 4.4 96.8 1.0 OP2 A:G1337 4.6 73.9 1.0 C2' A:C1336 4.8 94.7 1.0 C1' A:C1336 5.0 95.6 1.0

Magnesium binding site 8 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:95.0 occ:1.00 OP2 A:G1120 3.1 0.3 1.0 N7 A:G1120 3.8 0.5 1.0 C8 A:G1120 4.3 0.7 1.0 P A:G1120 4.5 0.4 1.0 O5' A:G1120 4.8 0.9 1.0 C5 A:G1120 4.9 0.9 1.0

Magnesium binding site 9 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:45.8 occ:1.00 OP1 A:G577 3.0 52.7 1.0 P A:G577 4.4 52.4 1.0 OP2 A:U813 4.5 66.4 1.0 O3' A:G576 4.6 61.1 1.0 N7 A:G577 4.7 54.6 1.0

Magnesium binding site 10 out of 194 in the 30S Ribosomal Subunit- Higb Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of 30S Ribosomal Subunit- Higb Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:61.6 occ:1.00 O2 A:C519 2.4 90.0 1.0 O2' A:C519 3.4 87.4 1.0 C2 A:C519 3.6 89.8 1.0 O4' A:A520 3.6 92.5 1.0 OP1 A:G517 3.8 0.3 1.0 O3' A:U516 4.0 91.3 1.0 C2' A:C519 4.2 87.0 1.0 O2' A:U516 4.2 90.8 1.0 C1' A:A520 4.3 93.2 1.0 C1' A:C519 4.4 87.5 1.0 N3 A:C519 4.4 90.6 1.0 C5' A:G517 4.4 0.1 1.0 N1 A:C519 4.5 88.5 1.0 P A:G517 4.6 0.9 1.0 C4' A:A520 4.6 91.7 1.0 N9 A:A520 5.0 92.8 1.0

M.A.Schureck, T.Maehigashi, S.J.Miles, J.Marquez, C.M.Dunham. Mrna Bound to the 30S Subunit Is A Higb Toxin Substrate. Rna V. 22 1261 2016.
ISSN: ESSN 1469-9001
PubMed: 27307497
DOI: 10.1261/RNA.056218.116