Magnesium in PDB 5wnv: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 5wnv was solved by H.Demirci, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.80 / 3.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.000, 400.000, 173.000, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.3

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus also contains other interesting chemical elements:

Potassium	(K)	22 atoms
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 - 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 - 251;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 5wnv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 251 binding sites of Magnesium where determined in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 5wnv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:0.8 occ:1.00 O6 A:G216 3.3 0.3 1.0 C6 A:U204 3.4 0.6 1.0 O2 A:U203 3.6 0.4 1.0 C1' A:U204 3.9 0.9 1.0 C6 A:G216 3.9 0.7 1.0 N1 A:U204 4.1 0.8 1.0 C5 A:U204 4.2 0.5 1.0 O4' A:U204 4.2 0.3 1.0 N1 A:G216 4.5 1.0 1.0 C5 A:G216 4.7 0.1 1.0 C2 A:U203 4.7 0.9 1.0

Magnesium binding site 2 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:1.0 occ:1.00 O A:HOH2060 2.1 0.7 1.0 O A:HOH2035 2.1 0.6 1.0 O A:HOH2029 2.1 71.5 1.0 O6 A:G377 4.6 0.7 1.0 N7 A:G376 4.6 0.9 1.0 N7 A:G377 4.8 0.5 1.0 O6 A:G376 4.9 0.8 1.0

Magnesium binding site 3 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:0.9 occ:1.00 O A:HOH2107 2.1 0.8 1.0 O A:HOH2067 2.1 0.6 1.0 O A:HOH2017 2.1 97.5 1.0 OP2 A:A753 3.7 0.1 1.0 N7 A:G650 3.8 0.9 1.0 O6 A:G650 4.0 0.0 1.0 N7 A:G649 4.3 0.8 1.0 O6 A:G649 4.5 0.6 1.0 C5 A:G650 4.6 0.1 1.0 OP1 A:A753 4.6 89.1 1.0 P A:A753 4.6 100.0 1.0 C6 A:G650 4.7 0.1 1.0 C5 A:G649 4.8 0.6 1.0 C8 A:G650 4.9 0.7 1.0 C6 A:G649 4.9 0.6 1.0

Magnesium binding site 4 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:0.5 occ:1.00 O A:HOH1926 2.1 0.1 1.0 O A:HOH1975 2.1 0.3 1.0 OP2 A:C749 3.0 0.5 1.0 OP2 A:G750 3.1 0.3 1.0 OP1 A:C749 3.3 0.9 1.0 P A:C749 3.6 0.3 1.0 P A:G750 4.4 0.8 1.0 O2' A:C748 4.5 0.9 1.0 O3' A:C748 4.6 0.3 1.0 O6 A:G752 4.8 0.6 1.0 O5' A:C749 4.9 0.5 1.0 OP2 A:A653 4.9 0.6 1.0 OP1 A:G750 5.0 1.0 1.0

Magnesium binding site 5 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:0.6 occ:1.00 O A:HOH1906 2.1 0.5 1.0 O A:HOH1907 2.1 70.3 1.0 O A:HOH1910 2.1 0.5 1.0 O A:HOH1911 2.1 0.1 1.0 OP2 A:G117 2.8 71.0 1.0 OP2 A:G289 3.3 98.3 1.0 OP1 A:A116 3.6 83.3 1.0 P A:G117 3.7 0.4 1.0 OP1 A:G117 3.7 0.2 1.0 O5' A:A288 4.2 88.1 1.0 C8 A:A288 4.2 0.1 1.0 OP2 A:A288 4.2 65.7 1.0 O4 A:U118 4.2 84.4 1.0 C3' A:A288 4.4 0.8 1.0 N7 A:A288 4.4 0.9 1.0 P A:G289 4.5 92.3 1.0 C5 A:U118 4.5 89.7 1.0 P A:A116 4.6 1.0 1.0 O5' A:G117 4.6 0.6 1.0 OP2 A:A116 4.7 0.9 1.0 P A:A288 4.8 86.7 1.0 C4 A:U118 4.8 93.9 1.0 N7 A:G117 4.8 0.8 1.0 O3' A:A288 4.9 0.3 1.0 N9 A:A288 4.9 0.8 1.0 O3' A:A116 4.9 0.2 1.0 C5' A:A116 4.9 89.0 1.0 C8 A:G117 5.0 0.7 1.0 OP1 A:G289 5.0 66.4 1.0

Magnesium binding site 6 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:0.7 occ:1.00 OP2 A:C48 3.0 0.9 1.0 OP2 A:U49 3.2 0.8 1.0 OP1 A:A51 3.3 0.8 1.0 OP1 A:G115 3.7 0.7 1.0 O3' A:C47 4.1 0.1 1.0 P A:C48 4.2 0.6 1.0 P A:A51 4.5 0.6 1.0 P A:U49 4.6 0.1 1.0 O2' A:C47 4.6 0.3 1.0 C5' A:C48 4.9 84.1 1.0 P A:G115 4.9 98.9 1.0 O5' A:C48 4.9 91.9 1.0 C5' A:A51 5.0 0.4 1.0 O3' A:U114 5.0 0.4 1.0 O5' A:A51 5.0 97.3 1.0

Magnesium binding site 7 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:0.7 occ:1.00 O A:HOH1951 2.1 0.6 1.0 O A:HOH2025 2.1 0.7 1.0 O A:HOH2021 2.1 0.8 1.0 O A:HOH2073 2.1 94.8 1.0 N7 A:G752 3.7 0.1 1.0 OP2 A:U751 4.1 0.6 1.0 OP2 A:U652 4.1 0.1 1.0 C8 A:G752 4.4 0.2 1.0 OP1 A:U751 4.5 0.8 1.0 OP2 A:G752 4.7 0.3 1.0 P A:U751 4.7 0.5 1.0 C5 A:G752 4.7 0.4 1.0 OP1 A:C651 4.8 0.1 1.0 O6 A:G752 4.9 0.6 1.0

Magnesium binding site 8 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:94.8 occ:1.00 O A:HOH1962 2.1 0.3 1.0 O A:HOH2092 2.1 0.6 1.0 O A:HOH2106 2.1 82.8 1.0 O6 A:G800 3.7 98.1 1.0 O A:HOH2005 3.8 0.3 1.0 N7 A:G799 4.1 90.6 1.0 O6 A:G799 4.4 0.1 1.0 C6 A:G800 4.4 0.6 1.0 OP2 A:A781 4.7 93.6 1.0 N7 A:G798 4.8 95.2 1.0 N1 A:G800 4.9 81.6 1.0 O6 A:G798 4.9 0.9 1.0 C5 A:G799 4.9 92.0 1.0 OP1 A:A781 5.0 0.9 1.0

Magnesium binding site 9 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:0.3 occ:1.00 O2 A:U1506 3.1 1.0 1.0 OP1 A:U1522 3.8 82.3 1.0 C2 A:U1506 3.8 88.1 1.0 OP2 A:U1522 4.1 0.3 1.0 O2' A:U1506 4.2 0.5 1.0 P A:U1522 4.4 93.6 1.0 OP2 A:G1508 4.5 0.9 1.0 C1' A:U1506 4.5 99.7 1.0 N1 A:U1506 4.5 84.8 1.0 N3 A:U1506 4.6 83.1 1.0 MG A:MG1788 5.0 91.2 1.0 C2' A:U1506 5.0 98.3 1.0

Magnesium binding site 10 out of 251 in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:71.3 occ:1.00 O A:HOH1912 2.1 0.5 1.0 O A:HOH1914 2.1 76.2 1.0 OP1 A:G1505 2.9 0.6 1.0 OP1 A:G1508 2.9 88.6 1.0 OP1 A:A1500 3.0 84.1 1.0 O3' A:A1507 3.0 83.5 1.0 O5' A:G1505 3.2 0.9 1.0 OP1 A:G1504 3.3 92.0 1.0 C5' A:G1505 3.6 0.7 1.0 P A:G1508 3.6 91.2 1.0 P A:G1505 3.6 89.0 1.0 C3' A:G1504 3.9 0.2 1.0 O5' A:G1504 4.0 0.1 1.0 O2' A:U1506 4.1 0.5 1.0 O3' A:G1504 4.1 0.2 1.0 P A:G1504 4.2 94.4 1.0 C5' A:G1508 4.2 87.2 1.0 P A:A1500 4.2 84.6 1.0 C3' A:A1507 4.2 83.5 1.0 O5' A:G1508 4.4 93.1 1.0 OP2 A:C1501 4.4 85.4 1.0 C4' A:A1507 4.5 84.5 1.0 O2' A:A1507 4.5 84.3 1.0 OP2 A:A1500 4.6 85.4 1.0 C2' A:U1506 4.6 98.3 1.0 MG A:MG1721 4.7 58.5 1.0 C2' A:G1504 4.8 0.5 1.0 OP2 A:G1508 4.8 0.9 1.0 OP2 A:G1504 4.8 0.2 1.0 O2' A:G1504 4.9 0.8 1.0 C4' A:G1504 5.0 87.7 1.0 C5' A:A1507 5.0 0.3 1.0 OP2 A:G1505 5.0 98.5 1.0

J.Choi, G.Indrisiunaite, H.Demirci, K.W.Ieong, J.Wang, A.Petrov, A.Prabhakar, G.Rechavi, D.Dominissini, C.He, M.Ehrenberg, J.D.Puglisi. 2'-O-Methylation in Mrna Disrupts Trna Decoding During Translation Elongation. Nat. Struct. Mol. Biol. V. 25 208 2018.
ISSN: ESSN 1545-9985
PubMed: 29459784
DOI: 10.1038/S41594-018-0030-Z