Magnesium in PDB 6ny6: Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome

The structure of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome, PDB code: 6ny6 was solved by I.J.Pavelich, E.D.Hoffer, T.Maehigashi, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.83 / 3.74
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.710, 401.710, 175.440, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.4

The structure of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Iron	(Fe)	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 - 184;

Binding sites:

The binding sites of Magnesium atom in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome (pdb code 6ny6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 184 binding sites of Magnesium where determined in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome, PDB code: 6ny6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1601 b:0.7 occ:1.00 O6 A:G157 2.6 0.1 1.0 O6 A:G158 2.8 0.3 1.0 O4 A:U164 3.4 0.7 1.0 C6 A:G157 3.7 0.3 1.0 C6 A:G158 4.0 0.0 1.0 O6 A:G156 4.1 0.5 1.0 N4 A:C165 4.2 0.9 1.0 C4 A:U164 4.4 0.5 1.0 C5 A:G157 4.6 0.8 1.0 N1 A:G157 4.6 0.2 1.0 N3 A:U164 4.6 0.7 1.0 N7 A:G157 4.7 0.6 1.0 N1 A:G158 4.8 0.8 1.0 C6 A:G156 4.8 0.3 1.0

Magnesium binding site 2 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:0.2 occ:1.00 OP2 A:G266 2.5 0.3 1.0 P A:G266 3.9 0.0 1.0 O6 A:G258 4.1 0.1 1.0 OP1 A:G266 4.3 0.5 1.0 O6 A:G257 4.4 0.3 1.0 O3' A:G265 4.8 0.8 1.0 N7 A:G257 4.9 0.2 1.0 O5' A:G266 4.9 0.6 1.0

Magnesium binding site 3 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:0.7 occ:1.00 O6 A:G78 4.2 0.2 1.0 N7 A:G78 4.6 0.2 1.0 C6 A:G78 5.0 0.2 1.0

Magnesium binding site 4 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:0.3 occ:1.00 N7 A:G731 4.0 0.5 1.0 OP1 A:G730 4.1 0.1 1.0 O6 A:G731 4.6 0.2 1.0 OP2 A:G818 4.8 0.3 1.0 OP2 A:G730 4.8 0.8 1.0 C8 A:G731 4.9 0.3 1.0 P A:G730 5.0 0.5 1.0

Magnesium binding site 5 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:0.5 occ:1.00 OP2 A:G942 2.6 0.6 1.0 OP1 A:G942 2.6 0.9 1.0 P A:G942 3.0 0.3 1.0 O2 A:C1336 3.6 0.4 1.0 O3' A:G941 3.9 0.9 1.0 N3 A:C1336 4.1 0.6 1.0 C2 A:C1336 4.3 0.5 1.0 O5' A:G942 4.3 0.2 1.0 C3' A:G941 4.8 0.1 1.0

Magnesium binding site 6 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:0.5 occ:1.00 O4 A:U1121 4.2 0.9 1.0 OP2 A:G1120 4.4 0.1 1.0 OP2 A:U1148 4.6 0.2 1.0 O4 A:U1150 4.7 0.5 1.0

Magnesium binding site 7 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:0.2 occ:1.00 OP1 A:G577 3.6 0.7 1.0 OP1 A:U813 3.8 97.4 1.0 N7 A:G577 4.3 96.0 1.0 P A:U813 4.8 1.0 1.0 C8 A:G577 5.0 99.2 1.0 OP2 A:U813 5.0 0.7 1.0

Magnesium binding site 8 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:56.4 occ:1.00 O6 A:G800 3.9 0.2 1.0 NZ K:LYS122 4.4 0.4 1.0 N7 A:G799 4.5 0.4 1.0 O6 A:G799 4.5 0.6 1.0 N7 A:G798 4.6 0.1 1.0 C6 A:G800 4.8 0.2 1.0 OP2 A:A781 4.9 0.5 1.0

Magnesium binding site 9 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:85.0 occ:1.00 N7 A:G758 3.6 0.1 1.0 OP2 A:U580 3.7 0.8 1.0 OP2 A:G581 3.7 0.1 1.0 N7 A:G581 3.9 0.9 1.0 OP2 A:U757 4.0 0.6 1.0 O6 A:G758 4.1 0.7 1.0 C5 A:G758 4.5 0.3 1.0 C8 A:G581 4.6 0.1 1.0 OP2 A:G758 4.6 0.6 1.0 C8 A:G758 4.6 1.0 1.0 C6 A:G758 4.7 1.0 1.0 P A:U580 4.8 0.3 1.0 C5 A:G581 4.9 0.1 1.0 O5' A:U580 4.9 0.6 1.0 O6 A:G581 5.0 0.6 1.0 P A:U757 5.0 0.2 1.0

Magnesium binding site 10 out of 184 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:0.7 occ:1.00 OP1 A:G438 3.0 0.2 1.0 OP2 A:G438 3.7 0.4 1.0 P A:G438 3.8 0.8 1.0 OP2 A:G492 4.0 1.0 1.0 O5' A:G438 4.4 0.5 1.0 O6 A:G494 4.9 0.3 1.0 MG A:MG1740 4.9 0.3 1.0

I.J.Pavelich, T.Maehigashi, E.D.Hoffer, A.Ruangprasert, S.J.Miles, C.M.Dunham. Monomeric Yoeb Toxin Retains Rnase Activity But Adopts An Obligate Dimeric Form For Thermal Stability. Nucleic Acids Res. V. 47 10400 2019.
ISSN: ESSN 1362-4962
PubMed: 31501867
DOI: 10.1093/NAR/GKZ760