Magnesium in PDB 4yhh: Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline, PDB code: 4yhh was solved by A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Dhimole, S.Zhou, J.P.Lopez-Alonso, S.R.Connell, P.Fucini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.72 / 3.42
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	409.590, 409.590, 171.730, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 28.7

The structure of Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline 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 - 103;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline (pdb code 4yhh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 103 binding sites of Magnesium where determined in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline, PDB code: 4yhh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1602 b:99.3 occ:1.00 OP1 A:A16 3.3 0.4 1.0 OP1 A:U13 3.4 0.9 1.0 C5 A:U14 3.6 0.3 1.0 OP2 A:A16 3.8 0.1 1.0 C6 A:U14 3.9 0.3 1.0 P A:A16 4.1 0.9 1.0 C4 A:U14 4.6 1.0 1.0 P A:U13 4.7 0.8 1.0 OP2 A:G15 4.8 0.1 1.0 OP2 A:U14 4.9 0.6 1.0 O5' A:U13 5.0 0.7 1.0 O5' A:U14 5.0 0.3 1.0

Magnesium binding site 2 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1603 b:0.3 occ:1.00 OP1 A:G21 2.7 0.9 1.0 N2 A:G567 3.3 0.3 1.0 N3 A:G567 3.6 0.8 1.0 O2' A:G567 3.6 0.6 1.0 P A:G21 3.7 0.1 1.0 N6 A:A563 3.8 0.4 1.0 OP2 A:G21 3.8 0.1 1.0 C2 A:G567 3.9 0.2 1.0 O3' A:U20 4.3 0.2 1.0 N7 A:A563 4.6 0.5 1.0 C2' A:G567 4.6 0.8 1.0 O4' A:G568 4.7 0.6 1.0 C4 A:G567 4.8 0.8 1.0 C6 A:A563 4.9 0.3 1.0 C1' A:G567 4.9 0.8 1.0

Magnesium binding site 3 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1604 b:0.3 occ:1.00 O6 A:G29 4.2 0.9 1.0 O4 A:U30 4.5 0.5 1.0 C6 A:G29 4.8 0.0 1.0

Magnesium binding site 4 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1605 b:0.9 occ:1.00 O4 A:U37 3.1 0.0 1.0 O6 A:G38 3.4 0.5 1.0 N7 A:G38 3.9 0.8 1.0 C4 A:U37 3.9 0.5 1.0 C6 A:G38 4.2 0.1 1.0 C5 A:U37 4.4 0.2 1.0 C5 A:G38 4.4 0.3 1.0 N3 A:U37 5.0 0.3 1.0

Magnesium binding site 5 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1606 b:0.5 occ:1.00 O6 A:G41 3.5 0.0 1.0 N7 A:G41 3.6 0.1 1.0 C6 A:G41 4.2 0.8 1.0 C5 A:G41 4.3 0.9 1.0 O6 A:G42 4.4 0.3 1.0 N4 A:C40 4.4 0.4 1.0 C4 A:C40 4.6 0.2 1.0 C8 A:G41 4.7 0.9 1.0 C5 A:C40 5.0 0.3 1.0

Magnesium binding site 6 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1607 b:98.7 occ:1.00 O4 A:U45 3.9 0.8 1.0 N4 A:C43 4.0 0.5 1.0 O6 A:G396 4.1 0.8 1.0 N4 A:C395 4.1 0.7 1.0 O6 A:G44 4.5 0.9 1.0 N7 A:G44 4.7 0.9 1.0 C4 A:U45 4.8 0.1 1.0 C4 A:C43 4.8 0.9 1.0 C5 A:C43 4.9 0.7 1.0

Magnesium binding site 7 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1608 b:0.5 occ:1.00 OP2 A:A53 2.8 0.7 1.0 OP1 A:A353 3.5 0.7 1.0 N7 A:A353 3.6 0.2 1.0 P A:A53 3.9 0.0 1.0 N6 A:A353 4.2 0.9 1.0 OP1 A:A53 4.2 0.1 1.0 C5 A:A353 4.3 0.2 1.0 C5' A:G316 4.3 0.4 1.0 C4' A:G316 4.4 0.7 1.0 C8 A:A353 4.4 0.5 1.0 O4' A:G316 4.4 0.8 1.0 O3' A:C352 4.5 0.7 1.0 O5' A:A53 4.5 0.9 1.0 C6 A:A353 4.6 0.1 1.0 P A:A353 4.7 0.3 1.0 C5' A:C352 4.7 0.9 1.0

Magnesium binding site 8 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:0.8 occ:1.00 O6 A:G96 3.0 0.3 1.0 O4 A:U95 3.4 0.3 1.0 C4 A:U95 3.7 0.9 1.0 C5 A:U95 3.8 0.4 1.0 N7 A:G96 3.9 0.2 1.0 C6 A:G96 4.0 0.5 1.0 C5 A:G96 4.3 0.6 1.0 N3 A:U95 4.6 0.0 1.0 C6 A:U95 4.7 0.0 1.0

Magnesium binding site 9 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:0.8 occ:1.00 O6 A:G112 3.1 0.3 1.0 OP2 A:G111 3.3 0.5 1.0 N7 A:G112 3.7 0.3 1.0 C6 A:G112 3.9 0.9 1.0 C5 A:G112 4.1 0.4 1.0 OP2 A:C110 4.2 0.8 1.0 O6 A:G113 4.6 0.0 1.0 P A:G111 4.6 0.6 1.0 N7 A:G113 4.8 0.8 1.0 C8 A:G112 4.8 0.3 1.0

Magnesium binding site 10 out of 103 in the Crystal Structure of the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline


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 the 30S Ribosomal Subunit From Thermus Thermophilus in Complex with Tigecycline within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:0.8 occ:1.00 OP2 A:C48 2.8 0.3 1.0 OP1 A:G115 3.3 0.7 1.0 O2' A:C47 3.5 0.9 1.0 O3' A:C47 3.5 0.3 1.0 OP1 A:A51 3.5 0.8 1.0 OP2 A:U49 3.7 0.1 1.0 P A:C48 3.8 0.6 1.0 O3' A:U114 4.0 0.6 1.0 P A:G115 4.2 0.8 1.0 C3' A:C47 4.4 0.7 1.0 C2' A:C47 4.5 0.8 1.0 O5' A:A51 4.6 0.2 1.0 P A:A51 4.7 0.8 1.0 OP2 A:G115 4.8 0.9 1.0 O5' A:C48 4.8 0.9 1.0 OP1 A:C48 4.9 1.0 1.0

A.Schedlbauer, T.Kaminishi, B.Ochoa-Lizarralde, N.Dhimole, S.Zhou, J.P.Lopez-Alonso, S.R.Connell, P.Fucini. Structural Characterization of An Alternative-Binding Mode For Tigecycline to the Bacterial Ribosome. Antimicrob.Agents Chemother. 2015.
ISSN: ESSN 1098-6596
PubMed: 25753625
DOI: 10.1128/AAC.04895-14