Magnesium in PDB 4khp: Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin

The structure of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin, PDB code: 4khp was solved by D.S.Tourigny, I.S.Fernandez, A.C.Kelley, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.67 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.000, 401.000, 176.000, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.6

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 Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin (pdb code 4khp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 103 binding sites of Magnesium where determined in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin, PDB code: 4khp:
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 Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1609 b:45.6 occ:1.00 OP1 A:G922 2.0 58.6 1.0 OP2 A:G923 2.3 53.7 1.0 P A:G922 3.0 59.8 1.0 OP2 A:G922 3.5 61.0 1.0 P A:G923 3.6 60.0 1.0 O5' A:G922 3.7 53.0 1.0 O5' A:G923 4.0 58.7 1.0 N7 A:A924 4.2 59.7 1.0 C5' A:G922 4.3 48.8 1.0 OP1 A:G923 4.3 59.0 1.0 O3' A:U921 4.4 48.3 1.0 OP2 A:A924 4.5 59.2 1.0 O6 A:G925 4.6 59.4 1.0 O6 A:G1215 4.7 85.5 1.0 O3' A:G922 4.7 47.5 1.0 C8 A:A924 4.8 62.6 1.0

Magnesium binding site 2 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1610 b:42.3 occ:1.00 OP1 A:G1206 1.9 65.2 1.0 P A:G1206 3.4 70.4 1.0 OP2 A:G1206 4.0 71.2 1.0 N6 A:A955 4.1 0.4 1.0 OP1 A:G929 4.2 63.1 1.0 N7 A:A955 4.3 99.0 1.0 O5' A:G1206 4.3 73.0 1.0 O3' A:C1205 4.4 85.2 1.0 O2' A:C1205 4.5 78.9 1.0 OP2 A:U930 4.6 53.6 1.0 C2' A:C1205 4.7 82.4 1.0 C6 A:A955 4.8 99.3 1.0 C5 A:A955 4.8 98.4 1.0 C2 A:A952 4.8 58.6 1.0

Magnesium binding site 3 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1611 b:37.2 occ:1.00 O6 A:G23 2.9 67.0 1.0 O4 A:U13 2.9 69.2 1.0 O6 A:G12 3.0 54.0 1.0 O6 A:G22 3.2 71.1 1.0 N4 A:C24 3.5 46.8 1.0 C6 A:G22 3.6 58.4 1.0 C4 A:U13 3.9 63.6 1.0 C6 A:G23 3.9 56.2 1.0 N1 A:G22 4.0 61.4 1.0 N3 A:U13 4.1 67.6 1.0 N7 A:G23 4.1 54.9 1.0 C6 A:G12 4.1 57.2 1.0 C5 A:G22 4.3 57.3 1.0 C5 A:G23 4.4 52.5 1.0 C4 A:C24 4.5 47.0 1.0 N7 A:G22 4.8 62.9 1.0 N1 A:G12 4.9 59.1 1.0 C2 A:G22 5.0 66.7 1.0

Magnesium binding site 4 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1612 b:46.6 occ:1.00 O6 A:G372 3.6 84.1 1.0 O6 A:G373 3.7 68.3 1.0 N7 A:G372 3.8 70.3 1.0 C6 A:G372 4.2 69.3 1.0 MG A:MG1652 4.2 50.0 1.0 N7 A:G373 4.2 72.1 1.0 C5 A:G372 4.3 62.4 1.0 C6 A:G373 4.6 68.5 1.0 C5 A:G373 4.8 66.3 1.0 C8 A:G372 4.8 69.1 1.0

Magnesium binding site 5 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1613 b:56.3 occ:0.89 OP2 A:G734 2.0 78.9 1.0 OP2 A:C733 2.4 86.5 1.0 P A:G734 3.5 83.3 1.0 P A:C733 3.7 90.9 1.0 O3' A:C732 3.8 91.2 1.0 N7 A:G734 4.3 73.0 1.0 OP1 A:G734 4.3 83.3 1.0 O5' A:G734 4.3 74.2 1.0 O3' A:C733 4.4 77.9 1.0 C3' A:C733 4.5 71.2 1.0 O5' A:C733 4.5 77.9 1.0 C8 A:G734 4.6 71.3 1.0 OP1 A:C733 4.9 89.7 1.0

Magnesium binding site 6 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1614 b:31.0 occ:1.00 OP2 A:A750 2.2 43.1 1.0 N4 A:C795 3.4 53.1 1.0 N3 A:C795 3.6 38.6 1.0 P A:A750 3.7 41.9 1.0 C4 A:C795 4.0 40.9 1.0 N3 A:C796 4.0 62.1 1.0 O2 A:C796 4.0 67.7 1.0 C2 A:C796 4.4 61.3 1.0 O5' A:A750 4.5 40.7 1.0 N6 A:A752 4.5 36.1 1.0 OP1 A:A750 4.6 35.0 1.0 O3' A:G749 4.7 42.4 1.0 N7 A:A751 4.7 43.5 1.0 C2 A:C795 4.7 40.8 1.0 C3' A:G749 4.8 42.8 1.0 O4 A:U797 4.8 42.0 1.0 OP2 A:A751 4.9 57.6 1.0 C4 A:C796 4.9 57.6 1.0 O2 A:C795 5.0 50.3 1.0

Magnesium binding site 7 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1615 b:38.8 occ:1.00 OP2 A:A752 2.3 57.2 1.0 P A:A752 3.8 50.6 1.0 OP2 A:A751 4.0 57.6 1.0 N7 A:A752 4.1 42.6 1.0 O5' A:A751 4.2 60.6 1.0 OP1 A:A751 4.3 63.5 1.0 P A:A751 4.4 53.6 1.0 O5' A:A752 4.4 41.9 1.0 C8 A:A752 4.4 43.8 1.0 C3' A:A751 4.5 53.0 1.0 O3' A:A751 4.5 52.9 1.0 OP1 A:U788 4.6 46.4 1.0 C5' A:A751 4.7 63.0 1.0 OP2 A:C789 4.7 47.5 1.0 N7 A:G753 4.7 38.3 1.0 OP1 A:A752 4.8 50.9 1.0

Magnesium binding site 8 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1616 b:40.8 occ:1.00 O4 A:U756 3.9 71.1 1.0 N7 A:G755 4.1 61.5 1.0 OP1 A:G787 4.4 44.0 1.0 O6 A:G755 4.4 60.2 1.0 C5 A:C754 4.6 50.7 1.0 N4 A:C754 4.7 54.6 1.0 OP2 A:U788 4.7 47.0 1.0 C4 A:C754 4.8 49.0 1.0 C4 A:U756 4.9 59.6 1.0 C5 A:G755 4.9 56.0 1.0

Magnesium binding site 9 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1617 b:35.9 occ:1.00 OP1 A:C562 2.1 58.1 1.0 P A:C562 3.5 52.4 1.0 O3' A:G561 3.7 59.2 1.0 OP2 A:G560 3.7 58.0 1.0 OP2 A:C801 4.1 40.2 1.0 OP1 A:U804 4.5 52.5 1.0 O5' A:C562 4.5 41.4 1.0 C5' A:C562 4.5 36.3 1.0 OP2 A:C562 4.6 40.0 1.0 O3' A:G559 4.7 53.2 1.0 O2' A:G559 4.8 47.3 1.0 P A:G560 4.9 51.5 1.0 C5' A:G805 4.9 45.1 1.0

Magnesium binding site 10 out of 103 in the Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Thermus Thermophilus 30S Ribosomal Subunit in Complex with De-6-Msa-Pactamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1618 b:56.2 occ:1.00 N7 A:G831 4.1 65.8 1.0 N7 A:G832 4.2 55.5 1.0 OP2 A:U849 4.2 55.9 1.0 O6 A:G832 4.2 54.7 1.0 OP1 A:U849 4.3 62.0 1.0 O6 A:G831 4.5 83.5 1.0 C5 A:U849 4.6 67.7 1.0 C5 A:G831 4.7 62.9 1.0 P A:U849 4.8 58.3 1.0 C6 A:G831 4.9 67.0 1.0 C8 A:G831 4.9 61.8 1.0 C5 A:G832 5.0 51.9 1.0 C6 A:G832 5.0 54.8 1.0

D.S.Tourigny, I.S.Fernandez, A.C.Kelley, R.R.Vakiti, A.K.Chattopadhyay, S.Dorich, S.Hanessian, V.Ramakrishnan. Crystal Structure of A Bioactive Pactamycin Analog Bound to the 30S Ribosomal Subunit. J.Mol.Biol. V. 425 3907 2013.
ISSN: ISSN 0022-2836
PubMed: 23702293
DOI: 10.1016/J.JMB.2013.05.004