Magnesium in PDB 4lf5: Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus

The structure of Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4lf5 was solved by H.Demirci, R.Belardinelli, J.Carr, F.Murphy Iv, G.Jogl, A.E.Dahlberg, S.T.Gregory, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.59 / 3.75
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.834, 401.834, 174.385, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.8

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

Potassium	(K)	8 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 - 118;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus (pdb code 4lf5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 118 binding sites of Magnesium where determined in the Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus, PDB code: 4lf5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 118 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:52.1 occ:1.00 O6 A:G800 4.0 0.8 1.0 O6 A:G799 4.2 90.5 1.0 N7 A:G798 4.2 96.2 1.0 N7 A:G799 4.4 0.1 1.0 C6 A:G800 4.7 0.9 1.0 O6 A:G798 4.7 0.8 1.0

Magnesium binding site 2 out of 118 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:54.3 occ:1.00 N7 A:G758 3.5 87.5 1.0 N7 A:G581 3.6 84.6 1.0 O6 A:G758 3.8 87.9 1.0 OP2 A:U757 3.9 88.5 1.0 OP2 A:U580 4.0 90.5 1.0 OP2 A:G581 4.2 89.7 1.0 C8 A:G581 4.3 85.4 1.0 OP2 A:G758 4.4 92.8 1.0 C5 A:G758 4.4 83.0 1.0 C6 A:G758 4.4 83.6 1.0 C8 A:G758 4.6 85.2 1.0 C5 A:G581 4.7 84.4 1.0 O6 A:G581 4.8 77.6 1.0 O5' A:U757 4.9 71.3 1.0 P A:U757 4.9 85.5 1.0

Magnesium binding site 3 out of 118 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:64.5 occ:1.00 O6 A:G592 2.8 0.7 1.0 O6 A:G593 2.8 98.9 1.0 O4 A:U646 3.3 94.0 1.0 C6 A:G592 3.5 0.6 1.0 O6 A:G594 3.6 0.6 1.0 C6 A:G593 3.8 0.5 1.0 N7 A:G593 3.8 0.5 1.0 C5 A:G592 4.1 0.6 1.0 C5 A:G593 4.2 0.4 1.0 N7 A:G592 4.2 0.5 1.0 C4 A:U646 4.3 92.4 1.0 C6 A:G594 4.4 0.7 1.0 N3 A:U646 4.4 91.0 1.0 N1 A:G592 4.5 0.4 1.0 N4 A:C645 4.5 87.0 1.0 N4 A:C647 4.7 0.8 1.0 N7 A:G594 4.9 0.6 1.0 C5 A:G594 4.9 100.0 1.0

Magnesium binding site 4 out of 118 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:98.9 occ:1.00 OP1 A:U264 2.3 0.3 1.0 OP2 A:U264 2.8 0.7 1.0 P A:U264 2.8 0.7 1.0 OP2 A:G265 3.2 0.4 1.0 O6 A:G260 3.3 0.5 1.0 O5' A:U264 3.5 94.5 1.0 O4 A:U261 3.7 0.4 1.0 N1 A:G260 3.9 0.0 1.0 C6 A:G260 4.0 0.0 1.0 O3' A:A263 4.3 96.7 1.0 N3 A:U261 4.3 0.9 1.0 C4 A:U261 4.4 0.4 1.0 N1 A:G190F 4.4 0.6 1.0 C5' A:U264 4.4 94.2 1.0 O6 A:G190F 4.6 0.7 1.0 P A:G265 4.7 0.8 1.0 C6 A:G190F 5.0 0.6 1.0

Magnesium binding site 5 out of 118 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:67.5 occ:1.00 O4 A:U12 2.6 0.2 1.0 O6 A:G22 3.0 92.5 1.0 O6 A:G21 3.1 92.3 1.0 O6 A:G11 3.3 87.8 1.0 N4 A:C23 3.6 0.8 1.0 C4 A:U12 3.7 0.5 1.0 C6 A:G21 3.7 87.0 1.0 C6 A:G22 4.1 84.7 1.0 N3 A:U12 4.2 0.5 1.0 N1 A:G21 4.2 85.0 1.0 C6 A:G11 4.4 84.3 1.0 C5 A:G21 4.6 77.7 1.0 N7 A:G22 4.6 87.0 1.0 C5 A:G22 4.8 81.0 1.0 C4 A:C23 4.8 0.1 1.0 C5 A:U12 4.9 0.3 1.0

Magnesium binding site 6 out of 118 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:99.6 occ:1.00 K A:K1704 3.6 0.7 1.0 O6 A:G476 3.7 0.9 1.0 O6 A:G475 3.8 1.0 1.0 N7 A:G475 4.4 0.2 1.0 C6 A:G475 4.4 0.4 1.0 N7 A:G476 4.5 0.5 1.0 C5 A:G475 4.7 0.8 1.0 C6 A:G476 4.7 0.0 1.0 OP2 A:G475 4.9 0.6 1.0 C5 A:G476 5.0 0.7 1.0

Magnesium binding site 7 out of 118 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:90.1 occ:1.00 O3' A:A665 2.7 0.8 1.0 OP2 A:G667 3.0 98.0 1.0 O2' A:A665 3.2 92.6 1.0 O5' A:G666 3.4 72.2 1.0 P A:G666 3.5 0.8 1.0 OP1 A:G666 3.6 0.8 1.0 C3' A:A665 3.8 97.0 1.0 C2' A:A665 4.1 92.3 1.0 C4' A:A665 4.3 0.7 1.0 C5' A:G666 4.3 78.3 1.0 P A:G667 4.4 0.6 1.0 C3' A:G666 4.5 83.6 1.0 O2' A:C732 4.8 99.5 1.0 O3' A:G666 4.8 88.8 1.0 C8 A:G666 4.8 0.4 1.0 OP2 A:G666 4.9 0.9 1.0 C4' A:G666 5.0 79.4 1.0 N7 A:G666 5.0 0.5 1.0

Magnesium binding site 8 out of 118 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:70.8 occ:1.00 O6 A:G741 3.2 94.5 1.0 O6 A:G664 3.3 90.0 1.0 O6 A:G742 3.5 0.3 1.0 N7 A:G741 3.8 0.4 1.0 C6 A:G741 4.1 95.0 1.0 C5 A:G741 4.3 96.9 1.0 C6 A:G664 4.4 90.0 1.0 C6 A:G742 4.4 0.7 1.0 O4 A:U740 4.5 0.1 1.0 O6 A:G666 4.5 0.3 1.0 N6 A:A663 4.7 97.6 1.0 N7 A:G742 4.8 0.1 1.0 N1 A:G664 4.8 92.8 1.0 C4 A:U740 4.9 0.7 1.0 C8 A:G741 4.9 95.0 1.0 C5 A:G742 4.9 0.2 1.0

Magnesium binding site 9 out of 118 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 N7 A:G1432 3.0 0.9 1.0 O6 A:G1432 3.3 0.3 1.0 O6 A:G1467 3.3 0.7 1.0 C5 A:G1432 3.6 0.5 1.0 C6 A:G1432 3.7 0.8 1.0 C8 A:G1432 4.0 0.1 1.0 OP2 A:C1466 4.1 0.2 1.0 C6 A:G1467 4.4 0.8 1.0 OP2 A:C1465 4.5 0.4 1.0 N7 A:G1467 4.8 0.5 1.0 C4 A:G1432 4.8 0.4 1.0 OP1 A:C1465 4.8 0.7 1.0 C5 A:G1467 5.0 0.2 1.0

Magnesium binding site 10 out of 118 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:62.2 occ:1.00 O6 A:G377 3.2 0.6 1.0 O6 A:G376 4.1 0.4 1.0 N7 A:G376 4.1 0.6 1.0 C6 A:G377 4.3 0.6 1.0 N7 A:G377 4.5 0.3 1.0 C6 A:G376 4.6 0.4 1.0 C5 A:G376 4.6 0.9 1.0 C5 A:G377 4.8 0.9 1.0

H.Demirci, R.Belardinelli, J.Carr, F.Murphy Iv, G.Jogl, A.E.Dahlberg, S.T.Gregory. Crystal Structure of 30S Ribosomal Subunit From Thermus Thermophilus To Be Published 2013.