Magnesium in PDB 3oto: Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto was solved by H.Demirci, F.Murphy Iv, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.84 / 3.69
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	402.089, 402.089, 173.254, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 23.1

The structure of Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) also contains other interesting chemical elements:

Potassium	(K)	42 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 - 94;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8) (pdb code 3oto). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 94 binding sites of Magnesium where determined in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8), PDB code: 3oto:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1545 b:75.1 occ:1.00 O2 A:C701 3.0 0.4 1.0 OP2 A:A702 3.4 0.1 1.0 O6 A:G703 3.5 0.3 1.0 C1' A:C701 4.1 0.0 1.0 C2 A:C701 4.2 0.5 1.0 C6 A:G703 4.2 0.4 1.0 OP1 A:A702 4.2 0.2 1.0 P A:A702 4.3 0.5 1.0 N1 A:C701 4.6 0.6 1.0 O2' A:C701 4.6 0.2 1.0 N1 A:G703 4.8 0.5 1.0 O4' A:C701 4.8 0.1 1.0 C5 A:G703 4.9 0.3 1.0 O3' A:C701 5.0 0.5 1.0 C2' A:C701 5.0 0.8 1.0

Magnesium binding site 2 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1546 b:76.2 occ:1.00 O6 A:G258 3.4 0.7 1.0 O6 A:G259 3.5 0.5 1.0 OP2 A:G265 4.0 87.3 1.0 C6 A:G258 4.2 0.4 1.0 N7 A:G258 4.2 0.4 1.0 OP2 A:G266 4.3 88.2 1.0 C5 A:G258 4.5 0.4 1.0 C6 A:G259 4.7 0.4 1.0 OP1 A:G265 4.8 93.5 1.0 N4 A:C267 4.8 77.0 1.0 P A:G265 4.8 90.4 1.0

Magnesium binding site 3 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1547 b:86.1 occ:1.00 N7 A:G724 3.7 83.2 1.0 OP2 A:G724 3.7 0.2 1.0 N7 A:G725 3.9 77.1 1.0 O6 A:G725 4.1 73.3 1.0 O6 A:G724 4.2 84.6 1.0 C5 A:G724 4.2 79.3 1.0 C8 A:G724 4.4 82.8 1.0 C6 A:G724 4.4 78.6 1.0 C5 A:G725 4.7 75.4 1.0 C6 A:G725 4.8 72.2 1.0 P A:G724 4.8 0.1 1.0 C8 A:G725 4.9 81.8 1.0 OP2 A:G725 4.9 0.8 1.0 OP1 A:G724 4.9 0.5 1.0

Magnesium binding site 4 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1548 b:81.9 occ:1.00 OP1 A:G438 3.5 0.2 1.0 OP2 A:G492 4.0 0.5 1.0 OP2 A:G438 4.1 0.4 1.0 P A:G438 4.2 0.0 1.0 O6 A:G494 4.2 0.8 1.0 N7 A:G494 4.5 0.1 1.0 O5' A:G438 4.6 0.9 1.0 C6 A:G494 4.9 0.5 1.0 P A:G492 5.0 0.5 1.0

Magnesium binding site 5 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1549 b:59.4 occ:1.00 O6 A:G309 3.4 89.4 1.0 N7 A:G309 3.6 82.7 1.0 C6 A:G309 3.9 82.6 1.0 C5 A:G309 4.1 82.8 1.0 C5 A:C308 4.1 67.7 1.0 O6 A:G310 4.1 73.4 1.0 N4 A:C308 4.2 71.5 1.0 OP2 A:C307 4.3 0.1 1.0 C4 A:C308 4.4 68.2 1.0 OP2 A:C308 4.4 0.0 1.0 C8 A:G309 4.7 81.1 1.0 N7 A:G310 4.9 72.1 1.0 C6 A:C308 4.9 67.8 1.0

Magnesium binding site 6 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1550 b:52.5 occ:1.00 O6 A:G22 2.9 77.5 1.0 O4 A:U12 2.9 89.7 1.0 O6 A:G11 3.2 86.1 1.0 O6 A:G21 3.4 82.6 1.0 N4 A:C23 3.6 79.3 1.0 C6 A:G21 3.8 76.0 1.0 C6 A:G22 4.0 72.3 1.0 C4 A:U12 4.0 89.4 1.0 N1 A:G21 4.3 72.8 1.0 N3 A:U12 4.3 82.7 1.0 C6 A:G11 4.3 78.4 1.0 N7 A:G22 4.4 71.6 1.0 C5 A:G21 4.5 67.9 1.0 C5 A:G22 4.6 67.5 1.0 C4 A:C23 4.8 76.2 1.0 N7 A:G21 4.9 67.5 1.0

Magnesium binding site 7 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1551 b:50.3 occ:1.00 K A:K1637 3.9 0.7 1.0 O6 A:G475 4.1 0.8 1.0 O6 A:G476 4.2 0.1 1.0 C6 A:G475 4.6 0.1 1.0 N7 A:G476 4.7 0.7 1.0 N7 A:G475 4.7 0.8 1.0 C5 A:G475 4.9 0.2 1.0 C6 A:G476 5.0 0.7 1.0

Magnesium binding site 8 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1552 b:80.8 occ:1.00 O3' A:A665 2.7 79.2 1.0 OP2 A:G667 3.4 94.2 1.0 O5' A:G666 3.4 67.2 1.0 P A:G666 3.4 80.0 1.0 OP1 A:G666 3.5 81.7 1.0 O2' A:A665 3.5 75.0 1.0 C3' A:A665 3.9 78.2 1.0 C2' A:A665 4.3 75.8 1.0 C4' A:A665 4.3 82.9 1.0 C8 A:G666 4.5 83.5 1.0 C5' A:G666 4.5 69.6 1.0 N7 A:G666 4.6 88.4 1.0 C3' A:G666 4.8 76.5 1.0 P A:G667 4.8 0.4 1.0 O5' A:A665 4.8 90.4 1.0 OP2 A:G666 4.8 77.3 1.0 N7 A:G667 5.0 85.9 1.0

Magnesium binding site 9 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1553 b:94.6 occ:1.00 O6 A:G890 2.9 98.6 1.0 OP2 A:G906 3.6 83.0 1.0 C6 A:G890 4.0 98.8 1.0 OP1 A:C883 4.7 76.3 1.0 N1 A:G890 4.7 95.7 1.0 OP1 A:U905 4.7 92.6 1.0 P A:G906 4.9 84.7 1.0 OP2 A:U905 4.9 89.8 1.0 C5 A:G890 5.0 97.4 1.0

Magnesium binding site 10 out of 94 in the Crystal Structure of the 30S Ribosomal Subunit From A Ksga Mutant of Thermus Thermophilus (HB8)


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 A Ksga Mutant of Thermus Thermophilus (HB8) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1554 b:59.8 occ:1.00 O6 A:G741 3.2 80.6 1.0 O6 A:G664 3.4 89.2 1.0 N7 A:G741 3.5 82.2 1.0 O6 A:G742 3.7 90.9 1.0 C6 A:G741 3.9 80.0 1.0 C5 A:G741 4.0 78.7 1.0 C6 A:G664 4.3 87.6 1.0 O6 A:G666 4.4 85.2 1.0 C6 A:G742 4.4 85.7 1.0 N1 A:G664 4.4 84.0 1.0 N7 A:G742 4.5 75.4 1.0 C8 A:G741 4.6 82.5 1.0 C5 A:G742 4.7 79.4 1.0 N6 A:A663 4.7 85.6 1.0 O4 A:U740 4.8 84.9 1.0

H.Demirci, F.Murphy, R.Belardinelli, A.C.Kelley, V.Ramakrishnan, S.T.Gregory, A.E.Dahlberg, G.Jogl. Modification of 16S Ribosomal Rna By the Ksga Methyltransferase Restructures the 30S Subunit to Optimize Ribosome Function. Rna V. 16 2319 2010.
ISSN: ISSN 1355-8382
PubMed: 20962038
DOI: 10.1261/RNA.2357210