Magnesium in PDB 1s72: Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

The structure of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72 was solved by D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.660, 299.670, 573.770, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.2

The structure of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 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 - 116;

Binding sites:

The binding sites of Magnesium atom in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution (pdb code 1s72). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 116 binding sites of Magnesium where determined in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8001 b:25.6 occ:1.00 OP2 0:C2534 1.9 29.0 1.0 O 0:HOH7282 2.0 21.7 1.0 OP2 0:A2483 2.1 29.3 1.0 OP2 0:C2533 2.1 31.3 1.0 O 0:HOH8694 2.1 31.0 1.0 O 0:HOH3137 2.2 17.6 1.0 P 0:A2483 3.1 27.1 1.0 O3' 0:G2482 3.3 28.7 1.0 P 0:C2534 3.3 28.4 1.0 P 0:C2533 3.5 30.5 1.0 O3' 0:A2532 3.9 29.2 1.0 OP1 0:A2483 4.0 30.1 1.0 O 0:HOH3851 4.0 34.7 1.0 O2' 0:A2532 4.0 29.9 1.0 O 0:HOH9158 4.1 37.0 1.0 O3' 0:C2533 4.1 26.1 1.0 OP1 0:C2534 4.1 30.6 1.0 O2' 0:G2482 4.2 25.3 1.0 OP2 0:U2484 4.2 34.0 1.0 O5' 0:C2533 4.2 31.0 1.0 O5' 0:C2534 4.3 25.3 1.0 C3' 0:C2533 4.4 25.6 1.0 O5' 0:A2483 4.4 31.0 1.0 O 0:HOH6987 4.4 34.1 1.0 O 0:HOH5895 4.5 40.7 1.0 C3' 0:G2482 4.6 26.5 1.0 OP1 0:C2533 4.6 29.8 1.0 C5' 0:A2483 4.7 27.1 1.0 MG 0:MG8002 4.7 28.2 1.0 C5 0:C2534 4.8 29.7 1.0 C2' 0:G2482 4.9 24.1 1.0 C3' 0:A2532 5.0 28.4 1.0

Magnesium binding site 2 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8002 b:28.2 occ:1.00 OP1 0:A2483 1.9 30.1 1.0 O 0:HOH3851 1.9 34.7 1.0 O 0:HOH7260 2.0 21.9 1.0 O6 0:G627 2.1 27.2 1.0 OP1 0:C2534 2.2 30.6 1.0 O 0:HOH7261 2.2 24.8 1.0 P 0:A2483 3.1 27.1 1.0 C6 0:G627 3.3 27.4 1.0 P 0:C2534 3.4 28.4 1.0 OP2 0:A2483 3.5 29.3 1.0 O 0:HOH6614 3.9 41.6 1.0 O4 0:U626 3.9 25.8 1.0 OP2 0:C2534 3.9 29.0 1.0 N1 0:G627 3.9 27.0 1.0 O5' 0:A2483 4.0 31.0 1.0 O3' 0:C2533 4.1 26.1 1.0 O 0:HOH5398 4.3 27.6 1.0 O2' 0:U625 4.3 21.0 1.0 O 0:HOH8780 4.3 26.1 1.0 O3' 0:G2482 4.3 28.7 1.0 OP2 0:U2535 4.4 26.9 1.0 C5 0:U626 4.4 25.8 1.0 C4 0:U626 4.4 25.4 1.0 C5 0:G627 4.5 26.3 1.0 O 0:HOH3052 4.5 44.2 1.0 O5' 0:C2534 4.6 25.3 1.0 MG 0:MG8001 4.7 25.6 1.0 C3' 0:G2482 4.8 26.5 1.0 OP2 0:C2533 4.9 31.3 1.0 N7 0:G627 5.0 26.5 1.0 C5' 0:C2534 5.0 25.8 1.0

Magnesium binding site 3 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8003 b:22.4 occ:1.00 OP1 0:A2624 2.0 19.1 1.0 OP2 0:A876 2.1 21.8 1.0 O A:HOH8512 2.1 15.5 1.0 OP2 0:G877 2.1 20.1 1.0 O 0:HOH3188 2.2 21.3 1.0 O A:HOH8535 2.4 22.0 1.0 P 0:G877 3.4 20.9 1.0 P 0:A2624 3.4 21.9 1.0 P 0:A876 3.4 24.3 1.0 OP1 0:G877 3.8 21.3 1.0 O3' 0:G2623 3.9 17.8 1.0 O5' 0:A876 3.9 20.5 1.0 O3' 0:A875 4.0 21.4 1.0 O 0:HOH5798 4.1 30.7 1.0 OD1 A:ASN195 4.2 18.9 1.0 O 0:HOH6675 4.2 34.8 1.0 O3' 0:A876 4.2 20.5 1.0 C5' 0:A876 4.3 20.3 1.0 OP2 0:A2624 4.3 21.1 1.0 O A:ALA193 4.3 23.3 1.0 O A:HOH8568 4.3 30.4 1.0 O A:HOH8625 4.4 29.7 1.0 O 0:HOH8541 4.4 18.7 1.0 O5' 0:A2624 4.4 23.6 1.0 O5' 0:G877 4.6 20.7 1.0 C5' 0:A2624 4.6 23.9 1.0 OP1 0:A876 4.6 23.4 1.0 C3' 0:A876 4.7 22.3 1.0 O A:HOH8546 4.7 39.6 1.0 CG A:ASN195 4.9 18.2 1.0

Magnesium binding site 4 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8004 b:22.2 occ:1.00 OP1 0:A459 1.9 20.5 1.0 O 0:HOH3305 1.9 13.7 1.0 O 0:HOH8567 2.0 18.9 1.0 O 0:HOH9300 2.1 12.3 1.0 O 0:HOH7267 2.1 22.8 1.0 O6 0:G456 2.1 21.1 1.0 C6 0:G456 3.2 25.1 1.0 P 0:A459 3.2 24.1 1.0 O5' 0:A459 3.8 23.2 1.0 OP2 0:A459 3.9 22.4 1.0 C5 0:G456 4.0 26.5 1.0 N7 0:G456 4.0 23.9 1.0 C5' 0:A459 4.1 25.2 1.0 O 0:HOH5484 4.2 43.8 1.0 O 0:HOH3225 4.2 26.5 1.0 CE C:LYS85 4.2 21.0 1.0 NZ C:LYS85 4.2 20.3 1.0 O 0:HOH8853 4.3 21.8 1.0 N1 0:G456 4.3 26.1 1.0 O3' 0:G458 4.4 25.1 1.0 OP1 0:A460 4.4 23.4 1.0 OP2 0:A455 4.4 25.1 1.0 O 0:HOH3039 4.5 34.1 1.0 N7 0:A455 4.5 28.0 1.0 OP1 0:A477 4.6 23.9 1.0 O 0:HOH4926 4.7 27.6 1.0 CD C:LYS85 4.9 20.1 1.0 OP2 0:A477 4.9 21.2 1.0 O 0:HOH7268 5.0 16.8 1.0

Magnesium binding site 5 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8005 b:24.6 occ:1.00 OP1 0:U1838 1.9 24.4 1.0 OP1 0:A1836 2.0 22.6 1.0 O 0:HOH3134 2.0 16.4 1.0 O 0:HOH7283 2.0 12.5 1.0 O 0:HOH7284 2.0 24.0 1.0 OP2 0:A1839 2.1 19.1 1.0 P 0:U1838 3.4 22.1 1.0 P 0:A1836 3.5 22.2 1.0 P 0:A1839 3.6 21.5 1.0 O 0:HOH5023 3.9 31.0 1.0 O 0:HOH5082 4.0 27.3 1.0 OP2 0:U1838 4.1 22.8 1.0 O 0:HOH8528 4.1 17.4 1.0 O3' 0:U1838 4.2 22.7 1.0 O5' 0:A1836 4.2 27.6 1.0 C3' 0:G1837 4.2 24.5 1.0 O5' 0:U1838 4.3 22.9 1.0 OP2 0:A1836 4.3 23.5 1.0 C2' 0:U1835 4.3 23.0 1.0 O5' 0:A1839 4.3 21.0 1.0 O3' 0:G1837 4.3 22.1 1.0 O3' 0:U1835 4.4 23.6 1.0 O 0:HOH7358 4.4 24.9 1.0 O 0:HOH9155 4.4 21.8 1.0 O 0:HOH9031 4.4 28.9 1.0 C3' 0:U1838 4.4 20.4 1.0 C3' 0:U1835 4.5 21.8 1.0 OP2 0:G1837 4.5 24.4 1.0 C5' 0:U1838 4.5 19.7 1.0 OP1 0:A1839 4.6 26.0 1.0 O2' 0:U1835 4.6 24.6 1.0 N7 0:A1839 4.7 20.2 1.0 C8 0:A1839 4.8 21.7 1.0

Magnesium binding site 6 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8006 b:27.7 occ:1.00 OP2 0:C822 1.9 30.6 1.0 O 0:HOH9332 1.9 24.3 1.0 OP1 0:G854 1.9 26.1 1.0 OP2 0:U821 2.0 26.5 1.0 O 0:HOH3139 2.1 25.8 1.0 O 0:HOH3276 2.3 32.0 1.0 P 0:G854 3.2 28.7 1.0 P 0:C822 3.3 31.3 1.0 P 0:U821 3.4 26.1 1.0 OP2 0:G854 3.8 27.8 1.0 O5' 0:G854 3.8 24.9 1.0 NA 0:NA8327 3.9 38.6 1.0 O5' 0:U821 3.9 33.0 1.0 O3' 0:U821 4.0 30.9 1.0 OP1 0:G856 4.0 29.2 1.0 O 0:HOH9724 4.0 31.1 1.0 C3' 0:U821 4.0 30.5 1.0 OP1 0:C822 4.0 29.9 1.0 OP1 0:U855 4.2 28.1 1.0 C5' 0:G854 4.3 24.4 1.0 O3' 0:G820 4.3 28.7 1.0 O5' 0:C822 4.3 31.4 1.0 O 0:HOH4519 4.4 26.6 1.0 O3' 0:C853 4.4 27.1 1.0 OP1 0:U821 4.5 26.6 1.0 O 0:HOH9253 4.7 40.4 1.0 O 0:HOH8828 4.9 36.6 1.0 C5 0:C822 5.0 28.4 1.0

Magnesium binding site 7 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8007 b:22.8 occ:1.00 OP2 0:U832 2.0 24.9 1.0 OP1 0:A1839 2.0 26.0 1.0 O 0:HOH7272 2.1 13.2 1.0 O 0:HOH9879 2.2 24.3 1.0 O 0:HOH8528 2.2 17.4 1.0 OP2 0:A1840 2.2 19.5 1.0 P 0:A1839 3.3 21.5 1.0 P 0:U832 3.4 25.1 1.0 P 0:A1840 3.5 23.1 1.0 O 0:HOH5873 3.7 46.7 1.0 OP2 0:A1839 3.8 19.1 1.0 O 0:HOH8621 3.8 19.2 1.0 OP1 0:A1840 3.9 19.5 1.0 O 0:HOH9155 4.0 21.8 1.0 O5' 0:U832 4.1 25.0 1.0 OP1 0:U832 4.1 24.3 1.0 O3' 0:U1838 4.2 22.7 1.0 O3' 0:A1839 4.3 22.6 1.0 O 0:HOH7358 4.4 24.9 1.0 O5' 0:A1839 4.4 21.0 1.0 O 0:HOH7390 4.5 41.1 1.0 O3' 0:U831 4.5 24.1 1.0 C3' 0:A1839 4.6 21.2 1.0 O5' 0:A1840 4.7 21.1 1.0 C5' 0:A1839 4.7 20.7 1.0 C5' 0:U832 4.8 25.3 1.0 OP2 0:G833 4.9 24.9 1.0 O 0:HOH7284 4.9 24.0 1.0 C3' 0:U831 4.9 23.5 1.0

Magnesium binding site 8 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8008 b:24.4 occ:1.00 O 0:HOH7276 2.0 18.2 1.0 OP1 0:C2464 2.0 24.7 1.0 O 0:HOH7359 2.0 29.2 1.0 O 0:HOH3151 2.1 19.5 1.0 OP1 0:U919 2.2 20.8 1.0 OP1 0:A2465 2.2 27.4 1.0 P 0:U919 3.2 23.6 1.0 P 0:C2464 3.3 25.1 1.0 P 0:A2465 3.6 27.6 1.0 OP2 0:U919 3.6 25.5 1.0 O5' 0:U919 3.8 24.1 1.0 O5' 0:C2464 3.9 28.1 1.0 O 0:HOH9869 4.0 22.4 1.0 O 0:HOH8968 4.0 30.0 1.0 C5' 0:C2464 4.0 28.8 1.0 OP2 0:C2464 4.1 29.9 1.0 O 0:HOH5410 4.1 34.8 1.0 O5' 0:A2465 4.2 28.7 1.0 OP2 0:A2465 4.2 29.1 1.0 C5' 0:U919 4.3 23.7 1.0 O 0:HOH9065 4.4 30.2 1.0 O3' 0:A2463 4.4 28.7 1.0 OP1 0:G2466 4.5 28.0 1.0 O3' 0:G918 4.5 23.9 1.0 O 0:HOH9444 4.6 37.0 1.0 C3' 0:A2465 4.7 25.8 1.0 O3' 0:C2464 4.7 27.4 1.0 C5' 0:A2465 4.9 26.6 1.0 C3' 0:C2464 5.0 28.1 1.0 C2' 0:A2465 5.0 26.9 1.0

Magnesium binding site 9 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8009 b:25.8 occ:1.00 OP1 0:G2611 1.9 24.2 1.0 O 0:HOH7278 1.9 21.2 1.0 O 0:HOH3261 2.0 17.9 1.0 OP1 0:A2612 2.0 21.3 1.0 O 0:HOH6939 2.0 23.5 1.0 O 0:HOH7277 2.4 20.9 1.0 P 0:G2611 3.1 22.9 1.0 O3' 0:U2610 3.3 24.8 1.0 NA 0:NA8358 3.4 67.1 1.0 P 0:A2612 3.4 21.8 1.0 O 0:HOH8854 3.7 21.6 1.0 OP2 0:G2093 4.0 26.1 1.0 O5' 0:G2611 4.0 24.8 1.0 C5' 0:G2611 4.0 22.4 1.0 OP2 0:A2612 4.1 25.0 1.0 OP2 0:G2094 4.1 20.7 1.0 O 0:HOH8987 4.2 31.3 1.0 OP1 0:G2094 4.2 20.7 1.0 O3' 0:G2611 4.3 22.1 1.0 O 0:HOH8825 4.3 17.8 1.0 OP2 0:G2611 4.3 23.5 1.0 O5' 0:A2612 4.4 24.4 1.0 C3' 0:G2611 4.5 20.6 1.0 P 0:G2094 4.6 21.3 1.0 C3' 0:U2610 4.6 25.0 1.0 C4' 0:U2610 4.8 25.5 1.0 C4' 0:G2611 4.8 20.8 1.0 O 0:HOH7293 4.8 28.9 1.0

Magnesium binding site 10 out of 116 in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ 0:Mg8010 b:25.2 occ:1.00 OP1 0:G836 2.0 20.7 1.0 O 0:HOH3360 2.0 24.2 1.0 O B:HOH8526 2.0 18.8 1.0 OP1 0:U2615 2.1 18.4 1.0 OE1 B:GLN230 2.2 24.3 1.0 O 0:HOH8881 2.2 18.1 1.0 CD B:GLN230 3.3 23.4 1.0 P 0:G836 3.4 24.1 1.0 P 0:U2615 3.5 20.4 1.0 CG B:GLN230 3.9 20.8 1.0 CB B:GLN230 4.0 21.0 1.0 O 0:HOH4562 4.0 30.4 1.0 C5' 0:G836 4.1 25.1 1.0 O5' 0:G836 4.2 24.9 1.0 O 0:HOH8724 4.3 22.2 1.0 OP2 0:G836 4.3 22.9 1.0 O 0:HOH6343 4.3 42.5 1.0 OP2 0:U2615 4.3 23.6 1.0 O3' 0:U835 4.3 22.1 1.0 O3' 0:C2614 4.4 22.0 1.0 C3' 0:U835 4.4 22.9 1.0 O5' 0:U2615 4.4 22.0 1.0 NE2 B:GLN230 4.4 21.1 1.0 CA B:GLN230 4.4 21.7 1.0 O 0:HOH3514 4.6 38.6 1.0 OP2 0:G2616 4.6 24.2 1.0 O B:GLN230 4.6 22.4 1.0 C5' 0:U835 4.7 23.6 1.0 N2 0:G2616 4.8 26.4 1.0 C5' 0:U2615 4.8 18.6 1.0

D.J.Klein, P.B.Moore, T.A.Steitz. The Roles of Ribosomal Proteins in the Structure, Assembly and Evolution of the Large Ribosomal Subunit J.Mol.Biol. V. 340 141 2004.
ISSN: ISSN 0022-2836
PubMed: 15184028
DOI: 10.1016/J.JMB.2004.03.076