Sodium 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:

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

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 86 binding sites of Sodium where determined in the Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1s72:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 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 Sodium with other atoms in the Na 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:Na8301 b:35.7 occ:1.00 OP2 0:C1069 2.1 24.1 1.0 N7 0:G1072 2.4 24.6 1.0 O 0:HOH4495 2.5 42.2 1.0 O 0:HOH9688 2.7 29.7 1.0 O 0:HOH9720 3.1 52.1 1.0 O6 0:G1087 3.2 30.1 1.0 C5 0:G1072 3.2 24.9 1.0 O6 0:G1072 3.2 24.1 1.0 C8 0:G1072 3.4 24.9 1.0 C6 0:G1072 3.5 24.5 1.0 P 0:C1069 3.5 24.1 1.0 O 0:HOH8589 3.8 27.0 1.0 C6 0:G1087 4.1 28.8 1.0 O 0:HOH3059 4.1 31.0 1.0 OP1 0:C1069 4.2 25.2 1.0 O3' 0:C1068 4.3 27.6 1.0 C4 0:G1072 4.4 25.4 1.0 C3' 0:C1068 4.4 26.6 1.0 N9 0:G1072 4.4 24.9 1.0 C5' 0:C1068 4.5 28.2 1.0 O5' 0:C1069 4.6 27.2 1.0 N1 0:G1087 4.6 28.2 1.0 N1 0:G1072 4.8 25.2 1.0 N6 0:A1070 4.9 22.0 1.0

Sodium binding site 2 out of 86 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 Sodium with other atoms in the Na 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:Na8302 b:45.4 occ:1.00 O2' 0:G1119 2.8 31.8 1.0 O6 0:G1121 2.8 30.4 1.0 OP2 0:U1120 3.0 31.3 1.0 O 0:HOH7297 3.1 36.1 1.0 O3' 0:G1119 3.1 31.3 1.0 O 0:HOH4072 3.1 37.4 1.0 O 0:HOH5209 3.2 54.4 1.0 N7 0:G1121 3.3 30.0 1.0 O 0:HOH3693 3.6 32.4 1.0 O4 0:U1122 3.6 34.9 1.0 C6 0:G1121 3.6 28.9 1.0 P 0:U1120 3.6 31.2 1.0 C5 0:G1121 3.8 29.2 1.0 C2' 0:G1119 3.8 29.8 1.0 MG 0:MG8025 3.9 37.5 1.0 C3' 0:G1119 4.0 31.8 1.0 O 0:HOH6451 4.0 74.4 1.0 C1' 0:G1119 4.3 29.5 1.0 C4 0:U1122 4.3 35.5 1.0 C8 0:G1121 4.5 30.1 1.0 OP1 0:U1120 4.5 33.9 1.0 C5 0:U1122 4.6 34.7 1.0 N4 0:C1243 4.8 30.7 1.0 O5' 0:U1120 4.9 31.1 1.0 OP1 0:C1238 4.9 43.0 1.0 N1 0:G1121 4.9 26.2 1.0

Sodium binding site 3 out of 86 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 Sodium with other atoms in the Na 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:Na8303 b:34.7 occ:1.00 OP2 0:A643 2.9 18.9 1.0 O4 0:U904 2.9 21.4 1.0 OP1 0:G644 3.1 27.3 1.0 OP1 0:G1354 3.1 25.3 1.0 NH2 L:ARG8 3.4 26.0 1.0 O 0:HOH9782 3.4 29.3 1.0 O5' 0:A643 3.4 20.6 1.0 P 0:A643 3.5 21.6 1.0 OP1 0:C1353 3.8 47.7 1.0 OP1 0:A643 3.8 24.6 1.0 C4 0:U904 3.9 21.4 1.0 O 0:HOH8949 3.9 23.7 1.0 N3 0:U904 4.1 22.1 1.0 P 0:G1354 4.1 23.6 1.0 O 0:HOH4126 4.2 88.2 1.0 C5' 0:A643 4.3 20.7 1.0 CZ L:ARG8 4.3 25.5 1.0 P 0:G644 4.3 27.2 1.0 OP2 0:G1354 4.4 19.7 1.0 C3' 0:A643 4.6 24.5 1.0 O3' 0:C1353 4.6 23.1 1.0 O3' 0:A643 4.7 28.2 1.0 P 0:C1353 4.8 49.5 1.0 NE L:ARG8 4.9 24.2 1.0 O5' 0:C1353 4.9 43.7 1.0 N6 0:A1355 4.9 19.8 1.0

Sodium binding site 4 out of 86 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 Sodium with other atoms in the Na 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:Na8305 b:33.1 occ:1.00 O 0:HOH5310 2.5 43.7 1.0 O 0:HOH4225 2.5 31.5 1.0 O2' 0:A630 2.6 25.7 1.0 N3 0:A630 2.7 24.7 1.0 O 0:HOH3612 2.7 31.3 1.0 O2' 0:A631 2.9 24.5 1.0 C1' 0:A630 3.5 23.9 1.0 C2 0:A630 3.6 25.9 1.0 C2' 0:A631 3.6 25.4 1.0 OP2 0:A2074 3.6 27.4 1.0 C4 0:A630 3.6 25.7 1.0 C2' 0:A630 3.6 24.6 1.0 OP1 0:A632 3.9 22.9 1.0 C3' 0:A631 3.9 22.8 1.0 N9 0:A630 3.9 24.4 1.0 O3' 0:A630 4.0 25.1 1.0 O3' 0:A631 4.1 22.4 1.0 N2 0:G2070 4.2 18.3 1.0 P 0:A632 4.4 23.1 1.0 OP2 0:G2072 4.5 39.0 1.0 C3' 0:A630 4.5 24.6 1.0 N1 0:A629 4.6 26.3 1.0 O 0:HOH8927 4.7 30.6 1.0 O 0:HOH9603 4.7 31.9 1.0 O4' 0:A630 4.7 25.9 1.0 OP2 0:A632 4.8 23.1 1.0 C2 0:A629 4.8 27.0 1.0 N1 0:A630 4.9 26.2 1.0 C2 0:1MA628 4.9 24.5 1.0 C2 0:G2070 4.9 22.6 1.0 C5 0:A630 5.0 25.3 1.0

Sodium binding site 5 out of 86 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 Sodium with other atoms in the Na 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:Na8306 b:31.2 occ:1.00 N7 0:G2094 2.8 24.9 1.0 N1 0:A2649 2.9 28.6 1.0 O 0:HOH8646 3.0 21.3 1.0 N7 0:G2093 3.1 26.5 1.0 O6 0:G2094 3.2 29.1 1.0 O2' 0:G2092 3.2 23.6 1.0 C2 0:A2649 3.3 28.4 1.0 N3 0:G2092 3.3 22.9 1.0 C5 0:G2094 3.6 26.0 1.0 C5 0:G2093 3.6 25.8 1.0 N2 0:G2092 3.6 24.0 1.0 O6 0:G2093 3.6 29.1 1.0 N6 0:A2612 3.7 21.3 1.0 C6 0:G2094 3.7 26.3 1.0 C2 0:G2092 3.7 24.1 1.0 C6 0:G2093 3.8 26.9 1.0 C8 0:G2094 3.9 23.8 1.0 C8 0:G2093 3.9 25.6 1.0 C6 0:A2612 3.9 24.8 1.0 C6 0:A2649 4.0 29.3 1.0 C4 0:G2092 4.2 24.2 1.0 N6 0:A2649 4.3 28.4 1.0 C5 0:A2612 4.4 26.4 1.0 C2' 0:G2092 4.4 22.2 1.0 N1 0:A2612 4.4 24.4 1.0 C1' 0:G2092 4.5 23.2 1.0 C4 0:G2093 4.5 23.6 1.0 N3 0:A2649 4.6 29.6 1.0 N9 0:G2092 4.7 24.4 1.0 N9 0:G2093 4.7 24.7 1.0 N7 0:A2612 4.8 26.1 1.0 N1 0:G2092 4.8 23.2 1.0 C4 0:G2094 4.9 25.3 1.0 N1 0:G2093 4.9 24.1 1.0 O3' 0:G2092 4.9 23.9 1.0

Sodium binding site 6 out of 86 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 Sodium with other atoms in the Na 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:Na8307 b:42.5 occ:1.00 O2 0:C40 2.7 39.3 1.0 O2 0:C443 2.8 44.7 1.0 O2' 0:C40 2.9 37.7 1.0 N1 0:A442 3.0 43.1 1.0 O4' 0:G41 3.1 36.8 1.0 C2' 0:C40 3.4 36.8 1.0 C2 0:A442 3.5 42.1 1.0 C1' 0:C40 3.5 37.5 1.0 C2 0:C443 3.6 44.0 1.0 C2 0:C40 3.8 38.5 1.0 C1' 0:G41 3.9 35.5 1.0 C6 0:A442 3.9 42.0 1.0 N1 0:C40 4.2 37.9 1.0 N2 0:G39 4.2 35.4 1.0 N6 0:A442 4.2 42.5 1.0 C4' 0:G41 4.3 35.1 1.0 N3 0:C443 4.3 43.1 1.0 N9 0:G41 4.3 35.1 1.0 N1 0:C443 4.5 44.0 1.0 C1' 0:C443 4.5 43.9 1.0 C5' 0:G41 4.5 34.6 1.0 N3 0:A442 4.7 42.2 1.0 O 0:HOH5392 4.7 40.0 1.0 C8 0:G41 4.7 34.5 1.0 O4' 0:C40 4.8 38.0 1.0 C2 0:G39 4.8 36.4 1.0 C4 0:G41 4.8 34.0 1.0 N1 0:G39 4.9 35.2 1.0 C3' 0:C40 4.9 35.5 1.0 N3 0:C40 4.9 39.2 1.0

Sodium binding site 7 out of 86 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 Sodium with other atoms in the Na 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:Na8308 b:43.3 occ:1.00 O2 0:C1394 2.2 32.2 1.0 O2 0:U1724 2.4 34.4 1.0 O 0:HOH9933 2.5 24.4 1.0 O4 0:U1432 2.5 29.8 1.0 C2 0:C1394 3.3 31.9 1.0 O6 0:G1433 3.4 37.3 1.0 C2 0:U1724 3.6 34.3 1.0 C4 0:U1432 3.7 30.3 1.0 C2' 0:C1394 3.9 33.5 1.0 O2' 0:C1394 4.0 30.3 1.0 C6 0:G1433 4.0 37.4 1.0 O 0:HOH8817 4.0 28.2 1.0 N3 0:C1394 4.2 30.8 1.0 C1' 0:C1394 4.2 32.7 1.0 N3 0:U1432 4.2 30.6 1.0 N1 0:C1394 4.2 31.6 1.0 N1 0:G1433 4.4 38.1 1.0 N3 0:U1724 4.4 33.7 1.0 C1' 0:U1724 4.4 33.0 1.0 O2' 0:U1724 4.4 33.2 1.0 N1 0:U1724 4.5 33.8 1.0 C2' 0:U1724 4.6 33.2 1.0 O 0:HOH6662 4.6 49.1 1.0 O 0:HOH4359 4.6 34.9 1.0 O 0:HOH4990 4.6 53.7 1.0 O2' 0:C1725 4.8 29.4 1.0 C5 0:U1432 4.9 29.9 1.0 C5 0:G1433 4.9 35.9 1.0

Sodium binding site 8 out of 86 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 Sodium with other atoms in the Na 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:Na8310 b:28.4 occ:1.00 O6 0:G2579 2.7 29.7 1.0 O 0:HOH4031 2.9 38.3 1.0 N7 0:G2579 3.0 31.0 1.0 N3 0:A2577 3.0 32.4 1.0 O4' 0:A2577 3.1 33.7 1.0 N7 0:G2578 3.2 29.4 1.0 C6 0:G2579 3.4 30.1 1.0 O6 0:G2578 3.5 29.1 1.0 C5 0:G2579 3.5 31.7 1.0 C5 0:G2578 3.6 29.7 1.0 O 0:HOH7242 3.7 65.0 1.0 C6 0:G2578 3.7 29.7 1.0 C1' 0:A2577 3.8 33.1 1.0 C2 0:A2577 3.8 31.7 1.0 C4 0:A2577 3.9 30.4 1.0 C8 0:G2578 4.0 29.5 1.0 C4' 0:A2577 4.1 34.0 1.0 O 0:HOH5814 4.2 53.6 1.0 C8 0:G2579 4.2 32.4 1.0 N9 0:A2577 4.2 30.8 1.0 C4 0:G2578 4.6 30.3 1.0 N4 0:C2556 4.6 30.7 1.0 N1 0:G2579 4.7 31.2 1.0 O6 0:G2580 4.8 33.8 1.0 N1 0:G2578 4.8 29.7 1.0 N9 0:G2578 4.8 31.1 1.0 C4 0:G2579 4.8 31.6 1.0 N3 0:U2554 4.9 22.6 1.0 O3' 0:A2577 5.0 33.4 1.0

Sodium binding site 9 out of 86 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 Sodium with other atoms in the Na 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:Na8311 b:48.9 occ:1.00 O6 0:G2525 2.2 32.7 1.0 O 0:HOH3097 2.3 27.8 1.0 O 0:HOH4178 2.6 45.0 1.0 N7 0:G2524 2.7 28.5 1.0 O 0:HOH8701 2.7 31.6 1.0 C6 0:G2525 3.2 29.8 1.0 O 0:HOH5891 3.6 51.3 1.0 C8 0:G2524 3.6 29.2 1.0 O 0:HOH3141 3.7 24.6 1.0 C5 0:G2524 3.8 27.7 1.0 O6 0:G2524 3.9 25.1 1.0 C5 0:G2525 4.0 31.1 1.0 N1 0:G2525 4.2 28.7 1.0 C5 0:U2523 4.2 35.1 1.0 N7 0:G2525 4.2 29.9 1.0 C6 0:G2524 4.2 27.1 1.0 C4 0:U2523 4.3 34.2 1.0 OP2 0:G2524 4.3 35.8 1.0 O2' 0:C2493 4.3 24.1 1.0 O4 0:U2523 4.4 35.9 1.0 C6 0:U2523 4.7 33.8 1.0 C2' 0:C2493 4.7 28.4 1.0 N3 0:U2523 4.8 33.2 1.0 N9 0:G2524 4.8 29.0 1.0 C4 0:G2524 4.9 28.8 1.0

Sodium binding site 10 out of 86 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 Sodium with other atoms in the Na 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:Na8313 b:48.9 occ:1.00 O 0:HOH4642 2.3 39.5 1.0 O 0:HOH3357 2.3 46.3 1.0 O6 0:G2399 2.5 36.6 1.0 O 0:HOH9475 2.5 28.5 1.0 O 0:HOH5585 3.0 42.2 1.0 O 0:HOH4594 3.1 38.9 1.0 N7 0:G2399 3.3 34.4 1.0 C6 0:G2399 3.4 35.0 1.0 O 0:HOH6033 3.5 47.7 1.0 C5 0:G2399 3.7 34.9 1.0 O 0:HOH9913 3.7 32.0 1.0 OP2 0:A2398 3.8 33.9 1.0 O4 0:U2389 3.9 31.7 1.0 O 0:HOH5806 3.9 56.5 1.0 O6 0:G2400 4.0 30.1 1.0 N3 0:U2389 4.4 33.7 1.0 C8 0:G2399 4.6 32.9 1.0 C4 0:U2389 4.6 33.8 1.0 N7 0:G2400 4.7 32.2 1.0 C6 0:G2400 4.7 28.5 1.0 N1 0:G2399 4.7 34.7 1.0 O2 0:U2390 4.8 31.9 1.0 C5 0:G2400 4.9 30.5 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