Sodium in PDB 1jj2: Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution

The structure of Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2 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 (%)	18.9 / 22.2

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

Magnesium	(Mg)	117 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 Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution (pdb code 1jj2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the Fully Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution, PDB code: 1jj2:
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 Fully 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 Fully 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:33.9 occ:1.00 OP2 0:C1069 2.2 22.4 1.0 N7 0:G1072 2.4 24.4 1.0 O 0:HOH4505 2.5 39.4 1.0 O 0:HOH9691 2.7 29.2 1.0 O 0:HOH9724 3.0 51.0 1.0 O6 0:G1087 3.1 28.7 1.0 C5 0:G1072 3.2 24.6 1.0 O6 0:G1072 3.2 24.3 1.0 C8 0:G1072 3.4 24.3 1.0 C6 0:G1072 3.5 24.5 1.0 P 0:C1069 3.6 22.5 1.0 O 0:HOH8589 3.9 26.9 1.0 C6 0:G1087 4.1 27.2 1.0 O 0:HOH3063 4.1 30.4 1.0 OP1 0:C1069 4.3 23.7 1.0 O3' 0:C1068 4.3 25.9 1.0 C4 0:G1072 4.3 25.1 1.0 C3' 0:C1068 4.4 25.2 1.0 N9 0:G1072 4.5 24.6 1.0 C5' 0:C1068 4.5 27.0 1.0 O5' 0:C1069 4.6 25.7 1.0 N1 0:G1087 4.6 26.6 1.0 N1 0:G1072 4.8 25.1 1.0 N6 0:A1070 4.9 20.8 1.0

Sodium binding site 2 out of 86 in the Fully 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 Fully 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:44.6 occ:1.00 O2' 0:G1119 2.8 30.2 1.0 O6 0:G1121 2.9 30.1 1.0 OP2 0:U1120 2.9 30.4 1.0 O 0:HOH7342 3.0 36.7 1.0 O3' 0:G1119 3.1 30.0 1.0 O 0:HOH5225 3.1 53.5 1.0 O 0:HOH4079 3.1 36.3 1.0 N7 0:G1121 3.3 29.5 1.0 O 0:HOH3696 3.5 31.5 1.0 P 0:U1120 3.6 30.4 1.0 O4 0:U1122 3.6 33.0 1.0 C6 0:G1121 3.7 28.2 1.0 C5 0:G1121 3.8 28.6 1.0 MG 0:MG8025 3.8 36.7 1.0 C2' 0:G1119 3.8 28.7 1.0 C3' 0:G1119 4.0 30.5 1.0 C4 0:U1122 4.3 33.9 1.0 O 0:HOH6479 4.3 67.4 1.0 C1' 0:G1119 4.3 28.4 1.0 C8 0:G1121 4.5 29.4 1.0 OP1 0:U1120 4.5 33.5 1.0 C5 0:U1122 4.6 33.5 1.0 O5' 0:U1120 4.8 29.9 1.0 OP1 0:C1238 4.9 41.4 1.0 N4 0:C1243 4.9 29.4 1.0 C5' 0:U1120 5.0 31.6 1.0

Sodium binding site 3 out of 86 in the Fully 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 Fully 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:32.4 occ:1.00 OP2 0:A643 2.9 17.6 1.0 O4 0:U904 2.9 21.4 1.0 OP1 0:G644 3.1 26.1 1.0 OP1 0:G1354 3.1 24.7 1.0 NH2 K:ARG8 3.4 23.6 1.0 O5' 0:A643 3.4 19.8 1.0 O 0:HOH9787 3.5 28.9 1.0 P 0:A643 3.5 20.9 1.0 OP1 0:C1353 3.8 46.1 1.0 C4 0:U904 3.9 21.3 1.0 OP1 0:A643 3.9 23.7 1.0 O 0:HOH8949 3.9 21.6 1.0 N3 0:U904 4.1 22.0 1.0 P 0:G1354 4.1 22.7 1.0 C5' 0:A643 4.3 20.8 1.0 CZ K:ARG8 4.3 23.4 1.0 P 0:G644 4.3 26.0 1.0 OP2 0:G1354 4.4 18.9 1.0 O 0:HOH4133 4.4 82.7 1.0 C3' 0:A643 4.5 24.0 1.0 O3' 0:C1353 4.6 22.6 1.0 O3' 0:A643 4.7 27.0 1.0 P 0:C1353 4.8 48.0 1.0 NE K:ARG8 4.9 21.8 1.0 N6 0:A1355 4.9 18.9 1.0 O5' 0:C1353 4.9 42.1 1.0

Sodium binding site 4 out of 86 in the Fully 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 Fully 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:32.1 occ:1.00 O 0:HOH5327 2.5 41.6 1.0 O 0:HOH4235 2.5 30.1 1.0 O2' 0:A630 2.7 24.1 1.0 N3 0:A630 2.7 23.8 1.0 O 0:HOH3616 2.7 29.9 1.0 O2' 0:A631 2.9 24.1 1.0 C1' 0:A630 3.5 23.0 1.0 OP2 0:A2074 3.5 26.4 1.0 C2' 0:A631 3.6 24.5 1.0 C2 0:A630 3.6 25.1 1.0 C2' 0:A630 3.6 23.8 1.0 C4 0:A630 3.7 24.9 1.0 C3' 0:A631 3.9 22.0 1.0 OP1 0:A632 3.9 21.8 1.0 N9 0:A630 4.0 23.6 1.0 O3' 0:A630 4.0 24.3 1.0 O3' 0:A631 4.1 21.4 1.0 N2 0:G2070 4.1 18.3 1.0 P 0:A632 4.4 21.9 1.0 C3' 0:A630 4.5 23.7 1.0 OP2 0:G2072 4.5 38.4 1.0 N1 0:A629 4.6 25.9 1.0 O 0:HOH8927 4.6 30.4 1.0 O 0:HOH9607 4.7 33.2 1.0 O4' 0:A630 4.7 24.8 1.0 C2 0:A629 4.8 26.7 1.0 OP2 0:A632 4.8 21.5 1.0 C2 0:A628 4.9 24.9 1.0 C2 0:G2070 4.9 22.2 1.0 N1 0:A630 4.9 25.7 1.0 C5 0:A630 5.0 24.6 1.0

Sodium binding site 5 out of 86 in the Fully 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 Fully 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:28.8 occ:1.00 N7 0:G2094 2.8 24.5 1.0 N1 0:A2649 2.9 28.4 1.0 O 0:HOH8646 2.9 19.9 1.0 N7 0:G2093 3.1 25.4 1.0 O2' 0:G2092 3.2 22.8 1.0 O6 0:G2094 3.2 28.1 1.0 N3 0:G2092 3.3 22.2 1.0 C2 0:A2649 3.3 28.0 1.0 C5 0:G2093 3.6 24.8 1.0 C5 0:G2094 3.6 25.4 1.0 N2 0:G2092 3.6 23.6 1.0 N6 0:A2612 3.7 20.3 1.0 O6 0:G2093 3.7 28.0 1.0 C2 0:G2092 3.7 23.5 1.0 C6 0:G2094 3.8 25.6 1.0 C6 0:G2093 3.8 26.0 1.0 C8 0:G2093 3.9 24.7 1.0 C8 0:G2094 3.9 23.6 1.0 C6 0:A2612 3.9 23.4 1.0 C6 0:A2649 4.0 28.8 1.0 C4 0:G2092 4.2 23.8 1.0 N6 0:A2649 4.3 27.8 1.0 C2' 0:G2092 4.4 21.8 1.0 C5 0:A2612 4.4 25.4 1.0 N1 0:A2612 4.4 23.0 1.0 C1' 0:G2092 4.5 22.7 1.0 C4 0:G2093 4.5 22.8 1.0 N3 0:A2649 4.6 28.9 1.0 N9 0:G2092 4.7 23.9 1.0 N9 0:G2093 4.7 23.8 1.0 N7 0:A2612 4.7 24.8 1.0 N1 0:G2092 4.8 22.3 1.0 C4 0:G2094 4.9 24.9 1.0 O3' 0:G2092 4.9 22.4 1.0 N1 0:G2093 4.9 23.4 1.0

Sodium binding site 6 out of 86 in the Fully 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 Fully 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:42.1 occ:1.00 O2 0:C40 2.6 37.9 1.0 O2 0:C443 2.8 43.0 1.0 O2' 0:C40 2.9 36.5 1.0 N1 0:A442 3.0 42.4 1.0 O4' 0:G41 3.2 36.5 1.0 C2' 0:C40 3.4 36.0 1.0 C2 0:A442 3.5 41.0 1.0 C1' 0:C40 3.5 36.4 1.0 C2 0:C443 3.6 42.3 1.0 C2 0:C40 3.7 36.9 1.0 C6 0:A442 3.9 41.3 1.0 C1' 0:G41 3.9 34.9 1.0 N1 0:C40 4.1 36.4 1.0 N2 0:G39 4.1 35.3 1.0 N6 0:A442 4.2 41.9 1.0 N3 0:C443 4.2 41.1 1.0 C4' 0:G41 4.3 34.8 1.0 N9 0:G41 4.3 34.5 1.0 N1 0:C443 4.4 42.4 1.0 C1' 0:C443 4.5 42.5 1.0 C5' 0:G41 4.6 34.3 1.0 N3 0:A442 4.7 41.3 1.0 O4' 0:C40 4.7 37.2 1.0 C2 0:G39 4.7 36.4 1.0 O 0:HOH5408 4.7 38.9 1.0 C8 0:G41 4.8 33.8 1.0 N1 0:G39 4.8 35.4 1.0 C4 0:G41 4.9 33.2 1.0 N3 0:C40 4.9 37.6 1.0 C3' 0:C40 4.9 34.8 1.0

Sodium binding site 7 out of 86 in the Fully 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 Fully 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:42.9 occ:1.00 O2 0:C1394 2.2 31.5 1.0 O2 0:U1724 2.4 33.6 1.0 O 0:HOH9937 2.5 23.3 1.0 O4 0:U1432 2.5 29.1 1.0 C2 0:C1394 3.3 31.0 1.0 O6 0:G1433 3.5 36.3 1.0 C2 0:U1724 3.6 33.4 1.0 C4 0:U1432 3.7 29.1 1.0 O2' 0:C1394 4.0 29.6 1.0 C2' 0:C1394 4.0 32.5 1.0 O 0:HOH8817 4.0 28.0 1.0 C6 0:G1433 4.1 36.2 1.0 C1' 0:C1394 4.2 31.8 1.0 N3 0:C1394 4.2 29.8 1.0 N3 0:U1432 4.2 29.4 1.0 N1 0:C1394 4.2 30.7 1.0 O2' 0:U1724 4.4 32.3 1.0 C1' 0:U1724 4.4 32.2 1.0 N3 0:U1724 4.4 32.7 1.0 N1 0:G1433 4.4 36.6 1.0 N1 0:U1724 4.5 32.8 1.0 C2' 0:U1724 4.5 32.3 1.0 O 0:HOH6692 4.6 47.5 1.0 O 0:HOH5002 4.6 51.1 1.0 O 0:HOH4369 4.7 32.6 1.0 O2' 0:C1725 4.7 28.5 1.0 C5 0:U1432 4.9 28.6 1.0 C5 0:G1433 4.9 34.7 1.0

Sodium binding site 8 out of 86 in the Fully 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 Fully 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:27.0 occ:1.00 O6 0:G2579 2.7 28.9 1.0 O 0:HOH4037 2.9 36.9 1.0 N7 0:G2579 3.0 30.3 1.0 N3 0:A2577 3.0 31.5 1.0 O4' 0:A2577 3.1 32.6 1.0 N7 0:G2578 3.2 28.4 1.0 C6 0:G2579 3.4 29.1 1.0 O6 0:G2578 3.5 27.8 1.0 C5 0:G2579 3.5 30.7 1.0 C5 0:G2578 3.6 28.4 1.0 C6 0:G2578 3.7 28.5 1.0 O 0:HOH7287 3.7 68.4 1.0 C2 0:A2577 3.8 30.9 1.0 C1' 0:A2577 3.8 32.1 1.0 C4 0:A2577 3.9 29.7 1.0 C8 0:G2578 4.0 28.5 1.0 C4' 0:A2577 4.1 33.2 1.0 C8 0:G2579 4.2 31.9 1.0 N9 0:A2577 4.2 29.9 1.0 O 0:HOH5834 4.3 52.3 1.0 C4 0:G2578 4.6 28.9 1.0 N4 0:C2556 4.6 29.6 1.0 N1 0:G2579 4.7 30.1 1.0 N1 0:G2578 4.8 28.2 1.0 O6 0:G2580 4.8 33.0 1.0 N9 0:G2578 4.8 29.8 1.0 C4 0:G2579 4.8 30.7 1.0 N3 0:U2554 4.9 21.3 1.0 O3' 0:A2577 5.0 32.4 1.0 O 0:HOH5511 5.0 56.7 1.0 N1 0:A2577 5.0 30.6 1.0

Sodium binding site 9 out of 86 in the Fully 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 Fully 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:48.8 occ:1.00 O6 0:G2525 2.2 32.5 1.0 O 0:HOH3101 2.4 28.1 1.0 O 0:HOH4188 2.5 42.9 1.0 O 0:HOH8701 2.7 31.2 1.0 N7 0:G2524 2.8 27.7 1.0 C6 0:G2525 3.2 29.2 1.0 O 0:HOH5911 3.5 51.9 1.0 O 0:HOH3146 3.7 24.0 1.0 C8 0:G2524 3.7 28.4 1.0 C5 0:G2524 3.8 27.0 1.0 O6 0:G2524 4.0 24.7 1.0 C5 0:G2525 4.0 30.2 1.0 N7 0:G2525 4.2 28.8 1.0 N1 0:G2525 4.2 27.6 1.0 C5 0:U2523 4.2 33.5 1.0 C6 0:G2524 4.3 26.3 1.0 OP2 0:G2524 4.3 34.5 1.0 C4 0:U2523 4.3 32.6 1.0 O2' 0:C2493 4.4 22.8 1.0 O4 0:U2523 4.5 34.8 1.0 C2' 0:C2493 4.7 27.6 1.0 C6 0:U2523 4.8 32.3 1.0 N3 0:U2523 4.9 31.4 1.0 N9 0:G2524 4.9 28.1 1.0 C4 0:G2524 5.0 28.1 1.0

Sodium binding site 10 out of 86 in the Fully 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 Fully 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:HOH3361 2.2 42.6 1.0 O 0:HOH4655 2.3 39.5 1.0 O6 0:G2399 2.5 35.4 1.0 O 0:HOH9478 2.5 28.3 1.0 O 0:HOH5604 3.1 41.2 1.0 O 0:HOH4605 3.1 36.5 1.0 N7 0:G2399 3.3 33.0 1.0 C6 0:G2399 3.4 33.6 1.0 O 0:HOH6054 3.6 47.0 1.0 C5 0:G2399 3.7 33.5 1.0 O 0:HOH9918 3.7 30.4 1.0 O4 0:U2389 3.9 30.9 1.0 O 0:HOH5826 3.9 54.1 1.0 OP2 0:A2398 3.9 33.0 1.0 O6 0:G2400 4.0 29.3 1.0 N3 0:U2389 4.4 32.8 1.0 C8 0:G2399 4.6 31.4 1.0 C4 0:U2389 4.6 33.1 1.0 C6 0:G2400 4.6 27.8 1.0 N7 0:G2400 4.6 31.2 1.0 N1 0:G2399 4.7 32.9 1.0 O2 0:U2390 4.8 30.8 1.0 C5 0:G2400 4.9 29.8 1.0 N4 0:C2388 5.0 23.2 1.0

D.J.Klein, T.M.Schmeing, P.B.Moore, T.A.Steitz. The Kink-Turn: A New Rna Secondary Structure Motif. Embo J. V. 20 4214 2001.
ISSN: ISSN 0261-4189
PubMed: 11483524
DOI: 10.1093/EMBOJ/20.15.4214