Sodium in PDB 2qa4: A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit

The structure of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit, PDB code: 2qa4 was solved by T.A.Steitz, J.M.Kavran, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	214.490, 302.432, 578.056, 90.00, 90.00, 90.00
R / Rfree (%)	24.1 / 28.8

The structure of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit 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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit (pdb code 2qa4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit, PDB code: 2qa4:
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 A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3032 b:30.6 occ:1.00 OP2 0:C1069 2.5 32.9 1.0 N7 0:G1072 2.9 33.6 1.0 O6 0:G1072 3.1 37.7 1.0 O6 0:G1087 3.4 38.1 1.0 C5 0:G1072 3.6 34.1 1.0 C6 0:G1072 3.7 35.2 1.0 P 0:C1069 3.9 35.4 1.0 C5' 0:C1068 3.9 43.4 1.0 C8 0:G1072 4.0 32.5 1.0 C6 0:G1087 4.4 36.2 1.0 OP2 0:C1068 4.4 46.7 1.0 C3' 0:C1068 4.4 41.5 1.0 O3' 0:C1068 4.5 37.9 1.0 N6 0:A1070 4.7 35.5 1.0 OP1 0:C1069 4.7 34.9 1.0 C4' 0:C1068 4.8 42.7 1.0 C4 0:G1072 4.9 33.5 1.0 O5' 0:C1069 4.9 34.3 1.0

Sodium binding site 2 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3033 b:60.5 occ:1.00 OP2 0:U1120 2.4 43.2 1.0 O2' 0:G1119 3.1 44.1 1.0 P 0:U1120 3.3 40.1 1.0 MG 0:MG2947 3.6 15.6 1.0 O3' 0:G1119 3.6 40.4 1.0 O6 0:G1121 3.7 41.4 1.0 OP1 0:U1120 3.7 40.4 1.0 N7 0:G1121 4.0 37.5 1.0 O4 0:U1122 4.0 44.4 1.0 C2' 0:G1119 4.2 39.9 1.0 C3' 0:G1119 4.4 40.7 1.0 C6 0:G1121 4.5 41.1 1.0 C5 0:G1121 4.6 38.9 1.0 O5' 0:U1120 4.8 37.8 1.0 C4 0:U1122 4.9 41.3 1.0 C1' 0:G1119 4.9 37.7 1.0 OP1 0:C1238 5.0 41.8 1.0

Sodium binding site 3 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3034 b:91.2 occ:1.00 OP2 0:A643 3.0 37.1 1.0 OP1 0:G1354 3.1 41.2 1.0 OP1 0:G644 3.1 29.6 1.0 NH2 L:ARG8 3.1 51.4 1.0 O4 0:U904 3.2 35.6 1.0 O5' 0:A643 3.5 34.4 1.0 P 0:A643 3.6 36.0 1.0 OP1 0:C1353 4.0 54.0 1.0 C4 0:U904 4.0 34.6 1.0 N3 0:U904 4.0 32.6 1.0 OP1 0:A643 4.1 38.6 1.0 P 0:G1354 4.1 41.8 1.0 CZ L:ARG8 4.3 52.3 1.0 C5' 0:A643 4.3 33.1 1.0 O3' 0:C1353 4.4 42.7 1.0 P 0:G644 4.4 31.0 1.0 OP2 0:G1354 4.5 41.3 1.0 N6 0:A1355 4.8 35.4 1.0 C3' 0:A643 4.8 31.3 1.0 NE L:ARG8 4.8 52.3 1.0 O3' 0:A643 4.9 32.9 1.0

Sodium binding site 4 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ C:Na247 b:41.2 occ:1.00 OD1 C:ASP45 2.5 50.3 1.0 OD2 C:ASP45 2.6 50.5 1.0 O C:LYS96 2.8 55.6 1.0 CG C:ASP45 2.9 49.7 1.0 C C:LYS96 3.8 53.3 1.0 CA C:ASP97 3.9 51.5 1.0 N C:ARG98 4.0 47.1 1.0 N C:ASP97 4.3 52.8 1.0 CB C:ASP45 4.4 48.1 1.0 O C:THR94 4.5 51.3 1.0 C C:ASP97 4.5 49.4 1.0 OD2 C:ASP97 4.5 57.6 1.0 CB C:ASP97 5.0 53.7 1.0 NE C:ARG98 5.0 46.8 1.0 CG C:ASP97 5.0 56.7 1.0

Sodium binding site 5 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3035 b:17.1 occ:1.00 N3 0:A630 2.6 48.5 1.0 O2' 0:A631 2.8 47.0 1.0 O2' 0:A630 3.0 45.0 1.0 OP2 0:A2074 3.3 39.3 1.0 C2 0:A630 3.4 47.4 1.0 C1' 0:A630 3.5 47.2 1.0 N2 0:G2070 3.6 33.4 1.0 C4 0:A630 3.6 48.4 1.0 C2' 0:A631 3.7 44.7 1.0 C2' 0:A630 3.9 46.6 1.0 N9 0:A630 4.0 48.5 1.0 N1 0:A629 4.1 39.2 1.0 O3' 0:A630 4.1 49.8 1.0 C3' 0:A631 4.3 44.6 1.0 C2 0:G2070 4.4 33.9 1.0 OP1 0:A632 4.4 49.3 1.0 C2 0:A629 4.5 39.8 1.0 O3' 0:A631 4.5 45.7 1.0 OP2 0:G2072 4.6 50.6 1.0 C3' 0:A630 4.6 46.2 1.0 O4' 0:A630 4.7 46.4 1.0 P 0:A2074 4.7 38.6 1.0 N1 0:A630 4.8 44.9 1.0 N3 0:G2070 4.9 36.0 1.0 C5 0:A630 4.9 46.8 1.0 C6 0:A629 4.9 38.3 1.0 P 0:A632 5.0 48.1 1.0

Sodium binding site 6 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3036 b:49.5 occ:1.00 O6 0:G2094 2.5 29.7 1.0 N7 0:G2094 2.6 28.4 1.0 O6 0:G2093 2.7 33.4 1.0 N7 0:G2093 2.7 28.2 1.0 C5 0:G2093 2.8 31.3 1.0 C6 0:G2093 2.9 32.5 1.0 C6 0:G2094 3.0 29.1 1.0 C5 0:G2094 3.1 28.8 1.0 N2 0:G2092 3.5 41.5 1.0 N1 0:A2649 3.5 51.7 1.0 C2 0:A2649 3.5 51.7 1.0 N3 0:G2092 3.6 43.5 1.0 C8 0:G2093 3.8 27.0 1.0 C8 0:G2094 3.8 28.7 1.0 C2 0:G2092 3.8 42.4 1.0 C4 0:G2093 4.0 30.2 1.0 N1 0:G2093 4.0 32.0 1.0 N1 0:G2094 4.3 29.3 1.0 N3 0:U2652 4.4 36.2 1.0 C4 0:G2094 4.4 28.8 1.0 N6 0:A2612 4.4 30.0 1.0 O2' 0:G2092 4.4 40.2 1.0 N9 0:G2093 4.4 28.5 1.0 N3 0:A2649 4.6 50.7 1.0 C4 0:G2092 4.6 43.6 1.0 C6 0:A2649 4.6 50.7 1.0 N9 0:G2094 4.7 27.9 1.0 N4 0:C2651 4.8 39.8 1.0 O4 0:U2652 4.8 38.5 1.0 C2 0:G2093 4.9 32.1 1.0 O2 0:U2652 4.9 37.8 1.0 C6 0:A2612 4.9 32.1 1.0 N1 0:G2092 4.9 43.8 1.0 N3 0:G2093 4.9 31.8 1.0 N1 0:A2612 5.0 31.9 1.0

Sodium binding site 7 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3037 b:61.4 occ:1.00 O2 0:C40 2.0 63.1 1.0 C2' 0:C40 2.4 67.2 1.0 O2' 0:C40 2.4 67.0 1.0 O4' 0:G41 2.7 59.7 1.0 C1' 0:C40 2.9 67.3 1.0 C2 0:C40 2.9 65.1 1.0 N1 0:C40 3.3 66.7 1.0 O2 0:C443 3.5 63.2 1.0 C1' 0:G41 3.7 60.5 1.0 C5' 0:G41 3.7 61.1 1.0 N1 0:A442 3.7 71.6 1.0 C4' 0:G41 3.7 60.8 1.0 N9 0:G41 3.8 60.1 1.0 C3' 0:C40 3.9 66.0 1.0 O5' 0:G41 3.9 61.7 1.0 C8 0:G41 4.0 60.0 1.0 N3 0:C40 4.1 64.7 1.0 O4' 0:C40 4.2 67.9 1.0 N2 0:G39 4.3 69.7 1.0 C2 0:A442 4.4 70.4 1.0 C2 0:C443 4.5 64.2 1.0 O3' 0:C40 4.5 63.6 1.0 C4 0:G41 4.6 59.7 1.0 C6 0:C40 4.6 67.2 1.0 C2 0:G39 4.6 69.3 1.0 N6 0:A442 4.6 72.4 1.0 C6 0:A442 4.7 71.8 1.0 C4' 0:C40 4.7 66.7 1.0 N7 0:G41 4.7 60.1 1.0 N1 0:G39 4.8 69.4 1.0 C3' 0:G41 4.9 61.5 1.0 N3 0:C443 4.9 62.6 1.0 P 0:G41 5.0 61.5 1.0

Sodium binding site 8 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3038 b:67.8 occ:1.00 O2 0:C1394 2.4 43.2 1.0 O2 0:U1724 2.5 39.5 1.0 O4 0:U1432 2.9 31.2 1.0 C2 0:U1724 3.6 40.2 1.0 C2 0:C1394 3.7 42.0 1.0 O2' 0:U1724 3.7 32.2 1.0 C4 0:U1432 4.0 29.8 1.0 C2' 0:U1724 4.1 37.9 1.0 O2' 0:C1394 4.2 43.6 1.0 C1' 0:U1724 4.2 40.0 1.0 O2' 0:C1725 4.3 36.0 1.0 C1' 0:C1394 4.4 42.4 1.0 N1 0:U1724 4.4 41.3 1.0 C2' 0:C1394 4.5 42.4 1.0 N3 0:C1394 4.5 41.6 1.0 N1 0:C1394 4.5 41.7 1.0 N3 0:U1724 4.6 39.6 1.0 O6 0:G1433 4.6 42.7 1.0 N3 0:U1432 4.6 32.1 1.0 OP2 0:U1722 4.7 45.9 1.0 O3' 0:C1725 4.8 38.8 1.0

Sodium binding site 9 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ H:Na172 b:43.9 occ:1.00 O H:ILE157 2.5 55.7 1.0 O2' 0:A1133 2.8 46.2 1.0 O H:PRO159 2.8 66.4 1.0 O3' 0:A1133 2.8 46.8 1.0 O H:THR158 3.3 58.0 1.0 O H:TYR154 3.4 63.6 1.0 OP1 0:G1134 3.5 46.4 1.0 C3' 0:A1133 3.6 46.8 1.0 C H:ILE157 3.7 56.0 1.0 C H:THR158 3.7 59.1 1.0 C2' 0:A1133 3.7 47.1 1.0 C H:PRO159 3.7 65.7 1.0 O2' 0:G2520 3.8 48.9 1.0 P 0:G1134 3.9 47.2 1.0 C4' 0:A1133 3.9 47.8 1.0 N H:PRO159 4.2 60.4 1.0 CA H:THR158 4.3 58.4 1.0 N H:THR158 4.4 57.6 1.0 CA H:PRO159 4.5 62.4 1.0 N H:ILE157 4.5 54.4 1.0 C H:TYR154 4.6 63.7 1.0 C5' 0:G1134 4.6 45.4 1.0 N H:SER160 4.6 68.7 1.0 O5' 0:G1134 4.7 45.9 1.0 CA H:ILE157 4.8 54.6 1.0 C1' 0:A1133 4.8 46.6 1.0 O4' 0:A1133 4.8 48.0 1.0 CA H:SER160 4.9 71.2 1.0 C H:ASN155 4.9 57.3 1.0 CA H:ASN155 5.0 59.2 1.0

Sodium binding site 10 out of 86 in the A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of A More Complete Structure of the the L7/L12 Stalk of the Haloarcula Marismortui 50S Large Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3039 b:29.3 occ:1.00 O6 0:G2579 2.8 40.7 1.0 O4' 0:A2577 3.0 48.5 1.0 O6 0:G2578 3.0 46.9 1.0 N3 0:A2577 3.1 49.8 1.0 N7 0:G2578 3.3 44.2 1.0 C6 0:G2578 3.4 46.8 1.0 N7 0:G2579 3.5 40.1 1.0 C5 0:G2578 3.5 45.2 1.0 C6 0:G2579 3.6 38.2 1.0 C4 0:A2577 3.8 49.2 1.0 C1' 0:A2577 3.8 48.6 1.0 C5 0:G2579 3.8 37.7 1.0 C2 0:A2577 3.9 48.8 1.0 N9 0:A2577 4.0 48.2 1.0 C4' 0:A2577 4.1 48.5 1.0 N3 0:U2554 4.3 41.5 1.0 C8 0:G2578 4.3 43.6 1.0 N1 0:G2578 4.5 47.9 1.0 N4 0:C2556 4.6 38.7 1.0 O4 0:U2554 4.6 47.5 1.0 C8 0:G2579 4.7 39.5 1.0 C4 0:G2578 4.7 45.0 1.0 N1 0:G2579 4.8 37.2 1.0 C5' 0:A2577 4.8 45.9 1.0 C5 0:A2577 4.8 49.5 1.0 N1 0:A2577 4.9 49.1 1.0 C4 0:U2554 4.9 43.5 1.0

J.M.Kavran, T.A.Steitz. Structure of the Base of the L7/L12 Stalk of the Haloarcula Marismortui Large Ribosomal Subunit: Analysis of L11 Movements J.Mol.Biol. V. 371 1047 2007.
ISSN: ISSN 0022-2836
PubMed: 17599351
DOI: 10.1016/J.JMB.2007.05.091