Sodium in PDB 3cc2: The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins

The structure of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins, PDB code: 3cc2 was solved by G.Gurel, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.95 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.646, 299.672, 573.773, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.1

The structure of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins 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 The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins (pdb code 3cc2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins, PDB code: 3cc2:
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 The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8301 b:34.6 occ:1.00 OP2 0:C1069 2.1 21.2 1.0 N7 0:G1072 2.3 23.6 1.0 O 0:HOH4534 2.5 43.5 1.0 O 0:HOH9713 2.7 31.1 1.0 C5 0:G1072 3.1 23.1 1.0 O 0:HOH9745 3.1 51.3 1.0 O6 0:G1087 3.2 27.3 1.0 O6 0:G1072 3.2 22.2 1.0 C8 0:G1072 3.3 23.5 1.0 C6 0:G1072 3.4 23.5 1.0 P 0:C1069 3.5 22.9 1.0 O 0:HOH8591 3.7 29.7 1.0 C6 0:G1087 4.1 26.3 1.0 O 0:HOH3086 4.1 28.2 1.0 OP1 0:C1069 4.2 23.5 1.0 O3' 0:C1068 4.3 24.9 1.0 C4 0:G1072 4.3 24.2 1.0 N9 0:G1072 4.4 24.5 1.0 C3' 0:C1068 4.4 23.9 1.0 C5' 0:C1068 4.5 27.2 1.0 O5' 0:C1069 4.6 24.9 1.0 N1 0:G1087 4.6 25.2 1.0 N1 0:G1072 4.8 23.6 1.0

Sodium binding site 2 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8302 b:44.1 occ:1.00 O6 0:G1121 2.8 28.1 1.0 O2' 0:G1119 2.8 29.9 1.0 O 0:HOH7355 3.0 34.8 1.0 O 0:HOH4111 3.0 35.1 1.0 O3' 0:G1119 3.1 31.7 1.0 OP2 0:U1120 3.2 31.7 1.0 O 0:HOH5257 3.3 58.4 1.0 N7 0:G1121 3.3 27.6 1.0 O4 0:U1122 3.4 32.6 1.0 C6 0:G1121 3.6 27.0 1.0 O 0:HOH3728 3.7 27.0 1.0 C5 0:G1121 3.8 27.7 1.0 P 0:U1120 3.8 31.9 1.0 C2' 0:G1119 3.8 29.4 1.0 O 0:HOH6505 4.0 74.7 1.0 C3' 0:G1119 4.0 31.1 1.0 MG 0:MG8025 4.1 32.9 1.0 C4 0:U1122 4.1 32.4 1.0 C1' 0:G1119 4.3 29.0 1.0 C5 0:U1122 4.5 31.0 1.0 C8 0:G1121 4.5 27.8 1.0 OP1 0:U1120 4.7 35.6 1.0 N4 0:C1243 4.8 28.8 1.0 N6 0:A1242 4.9 28.1 1.0 N1 0:G1121 4.9 24.6 1.0 CL 0:CL8516 5.0 41.3 1.0 O5' 0:U1120 5.0 31.2 1.0

Sodium binding site 3 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8303 b:32.9 occ:1.00 O4 0:U904 2.9 21.8 1.0 OP2 0:A643 3.0 17.8 1.0 OP1 0:G644 3.0 24.8 1.0 OP1 0:G1354 3.1 25.8 1.0 NH2 L:ARG8 3.4 25.6 1.0 O 0:HOH9806 3.4 28.8 1.0 O5' 0:A643 3.5 20.0 1.0 P 0:A643 3.5 20.9 1.0 OP1 0:C1353 3.7 43.7 1.0 O 0:HOH4166 3.8 81.6 1.0 OP1 0:A643 3.8 22.4 1.0 C4 0:U904 3.9 20.7 1.0 N3 0:U904 4.1 21.1 1.0 O 0:HOH8964 4.1 27.1 1.0 P 0:G1354 4.1 23.4 1.0 CZ L:ARG8 4.2 24.6 1.0 P 0:G644 4.3 24.9 1.0 C5' 0:A643 4.3 19.3 1.0 OP2 0:G1354 4.4 19.8 1.0 C3' 0:A643 4.5 22.4 1.0 O3' 0:C1353 4.6 23.2 1.0 O3' 0:A643 4.7 25.1 1.0 NE L:ARG8 4.8 23.0 1.0 P 0:C1353 4.8 47.9 1.0 N6 0:A1355 5.0 16.7 1.0 OP2 0:G644 5.0 25.2 1.0

Sodium binding site 4 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8305 b:33.1 occ:1.00 O 0:HOH4265 2.5 27.9 1.0 O 0:HOH5358 2.6 48.5 1.0 O2' 0:A630 2.6 26.6 1.0 N3 0:A630 2.7 24.1 1.0 O 0:HOH3647 2.8 28.5 1.0 O2' 0:A631 2.9 25.3 1.0 C1' 0:A630 3.5 24.0 1.0 C2 0:A630 3.5 25.2 1.0 OP2 0:A2074 3.5 26.9 1.0 C2' 0:A631 3.6 24.4 1.0 C2' 0:A630 3.6 25.7 1.0 C4 0:A630 3.6 25.2 1.0 C3' 0:A631 3.9 22.6 1.0 OP1 0:A632 3.9 23.8 1.0 N9 0:A630 4.0 24.6 1.0 O3' 0:A630 4.0 24.9 1.0 N2 0:G2070 4.1 18.6 1.0 O3' 0:A631 4.2 22.4 1.0 P 0:A632 4.5 23.6 1.0 N1 0:A629 4.5 26.3 1.0 C3' 0:A630 4.5 24.8 1.0 OP2 0:G2072 4.5 39.8 1.0 O 0:HOH9629 4.6 36.4 1.0 O 0:HOH8941 4.7 30.3 1.0 C2 0:A629 4.7 27.1 1.0 O4' 0:A630 4.7 26.3 1.0 C2 0:G2070 4.8 21.7 1.0 N1 0:A630 4.8 25.7 1.0 OP2 0:A632 4.9 25.2 1.0 C5 0:A630 5.0 24.4 1.0 C2 0:1MA628 5.0 22.9 1.0

Sodium binding site 5 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8306 b:29.8 occ:1.00 N7 0:G2094 2.7 23.8 1.0 O 0:HOH8650 2.9 16.7 1.0 N1 0:A2649 2.9 24.9 1.0 N7 0:G2093 3.1 24.5 1.0 O6 0:G2094 3.1 26.8 1.0 O2' 0:G2092 3.3 22.6 1.0 C2 0:A2649 3.4 24.9 1.0 N3 0:G2092 3.4 23.2 1.0 C5 0:G2094 3.5 24.9 1.0 C5 0:G2093 3.5 23.3 1.0 O6 0:G2093 3.6 26.9 1.0 C6 0:G2094 3.6 24.6 1.0 N6 0:A2612 3.7 20.5 1.0 N2 0:G2092 3.7 25.3 1.0 C6 0:G2093 3.7 24.9 1.0 C2 0:G2092 3.8 25.4 1.0 C8 0:G2094 3.9 22.8 1.0 C8 0:G2093 3.9 24.1 1.0 C6 0:A2612 4.0 24.2 1.0 C6 0:A2649 4.0 26.0 1.0 C4 0:G2092 4.3 25.6 1.0 N6 0:A2649 4.3 25.6 1.0 C2' 0:G2092 4.5 22.2 1.0 C4 0:G2093 4.5 21.7 1.0 C5 0:A2612 4.5 25.5 1.0 N1 0:A2612 4.5 23.0 1.0 C1' 0:G2092 4.5 23.3 1.0 N9 0:G2093 4.6 23.6 1.0 N3 0:A2649 4.7 25.3 1.0 N9 0:G2092 4.8 25.6 1.0 C4 0:G2094 4.8 24.0 1.0 N7 0:A2612 4.8 24.8 1.0 N1 0:G2093 4.8 22.9 1.0 O3' 0:G2092 4.9 23.2 1.0 N1 0:G2092 4.9 23.7 1.0 N9 0:G2094 5.0 22.8 1.0

Sodium binding site 6 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8307 b:42.1 occ:1.00 O2 0:C40 2.7 39.1 1.0 O2' 0:C40 2.8 36.7 1.0 N1 0:A442 3.0 41.6 1.0 O2 0:C443 3.0 43.8 1.0 O4' 0:G41 3.0 34.8 1.0 C2' 0:C40 3.3 35.9 1.0 C2 0:A442 3.4 39.9 1.0 C1' 0:C40 3.5 36.8 1.0 C2 0:C443 3.8 42.0 1.0 C2 0:C40 3.8 38.5 1.0 C1' 0:G41 3.9 33.5 1.0 C6 0:A442 4.0 40.2 1.0 N1 0:C40 4.2 37.9 1.0 C4' 0:G41 4.2 33.6 1.0 N2 0:G39 4.2 33.6 1.0 N9 0:G41 4.2 34.1 1.0 N6 0:A442 4.3 40.9 1.0 N3 0:C443 4.3 41.6 1.0 C5' 0:G41 4.5 32.5 1.0 N1 0:C443 4.6 41.8 1.0 C1' 0:C443 4.6 41.6 1.0 N3 0:A442 4.7 40.0 1.0 C8 0:G41 4.7 33.9 1.0 O4' 0:C40 4.7 37.7 1.0 C2 0:G39 4.8 34.8 1.0 O 0:HOH5440 4.8 43.6 1.0 C4 0:G41 4.8 33.2 1.0 C3' 0:C40 4.8 34.8 1.0 O5' 0:G41 4.9 33.8 1.0 N1 0:G39 4.9 34.7 1.0 N3 0:C40 5.0 39.1 1.0

Sodium binding site 7 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8308 b:45.2 occ:1.00 O2 0:C1394 2.2 30.1 1.0 O2 0:U1724 2.3 32.0 1.0 O 0:HOH9956 2.6 25.7 1.0 O4 0:U1432 2.6 30.0 1.0 O6 0:G1433 3.3 38.4 1.0 C2 0:C1394 3.3 29.6 1.0 C2 0:U1724 3.6 30.8 1.0 C4 0:U1432 3.7 30.0 1.0 C6 0:G1433 3.9 37.1 1.0 C2' 0:C1394 3.9 31.6 1.0 O2' 0:C1394 3.9 29.6 1.0 O 0:HOH8827 4.0 28.9 1.0 N3 0:C1394 4.2 28.7 1.0 C1' 0:C1394 4.2 30.4 1.0 N3 0:U1432 4.2 30.6 1.0 N1 0:C1394 4.2 29.7 1.0 N1 0:G1433 4.3 37.5 1.0 O 0:HOH6718 4.4 52.9 1.0 N3 0:U1724 4.4 29.6 1.0 C1' 0:U1724 4.5 29.6 1.0 O2' 0:U1724 4.5 30.3 1.0 O 0:HOH4398 4.5 36.1 1.0 N1 0:U1724 4.5 30.1 1.0 O 0:HOH5038 4.6 56.2 1.0 C2' 0:U1724 4.6 30.1 1.0 O2' 0:C1725 4.8 28.0 1.0 C5 0:G1433 4.9 35.0 1.0 C5 0:U1432 4.9 29.8 1.0

Sodium binding site 8 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8309 b:25.7 occ:1.00 O H:PRO162 2.7 41.0 1.0 O3' 0:A1133 2.7 36.2 1.0 O H:ILE160 2.8 39.5 1.0 O H:TYR157 2.9 42.7 1.0 OP1 0:G1134 2.9 35.0 1.0 O2' 0:A1133 3.1 34.5 1.0 O H:THR161 3.4 36.5 1.0 P 0:G1134 3.5 36.3 1.0 C H:PRO162 3.5 42.0 1.0 C3' 0:A1133 3.8 35.1 1.0 C H:THR161 3.9 38.1 1.0 C2' 0:A1133 4.0 34.6 1.0 C H:ILE160 4.0 38.2 1.0 C H:TYR157 4.1 43.8 1.0 C5' 0:G1134 4.3 36.8 1.0 N H:SER163 4.3 44.5 1.0 N H:PRO162 4.3 38.7 1.0 C4' 0:A1133 4.3 34.4 1.0 CA H:PRO162 4.4 39.5 1.0 O5' 0:G1134 4.4 35.6 1.0 CA H:SER163 4.5 47.4 1.0 O2' 0:G2520 4.5 34.3 1.0 CA H:THR161 4.6 37.6 1.0 OP2 0:G1134 4.7 34.4 1.0 CA H:ASN158 4.8 43.2 1.0 N H:THR161 4.8 37.7 1.0 N H:ASN158 4.9 43.0 1.0 N H:ILE160 4.9 39.4 1.0

Sodium binding site 9 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8310 b:30.1 occ:1.00 O6 0:G2579 2.8 27.5 1.0 N3 0:A2577 3.0 29.7 1.0 O 0:HOH4068 3.0 37.5 1.0 N7 0:G2579 3.0 30.6 1.0 O4' 0:A2577 3.1 33.6 1.0 N7 0:G2578 3.2 29.8 1.0 C6 0:G2579 3.5 29.2 1.0 C5 0:G2579 3.6 31.2 1.0 O6 0:G2578 3.6 30.8 1.0 C5 0:G2578 3.6 30.4 1.0 C1' 0:A2577 3.7 33.0 1.0 C6 0:G2578 3.8 30.7 1.0 C2 0:A2577 3.8 29.5 1.0 O 0:HOH5862 3.8 60.5 1.0 O 0:HOH7300 3.9 66.1 1.0 C4 0:A2577 3.9 29.2 1.0 C8 0:G2578 4.0 30.2 1.0 C4' 0:A2577 4.0 34.9 1.0 N9 0:A2577 4.2 29.7 1.0 C8 0:G2579 4.2 32.5 1.0 C4 0:G2578 4.6 30.3 1.0 N4 0:C2556 4.6 28.4 1.0 N9 0:G2578 4.8 31.6 1.0 N1 0:G2579 4.8 29.6 1.0 N1 0:G2578 4.9 29.5 1.0 N3 0:U2554 4.9 22.9 1.0 C4 0:G2579 4.9 30.8 1.0 O3' 0:A2577 4.9 35.2 1.0 O6 0:G2580 4.9 31.4 1.0 C3' 0:A2577 5.0 35.0 1.0

Sodium binding site 10 out of 86 in the The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of The Refined Crystal Structure of the Haloarcula Marismortui Large Ribosomal Subunit at 2.4 Angstrom Resolution with Rrna Sequence For the 23S Rrna and Genome-Derived Sequences For R-Proteins within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8311 b:52.9 occ:1.00 O6 0:G2525 2.2 32.7 1.0 O 0:HOH3127 2.4 28.3 1.0 O 0:HOH4218 2.5 35.6 1.0 O 0:HOH8708 2.7 33.9 1.0 N7 0:G2524 2.9 26.4 1.0 C6 0:G2525 3.2 29.9 1.0 O 0:HOH5938 3.3 57.6 1.0 O 0:HOH3173 3.5 27.9 1.0 C8 0:G2524 3.8 26.1 1.0 C5 0:G2524 3.9 25.6 1.0 O6 0:G2524 4.0 24.4 1.0 C5 0:G2525 4.1 30.8 1.0 N1 0:G2525 4.2 28.3 1.0 N7 0:G2525 4.3 30.1 1.0 O2' 0:C2493 4.3 26.0 1.0 C6 0:G2524 4.4 24.1 1.0 C5 0:U2523 4.4 32.9 1.0 OP2 0:G2524 4.4 33.0 1.0 C4 0:U2523 4.5 32.5 1.0 O4 0:U2523 4.6 35.1 1.0 C2' 0:C2493 4.6 29.4 1.0 C6 0:U2523 4.9 31.0 1.0 O2 0:C2493 5.0 29.0 1.0

G.Blaha, G.Gurel, S.J.Schroeder, P.B.Moore, T.A.Steitz. Mutations Outside the Anisomycin-Binding Site Can Make Ribosomes Drug-Resistant. J.Mol.Biol. V. 379 505 2008.
ISSN: ISSN 0022-2836
PubMed: 18455733
DOI: 10.1016/J.JMB.2008.03.075