Sodium in PDB 1qvf: Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf was solved by 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)	50.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.522, 300.817, 574.861, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.9

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	119 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1qvf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf:
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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8301 b:44.3 occ:1.00 OP2 0:C1069 2.2 34.9 1.0 O 0:HOH4465 2.4 77.9 1.0 N7 0:G1072 2.6 38.3 1.0 O 0:HOH9716 2.9 58.7 1.0 O 0:HOH9686 3.0 28.9 1.0 O6 0:G1087 3.1 42.5 1.0 O6 0:G1072 3.2 36.4 1.0 C5 0:G1072 3.3 37.0 1.0 C6 0:G1072 3.6 36.0 1.0 C8 0:G1072 3.6 37.8 1.0 P 0:C1069 3.7 34.9 1.0 O 0:HOH8589 3.8 15.5 1.0 C6 0:G1087 4.1 44.8 1.0 O 0:HOH3054 4.2 47.9 1.0 C5' 0:C1068 4.3 42.8 1.0 C3' 0:C1068 4.3 39.9 1.0 O3' 0:C1068 4.3 37.3 1.0 OP1 0:C1069 4.4 33.7 1.0 C4 0:G1072 4.5 36.7 1.0 N9 0:G1072 4.6 36.9 1.0 O5' 0:C1069 4.7 33.8 1.0 N1 0:G1087 4.7 44.2 1.0 OP2 0:C1068 4.8 48.3 1.0 N1 0:G1072 4.9 35.2 1.0 C4' 0:C1068 4.9 41.1 1.0 O 0:HOH3781 4.9 61.3 1.0 N6 0:A1070 4.9 36.4 1.0

Sodium binding site 2 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8302 b:52.4 occ:1.00 O2' 0:G1119 2.5 45.6 1.0 O 0:HOH5171 2.7 88.9 1.0 OP2 0:U1120 2.8 43.2 1.0 O3' 0:G1119 2.9 45.2 1.0 O6 0:G1121 3.1 40.3 1.0 O 0:HOH4045 3.1 57.5 1.0 O 0:HOH7243 3.2 53.3 1.0 O 0:HOH3680 3.2 80.1 1.0 N7 0:G1121 3.4 39.7 1.0 P 0:U1120 3.4 43.7 1.0 C2' 0:G1119 3.7 43.9 1.0 O4 0:U1122 3.8 45.5 1.0 C6 0:G1121 3.9 40.1 1.0 MG 0:MG8025 3.9 32.5 1.0 C3' 0:G1119 3.9 45.3 1.0 C5 0:G1121 4.0 39.5 1.0 O 0:HOH6410 4.2 54.2 1.0 OP1 0:U1120 4.2 44.4 1.0 C1' 0:G1119 4.4 43.2 1.0 C4 0:U1122 4.6 43.9 1.0 C8 0:G1121 4.6 38.4 1.0 O5' 0:U1120 4.7 41.3 1.0 C5' 0:U1120 4.8 42.2 1.0 C5 0:U1122 4.9 43.5 1.0 OP1 0:C1238 5.0 42.1 1.0

Sodium binding site 3 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8303 b:58.5 occ:1.00 OP2 0:A643 2.9 40.1 1.0 O4 0:U904 3.0 30.5 1.0 OP1 0:G644 3.1 35.4 1.0 OP1 0:G1354 3.2 39.1 1.0 O 0:HOH9778 3.2 56.1 1.0 O5' 0:A643 3.4 38.5 1.0 P 0:A643 3.4 39.9 1.0 NH2 K:ARG8 3.6 36.2 1.0 OP1 0:C1353 3.7 58.6 1.0 OP1 0:A643 3.7 39.7 1.0 O 0:HOH8950 4.0 15.6 1.0 C4 0:U904 4.0 29.5 1.0 N3 0:U904 4.2 29.1 1.0 C5' 0:A643 4.2 37.8 1.0 P 0:G1354 4.3 38.8 1.0 P 0:G644 4.4 35.3 1.0 O 0:HOH4100 4.4 80.5 1.0 CZ K:ARG8 4.5 36.3 1.0 C3' 0:A643 4.6 37.2 1.0 OP2 0:G1354 4.7 38.2 1.0 P 0:C1353 4.7 59.2 1.0 O3' 0:A643 4.8 36.9 1.0 O3' 0:C1353 4.8 41.7 1.0 O5' 0:C1353 5.0 54.5 1.0 O3' 0:G642 5.0 39.3 1.0

Sodium binding site 4 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8305 b:44.8 occ:1.00 O 0:HOH5272 2.3 62.7 1.0 O 0:HOH4197 2.5 38.2 1.0 O 0:HOH3600 2.5 41.8 1.0 O2' 0:A630 2.6 36.7 1.0 N3 0:A630 2.7 36.5 1.0 O2' 0:A631 3.0 39.4 1.0 OP2 0:A2074 3.5 36.3 1.0 C2 0:A630 3.5 38.2 1.0 C1' 0:A630 3.6 33.7 1.0 C2' 0:A631 3.6 37.7 1.0 C2' 0:A630 3.7 34.1 1.0 C4 0:A630 3.7 35.6 1.0 C3' 0:A631 4.0 37.3 1.0 N2 0:G2070 4.0 26.7 1.0 N9 0:A630 4.0 35.4 1.0 OP1 0:A632 4.1 37.8 1.0 O3' 0:A631 4.2 36.5 1.0 O3' 0:A630 4.2 33.6 1.0 OP2 0:G2072 4.4 42.1 1.0 O 0:HOH9600 4.6 39.3 1.0 P 0:A632 4.6 37.4 1.0 N1 0:A629 4.6 33.9 1.0 C3' 0:A630 4.7 33.3 1.0 O 0:HOH8928 4.7 32.2 1.0 O4' 0:A630 4.7 32.0 1.0 C2 0:G2070 4.8 26.0 1.0 N1 0:A630 4.9 37.3 1.0 OP2 0:A632 4.9 36.9 1.0 C2 0:A629 4.9 34.3 1.0 P 0:A2074 4.9 35.1 1.0 C2 0:A628 5.0 35.0 1.0

Sodium binding site 5 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8306 b:57.3 occ:1.00 N7 0:G2094 2.6 34.2 1.0 O6 0:G2094 2.9 35.4 1.0 N7 0:G2093 3.0 38.0 1.0 N1 0:A2649 3.0 40.2 1.0 C5 0:G2094 3.3 35.4 1.0 O 0:HOH8648 3.3 34.0 1.0 C5 0:G2093 3.4 40.4 1.0 O2' 0:G2092 3.4 39.0 1.0 C2 0:A2649 3.4 39.1 1.0 C6 0:G2094 3.4 35.2 1.0 O6 0:G2093 3.4 43.6 1.0 N3 0:G2092 3.5 42.5 1.0 C6 0:G2093 3.6 41.7 1.0 N2 0:G2092 3.6 41.7 1.0 N6 0:A2612 3.6 40.3 1.0 C8 0:G2094 3.7 33.7 1.0 C2 0:G2092 3.8 42.2 1.0 C8 0:G2093 3.8 36.9 1.0 C6 0:A2612 4.1 40.5 1.0 C6 0:A2649 4.2 40.3 1.0 C4 0:G2093 4.3 40.2 1.0 C4 0:G2092 4.4 42.3 1.0 N6 0:A2649 4.5 40.7 1.0 N1 0:A2612 4.6 42.0 1.0 N9 0:G2093 4.6 38.1 1.0 C4 0:G2094 4.6 36.0 1.0 C5 0:A2612 4.6 39.2 1.0 C2' 0:G2092 4.6 40.0 1.0 N1 0:G2093 4.7 41.2 1.0 N3 0:A2649 4.7 39.2 1.0 N9 0:G2094 4.8 33.8 1.0 N1 0:G2094 4.8 36.0 1.0 C1' 0:G2092 4.8 41.4 1.0 N1 0:G2092 4.9 42.1 1.0 N7 0:A2612 4.9 40.5 1.0 N9 0:G2092 5.0 41.7 1.0

Sodium binding site 6 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8307 b:55.8 occ:1.00 O2' 0:C40 2.7 65.3 1.0 O2 0:C40 2.8 62.2 1.0 O4' 0:G41 3.0 59.5 1.0 O2 0:C443 3.0 71.6 1.0 N1 0:A442 3.2 72.1 1.0 C2' 0:C40 3.2 65.2 1.0 C1' 0:C40 3.5 64.5 1.0 C2 0:A442 3.7 71.4 1.0 C2 0:C40 3.8 63.7 1.0 C1' 0:G41 3.9 59.0 1.0 C2 0:C443 3.9 70.9 1.0 C4' 0:G41 4.1 59.3 1.0 N1 0:C40 4.1 64.3 1.0 C6 0:A442 4.2 70.8 1.0 N9 0:G41 4.2 59.8 1.0 C5' 0:G41 4.3 59.1 1.0 N2 0:G39 4.4 64.6 1.0 N6 0:A442 4.5 71.5 1.0 N3 0:C443 4.5 71.2 1.0 O 0:HOH5354 4.6 59.3 1.0 C1' 0:C443 4.6 69.3 1.0 N1 0:C443 4.6 70.2 1.0 C8 0:G41 4.7 60.0 1.0 O4' 0:C40 4.7 64.7 1.0 O5' 0:G41 4.7 60.9 1.0 C3' 0:C40 4.7 64.5 1.0 N3 0:A442 4.9 70.8 1.0 C4 0:G41 4.9 60.7 1.0 C2 0:G39 5.0 65.0 1.0 O 0:HOH6454 5.0 44.5 1.0

Sodium binding site 7 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8308 b:46.5 occ:1.00 O2 0:U1724 2.2 56.6 1.0 O2 0:C1394 2.3 54.9 1.0 O4 0:U1432 2.6 45.6 1.0 O 0:HOH9930 2.7 49.0 1.0 C2 0:U1724 3.4 55.1 1.0 O6 0:G1433 3.5 51.8 1.0 C2 0:C1394 3.5 52.4 1.0 C4 0:U1432 3.8 46.0 1.0 O2' 0:C1394 3.9 49.8 1.0 O 0:HOH8818 3.9 45.4 1.0 C2' 0:C1394 4.0 51.9 1.0 C6 0:G1433 4.1 51.5 1.0 O 0:HOH6620 4.2 0.6 1.0 N3 0:U1724 4.2 56.5 1.0 C1' 0:C1394 4.3 52.1 1.0 O2' 0:U1724 4.3 46.5 1.0 C1' 0:U1724 4.3 50.5 1.0 N1 0:U1724 4.3 53.0 1.0 N3 0:C1394 4.3 51.1 1.0 N1 0:C1394 4.4 52.4 1.0 N3 0:U1432 4.4 46.4 1.0 C2' 0:U1724 4.4 48.7 1.0 O 0:HOH4328 4.5 80.7 1.0 N1 0:G1433 4.5 51.7 1.0 O 0:HOH4950 4.6 54.5 1.0 O2' 0:C1725 4.8 45.0 1.0 C5 0:U1432 5.0 47.7 1.0 OP2 0:U1722 5.0 50.0 1.0

Sodium binding site 8 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8310 b:35.5 occ:1.00 O6 0:G2579 2.6 47.8 1.0 N7 0:G2579 2.9 46.9 1.0 O 0:HOH4006 2.9 36.5 1.0 N7 0:G2578 3.1 52.1 1.0 N3 0:A2577 3.2 49.2 1.0 C6 0:G2579 3.3 47.1 1.0 O4' 0:A2577 3.3 50.5 1.0 C5 0:G2579 3.4 46.4 1.0 O6 0:G2578 3.4 53.0 1.0 C5 0:G2578 3.5 51.2 1.0 C6 0:G2578 3.6 51.5 1.0 C1' 0:A2577 3.9 50.4 1.0 C2 0:A2577 3.9 48.3 1.0 O 0:HOH7192 4.0 87.1 1.0 C8 0:G2578 4.0 50.3 1.0 C4' 0:A2577 4.0 51.8 1.0 C8 0:G2579 4.1 46.6 1.0 C4 0:A2577 4.1 49.4 1.0 O 0:HOH5775 4.2 67.1 1.0 N9 0:A2577 4.4 49.2 1.0 C4 0:G2578 4.5 50.5 1.0 N1 0:G2579 4.6 47.9 1.0 N4 0:C2556 4.7 46.6 1.0 N1 0:G2578 4.7 51.7 1.0 O6 0:G2580 4.7 47.6 1.0 C4 0:G2579 4.7 46.2 1.0 N9 0:G2578 4.7 50.4 1.0 O 0:HOH5458 4.8 55.9 1.0

Sodium binding site 9 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8311 b:48.8 occ:1.00 O6 0:G2525 2.2 44.0 1.0 O 0:HOH3093 2.4 21.9 1.0 O 0:HOH4154 2.5 37.0 1.0 O 0:HOH8706 2.8 40.8 1.0 N7 0:G2524 2.9 37.0 1.0 C6 0:G2525 3.3 43.1 1.0 O 0:HOH5851 3.5 41.4 1.0 O 0:HOH3139 3.7 25.3 1.0 C8 0:G2524 3.7 37.3 1.0 C5 0:G2524 3.9 36.6 1.0 O6 0:G2524 4.0 33.1 1.0 C5 0:G2525 4.0 42.1 1.0 N7 0:G2525 4.1 42.4 1.0 C5 0:U2523 4.2 46.3 1.0 OP2 0:G2524 4.2 41.8 1.0 N1 0:G2525 4.3 41.5 1.0 C4 0:U2523 4.3 46.1 1.0 C6 0:G2524 4.3 35.6 1.0 O4 0:U2523 4.5 47.0 1.0 C6 0:U2523 4.7 44.9 1.0 C2' 0:C2493 4.8 41.5 1.0 O2' 0:C2493 4.8 41.2 1.0 N3 0:U2523 4.9 45.5 1.0 N9 0:G2524 4.9 37.3 1.0 OP2 0:U2523 5.0 41.7 1.0

Sodium binding site 10 out of 86 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8313 b:57.8 occ:1.00 O 0:HOH4614 2.1 69.5 1.0 O 0:HOH3348 2.2 48.1 1.0 O6 0:G2399 2.4 39.1 1.0 O 0:HOH9471 2.7 62.1 1.0 O 0:HOH4565 3.1 46.9 1.0 O 0:HOH5547 3.2 91.3 1.0 N7 0:G2399 3.3 42.2 1.0 C6 0:G2399 3.3 40.2 1.0 O 0:HOH5990 3.5 81.6 1.0 C5 0:G2399 3.6 41.5 1.0 O 0:HOH9910 3.7 40.7 1.0 O4 0:U2389 3.9 40.7 1.0 OP2 0:A2398 3.9 48.6 1.0 O 0:HOH5767 4.0 74.2 1.0 O6 0:G2400 4.0 39.3 1.0 N3 0:U2389 4.4 40.8 1.0 C8 0:G2399 4.5 43.2 1.0 N7 0:G2400 4.6 41.2 1.0 N1 0:G2399 4.6 41.0 1.0 C6 0:G2400 4.6 39.3 1.0 C4 0:U2389 4.7 40.1 1.0 C5 0:G2400 4.9 40.8 1.0 O2 0:U2390 4.9 49.7 1.0 C4 0:G2399 5.0 41.8 1.0

T.M.Schmeing, P.B.Moore, T.A.Steitz. Structures of Deacylated Trna Mimics Bound to the E Site of the Large Ribosomal Subunit Rna V. 9 1345 2003.
ISSN: ISSN 1355-8382
PubMed: 14561884
DOI: 10.1261/RNA.5120503