Sodium in PDB 1n8r: Structure of Large Ribosomal Subunit in Complex with Virginiamycin M

The structure of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r was solved by J.L.Hansen, 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)	20.00 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.902, 300.474, 575.176, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 24.2

The structure of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	1 atom
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 Large Ribosomal Subunit in Complex with Virginiamycin M (pdb code 1n8r). 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 Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r:
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 Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8301 b:21.9 occ:1.00 O A:HOH5360 2.1 40.5 1.0 OP2 A:C1069 2.5 9.8 1.0 N7 A:G1072 2.5 18.7 1.0 O A:HOH3558 2.6 20.9 1.0 O A:HOH3590 2.8 50.2 1.0 O6 A:G1087 3.1 28.4 1.0 O6 A:G1072 3.2 22.1 1.0 C5 A:G1072 3.3 19.8 1.0 O A:HOH9473 3.3 2.9 1.0 C6 A:G1072 3.5 20.6 1.0 C8 A:G1072 3.6 19.1 1.0 P A:C1069 3.8 13.9 1.0 O A:HOH3930 4.0 19.6 1.0 C6 A:G1087 4.1 26.5 1.0 O3' A:C1068 4.4 14.4 1.0 C5' A:C1068 4.5 21.6 1.0 C3' A:C1068 4.5 16.8 1.0 C4 A:G1072 4.5 19.6 1.0 OP1 A:C1069 4.6 10.9 1.0 N9 A:G1072 4.6 18.8 1.0 N1 A:G1087 4.7 26.1 1.0 N1 A:G1072 4.9 19.2 1.0 O A:HOH4661 4.9 52.5 1.0 OP2 A:C1068 4.9 28.5 1.0 O5' A:C1069 4.9 12.3 1.0 N6 A:A1070 5.0 25.8 1.0

Sodium binding site 2 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8302 b:19.6 occ:1.00 O2' A:G1119 2.8 22.2 1.0 O A:HOH6070 2.9 70.0 1.0 OP2 A:U1120 2.9 25.1 1.0 O6 A:G1121 3.0 27.6 1.0 O A:HOH4933 3.1 27.7 1.0 O A:HOH8278 3.1 42.2 1.0 O3' A:G1119 3.2 24.2 1.0 O A:HOH4561 3.3 27.2 1.0 N7 A:G1121 3.4 26.4 1.0 P A:U1120 3.7 25.7 1.0 O4 A:U1122 3.7 26.1 1.0 MG A:MG8025 3.7 33.2 1.0 C6 A:G1121 3.8 26.2 1.0 C2' A:G1119 3.9 22.3 1.0 C5 A:G1121 4.0 25.9 1.0 C3' A:G1119 4.0 23.4 1.0 O A:HOH7314 4.1 49.5 1.0 C1' A:G1119 4.4 21.3 1.0 C4 A:U1122 4.4 27.2 1.0 OP1 A:U1120 4.5 26.8 1.0 C8 A:G1121 4.6 26.8 1.0 O A:HOH8277 4.7 24.5 1.0 C5 A:U1122 4.8 27.4 1.0 N4 A:C1243 4.9 27.9 1.0 OP1 A:C1238 4.9 26.7 1.0 O5' A:U1120 4.9 25.5 1.0 N6 A:A1242 5.0 22.4 1.0

Sodium binding site 3 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8303 b:39.5 occ:1.00 O4 A:U904 2.9 20.2 1.0 OP1 A:G1354 3.0 25.8 1.0 OP2 A:A643 3.1 16.7 1.0 OP1 A:G644 3.2 10.8 1.0 NH2 M:ARG8 3.3 29.3 1.0 O A:HOH3652 3.5 35.6 1.0 O5' A:A643 3.6 16.3 1.0 P A:A643 3.6 18.2 1.0 O A:HOH9825 3.7 25.2 1.0 OP1 A:C1353 3.7 38.2 1.0 OP1 A:A643 3.8 19.0 1.0 C4 A:U904 3.9 17.6 1.0 P A:G1354 4.0 26.1 1.0 N3 A:U904 4.0 15.2 1.0 O A:HOH4990 4.2 91.4 1.0 OP2 A:G1354 4.3 23.2 1.0 CZ M:ARG8 4.3 27.7 1.0 P A:G644 4.4 14.3 1.0 C5' A:A643 4.5 15.0 1.0 O3' A:C1353 4.6 26.4 1.0 C3' A:A643 4.7 13.3 1.0 P A:C1353 4.7 39.9 1.0 O5' A:C1353 4.9 35.5 1.0 NE M:ARG8 4.9 28.3 1.0 O3' A:A643 4.9 13.9 1.0 OP2 A:G644 5.0 10.2 1.0

Sodium binding site 4 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8305 b:22.8 occ:1.00 O A:HOH6173 2.4 40.1 1.0 O A:HOH4484 2.5 19.7 1.0 O A:HOH5090 2.5 30.9 1.0 O2' A:A630 2.6 26.1 1.0 N3 A:A630 2.7 26.6 1.0 O2' A:A631 3.0 18.9 1.0 C1' A:A630 3.4 24.6 1.0 C2' A:A630 3.5 25.1 1.0 C2 A:A630 3.6 26.3 1.0 C4 A:A630 3.6 26.0 1.0 C2' A:A631 3.7 18.5 1.0 OP2 A:A2074 3.8 21.6 1.0 O3' A:A630 3.8 22.3 1.0 N9 A:A630 3.9 25.4 1.0 OP1 A:A632 4.0 21.2 1.0 C3' A:A631 4.0 18.4 1.0 N2 A:G2070 4.3 21.4 1.0 C3' A:A630 4.3 23.4 1.0 O3' A:A631 4.4 20.0 1.0 O A:HOH3473 4.5 43.1 1.0 O A:HOH9803 4.5 18.4 1.0 O4' A:A630 4.6 25.8 1.0 P A:A632 4.7 22.1 1.0 N1 A:A629 4.7 18.0 1.0 C2 A:A628 4.8 16.9 1.0 N1 A:A630 4.9 25.2 1.0 OP2 A:G2072 4.9 33.8 1.0 C2 A:A629 4.9 19.0 1.0 C5 A:A630 4.9 25.4 1.0

Sodium binding site 5 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8306 b:28.1 occ:1.00 N1 A:A2649 2.8 30.8 1.0 N7 A:G2094 2.9 21.0 1.0 N7 A:G2093 3.0 22.4 1.0 O6 A:G2094 3.2 21.0 1.0 O2' A:G2092 3.2 18.3 1.0 O A:HOH9528 3.2 25.9 1.0 N3 A:G2092 3.2 23.6 1.0 C2 A:A2649 3.3 30.8 1.0 O6 A:G2093 3.4 24.9 1.0 C5 A:G2093 3.5 24.0 1.0 C2 A:G2092 3.6 23.2 1.0 C6 A:G2093 3.7 25.1 1.0 N2 A:G2092 3.7 23.6 1.0 C5 A:G2094 3.7 21.0 1.0 C6 A:G2094 3.8 21.4 1.0 N6 A:A2612 3.8 20.3 1.0 C8 A:G2093 3.9 21.9 1.0 C6 A:A2649 3.9 31.4 1.0 C8 A:G2094 4.1 20.2 1.0 C4 A:G2092 4.1 23.1 1.0 N6 A:A2649 4.2 31.8 1.0 C6 A:A2612 4.3 22.9 1.0 C2' A:G2092 4.3 17.8 1.0 C1' A:G2092 4.4 19.1 1.0 C4 A:G2093 4.5 23.0 1.0 N9 A:G2092 4.6 22.0 1.0 N3 A:A2649 4.6 30.5 1.0 N1 A:G2092 4.6 23.0 1.0 N9 A:G2093 4.7 22.0 1.0 N1 A:A2612 4.8 23.2 1.0 C5 A:A2612 4.8 22.9 1.0 N1 A:G2093 4.8 25.8 1.0 O3' A:G2092 4.8 17.6 1.0 C4 A:G2094 5.0 20.3 1.0

Sodium binding site 6 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8307 b:42.0 occ:1.00 O2 A:C40 2.5 40.5 1.0 O2' A:C40 2.8 42.9 1.0 O4' A:G41 2.9 33.7 1.0 N1 A:A442 3.0 43.2 1.0 O2 A:C443 3.0 48.0 1.0 C2' A:C40 3.2 41.4 1.0 C1' A:C40 3.4 42.0 1.0 C2 A:C40 3.6 42.0 1.0 C2 A:A442 3.6 43.3 1.0 C1' A:G41 3.7 34.2 1.0 C2 A:C443 3.8 46.5 1.0 N1 A:C40 4.0 42.0 1.0 C6 A:A442 4.0 41.8 1.0 N9 A:G41 4.0 35.5 1.0 C4' A:G41 4.0 33.9 1.0 N6 A:A442 4.2 43.7 1.0 C5' A:G41 4.3 35.5 1.0 N2 A:G39 4.3 38.0 1.0 N3 A:C443 4.4 46.0 1.0 C8 A:G41 4.4 35.6 1.0 N1 A:C443 4.6 45.7 1.0 O5' A:G41 4.6 37.4 1.0 O4' A:C40 4.7 41.5 1.0 C1' A:C443 4.7 43.4 1.0 C4 A:G41 4.7 36.2 1.0 C3' A:C40 4.7 40.8 1.0 N3 A:C40 4.7 40.9 1.0 O A:HOH6253 4.8 27.1 1.0 C2 A:G39 4.8 37.9 1.0 N3 A:A442 4.8 42.5 1.0 O A:HOH7359 4.9 45.5 1.0 N1 A:G39 5.0 38.7 1.0

Sodium binding site 7 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8308 b:53.2 occ:1.00 O2 A:U1724 2.1 33.9 1.0 O2 A:C1394 2.4 35.0 1.0 O4 A:U1432 2.7 30.6 1.0 O A:HOH3802 2.8 27.6 1.0 C2 A:U1724 3.3 31.3 1.0 C2 A:C1394 3.6 33.5 1.0 O6 A:G1433 3.7 34.0 1.0 O A:HOH9693 3.8 32.9 1.0 O2' A:C1394 3.8 27.2 1.0 C4 A:U1432 3.9 30.6 1.0 O A:HOH7529 3.9 71.8 1.0 C2' A:C1394 4.1 30.2 1.0 N3 A:U1724 4.2 31.6 1.0 C1' A:U1724 4.2 28.9 1.0 O2' A:U1724 4.3 26.9 1.0 N1 A:U1724 4.3 30.5 1.0 C6 A:G1433 4.3 32.4 1.0 C2' A:U1724 4.4 27.7 1.0 O A:HOH5220 4.4 33.8 1.0 C1' A:C1394 4.4 30.9 1.0 N3 A:C1394 4.5 33.2 1.0 N3 A:U1432 4.5 30.8 1.0 N1 A:C1394 4.5 32.6 1.0 O A:HOH5852 4.7 52.2 1.0 N1 A:G1433 4.7 32.1 1.0 OP2 A:U1722 4.9 35.7 1.0 O2' A:C1725 4.9 30.1 1.0

Sodium binding site 8 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8310 b:27.9 occ:1.00 N3 A:A2577 2.7 27.7 1.0 O6 A:G2579 2.8 29.1 1.0 O A:HOH4894 2.9 21.9 1.0 O4' A:A2577 3.0 28.0 1.0 N7 A:G2579 3.2 31.2 1.0 C1' A:A2577 3.4 27.7 1.0 C2 A:A2577 3.5 27.6 1.0 C4 A:A2577 3.5 27.1 1.0 N7 A:G2578 3.6 28.2 1.0 C6 A:G2579 3.6 29.4 1.0 C5 A:G2579 3.8 29.4 1.0 O6 A:G2578 3.8 30.3 1.0 N9 A:A2577 3.8 26.6 1.0 O A:HOH8223 3.9 85.5 1.0 C5 A:G2578 4.0 28.8 1.0 O A:HOH6675 4.0 67.0 1.0 C4' A:A2577 4.1 28.9 1.0 C6 A:G2578 4.1 29.8 1.0 O6 A:G2580 4.4 31.9 1.0 C8 A:G2578 4.4 29.1 1.0 C8 A:G2579 4.4 29.8 1.0 N1 A:A2577 4.7 26.9 1.0 N3 A:U2554 4.7 26.1 1.0 N4 A:C2556 4.8 32.8 1.0 C5 A:A2577 4.8 26.9 1.0 C2' A:A2577 4.8 28.6 1.0 O A:HOH6356 4.9 56.8 1.0 O A:HOH5088 4.9 35.5 1.0 C3' A:A2577 4.9 29.0 1.0 N1 A:G2579 4.9 28.4 1.0 O3' A:A2577 4.9 29.5 1.0 C4 A:G2578 5.0 28.3 1.0

Sodium binding site 9 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8311 b:37.2 occ:1.00 O6 A:G2525 2.3 35.6 1.0 O A:HOH3970 2.3 21.8 1.0 O A:HOH9584 2.7 33.6 1.0 O A:HOH5043 2.7 23.8 1.0 N7 A:G2524 2.9 27.2 1.0 C6 A:G2525 3.4 35.2 1.0 O A:HOH4015 3.5 29.7 1.0 O A:HOH6754 3.5 57.6 1.0 C8 A:G2524 3.8 26.1 1.0 C5 A:G2524 4.0 26.4 1.0 O6 A:G2524 4.1 22.6 1.0 C5 A:G2525 4.2 34.5 1.0 C5 A:U2523 4.2 30.4 1.0 N7 A:G2525 4.3 33.8 1.0 O2' A:C2493 4.3 27.6 1.0 N1 A:G2525 4.4 34.4 1.0 C6 A:G2524 4.4 25.9 1.0 C4 A:U2523 4.4 31.4 1.0 OP2 A:G2524 4.4 31.6 1.0 O4 A:U2523 4.6 32.8 1.0 C6 A:U2523 4.7 29.8 1.0 C2' A:C2493 4.7 28.8 1.0 OP2 A:U2523 5.0 26.9 1.0

Sodium binding site 10 out of 86 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of Large Ribosomal Subunit in Complex with Virginiamycin M within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8313 b:50.5 occ:1.00 O A:HOH5512 2.1 52.5 1.0 O A:HOH4231 2.3 33.1 1.0 O6 A:G2399 2.4 29.8 1.0 O A:HOH3341 2.4 19.2 1.0 N7 A:G2399 3.2 27.8 1.0 O A:HOH5461 3.2 33.5 1.0 C6 A:G2399 3.3 28.4 1.0 O A:HOH6446 3.4 45.1 1.0 O A:HOH6897 3.4 58.1 1.0 C5 A:G2399 3.6 28.2 1.0 O A:HOH3782 3.6 28.1 1.0 O4 A:U2389 3.9 32.4 1.0 OP2 A:A2398 4.0 31.1 1.0 O6 A:G2400 4.0 32.8 1.0 O A:HOH6667 4.2 45.3 1.0 N3 A:U2389 4.4 31.4 1.0 C8 A:G2399 4.5 27.9 1.0 N7 A:G2400 4.5 33.3 1.0 N1 A:G2399 4.6 28.3 1.0 C4 A:U2389 4.7 31.0 1.0 C6 A:G2400 4.7 31.6 1.0 O2 A:U2390 4.8 30.9 1.0 C5 A:G2400 4.9 32.6 1.0 C4 A:G2399 4.9 28.4 1.0

J.Hansen, P.B.Moore, T.A.Steitz. Structures of Five Antibiotics Bound at the Peptidyl Transferase Center of the Large Ribosomal Subunit J.Mol.Biol. V. 330 1061 2003.
ISSN: ISSN 0022-2836
PubMed: 12860128
DOI: 10.1016/S0022-2836(03)00668-5