Sodium in PDB 1yit: Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yit was solved by D.Tu, G.Blaha, 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)	29.99 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	212.583, 299.758, 573.560, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.1

The structure of Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	118 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 - 85;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yit). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 85 binding sites of Sodium where determined in the Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yit:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8501 b:23.5 occ:1.00 OP2 0:C1069 2.3 25.0 1.0 N7 0:G1072 2.4 28.2 1.0 O6 0:G1072 3.2 29.4 1.0 C5 0:G1072 3.2 27.8 1.0 O6 0:G1087 3.4 32.9 1.0 C8 0:G1072 3.5 29.3 1.0 C6 0:G1072 3.6 27.9 1.0 P 0:C1069 3.7 28.2 1.0 C6 0:G1087 4.3 31.1 1.0 O3' 0:C1068 4.4 27.3 1.0 C3' 0:C1068 4.4 29.9 1.0 C4 0:G1072 4.5 28.2 1.0 OP1 0:C1069 4.5 25.7 1.0 C5' 0:C1068 4.5 32.8 1.0 N9 0:G1072 4.5 29.1 1.0 O5' 0:C1069 4.7 27.8 1.0 N1 0:G1087 4.9 28.7 1.0 N1 0:G1072 4.9 27.1 1.0 N6 0:A1070 4.9 37.6 1.0

Sodium binding site 2 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8502 b:44.3 occ:1.00 O2' 0:G1119 2.6 31.3 1.0 O6 0:G1121 2.9 28.5 1.0 OP2 0:U1120 3.2 36.4 1.0 O3' 0:G1119 3.2 36.8 1.0 O4 0:U1122 3.4 37.9 1.0 N7 0:G1121 3.5 30.7 1.0 C2' 0:G1119 3.7 32.4 1.0 C6 0:G1121 3.7 28.7 1.0 P 0:U1120 3.8 38.5 1.0 C5 0:G1121 4.0 28.5 1.0 C3' 0:G1119 4.0 34.7 1.0 C1' 0:G1119 4.2 31.4 1.0 C4 0:U1122 4.2 36.8 1.0 MG 0:MG8025 4.5 31.8 1.0 OP1 0:U1120 4.5 40.1 1.0 N4 0:C1243 4.6 35.3 1.0 C5 0:U1122 4.6 36.7 1.0 CL 0:CL8816 4.7 57.1 1.0 N6 0:A1242 4.7 31.8 1.0 C8 0:G1121 4.7 30.4 1.0 N9 0:G1119 5.0 30.6 1.0

Sodium binding site 3 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8503 b:45.2 occ:1.00 OP2 0:A643 3.0 24.2 1.0 OP1 0:G1354 3.1 28.6 1.0 OP1 0:G644 3.2 26.0 1.0 O4 0:U904 3.3 31.9 1.0 OP1 0:C1353 3.4 45.3 1.0 P 0:A643 3.5 26.4 1.0 NH2 L:ARG8 3.5 33.5 1.0 O5' 0:A643 3.6 22.5 1.0 OP1 0:A643 3.8 30.0 1.0 P 0:G1354 4.1 29.1 1.0 C4 0:U904 4.2 31.1 1.0 N3 0:U904 4.2 30.6 1.0 OP2 0:G1354 4.3 27.2 1.0 C5' 0:A643 4.4 21.0 1.0 CZ L:ARG8 4.5 33.4 1.0 O3' 0:C1353 4.5 31.4 1.0 P 0:G644 4.6 27.7 1.0 P 0:C1353 4.7 50.4 1.0 C3' 0:A643 4.8 24.5 1.0 O5' 0:C1353 4.9 46.1 1.0

Sodium binding site 4 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8505 b:32.4 occ:1.00 N3 0:A630 2.8 34.0 1.0 O2' 0:A631 2.8 28.9 1.0 O2' 0:A630 3.1 30.9 1.0 OP2 0:A2074 3.1 30.3 1.0 C2' 0:A631 3.5 29.5 1.0 C2 0:A630 3.6 33.7 1.0 N2 0:G2070 3.6 32.4 1.0 C1' 0:A630 3.6 31.5 1.0 C4 0:A630 3.8 33.3 1.0 C2' 0:A630 3.9 31.5 1.0 O3' 0:A630 4.0 30.1 1.0 C3' 0:A631 4.1 29.8 1.0 N9 0:A630 4.1 33.1 1.0 N1 0:A629 4.2 28.8 1.0 C2 0:A629 4.4 28.8 1.0 C2 0:G2070 4.4 31.6 1.0 P 0:A2074 4.5 29.4 1.0 O3' 0:A631 4.6 29.2 1.0 OP1 0:A632 4.6 30.3 1.0 C3' 0:A630 4.7 29.8 1.0 OP2 0:G2072 4.7 39.6 1.0 O4' 0:A630 4.8 31.2 1.0 N1 0:A630 4.9 33.9 1.0 C1' 0:A631 4.9 28.5 1.0 N3 0:G2070 5.0 31.2 1.0

Sodium binding site 5 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8506 b:41.9 occ:1.00 N7 0:G2094 2.8 34.1 1.0 N7 0:G2093 3.0 30.7 1.0 N1 0:A2649 3.0 41.0 1.0 O2' 0:G2092 3.2 25.7 1.0 O6 0:G2094 3.2 36.4 1.0 N3 0:G2092 3.3 33.3 1.0 C2 0:A2649 3.4 40.1 1.0 C5 0:G2093 3.4 31.0 1.0 O6 0:G2093 3.5 33.5 1.0 C5 0:G2094 3.6 34.5 1.0 C6 0:G2093 3.6 32.1 1.0 N2 0:G2092 3.6 34.4 1.0 C2 0:G2092 3.7 33.4 1.0 C6 0:G2094 3.7 35.0 1.0 C8 0:G2093 3.8 29.8 1.0 C8 0:G2094 3.9 33.1 1.0 N6 0:A2612 3.9 30.1 1.0 C6 0:A2649 4.1 41.4 1.0 C4 0:G2092 4.2 32.9 1.0 C6 0:A2612 4.3 32.2 1.0 C2' 0:G2092 4.3 28.9 1.0 C4 0:G2093 4.4 30.4 1.0 C1' 0:G2092 4.4 29.6 1.0 N6 0:A2649 4.5 43.4 1.0 N9 0:G2093 4.6 30.3 1.0 N3 0:A2649 4.6 40.0 1.0 N9 0:G2092 4.6 31.4 1.0 N1 0:G2093 4.7 33.0 1.0 C5 0:A2612 4.7 31.6 1.0 N1 0:A2612 4.8 31.8 1.0 O3' 0:G2092 4.8 28.3 1.0 N1 0:G2092 4.8 31.2 1.0 C4 0:G2094 4.9 33.7 1.0

Sodium binding site 6 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8507 b:59.4 occ:1.00 O2 0:C40 2.4 48.0 1.0 O2' 0:C40 2.7 48.2 1.0 O4' 0:G41 2.7 45.6 1.0 N1 0:A442 3.0 50.3 1.0 C2' 0:C40 3.0 48.4 1.0 O2 0:C443 3.3 51.2 1.0 C1' 0:C40 3.3 49.0 1.0 C2 0:C40 3.4 48.8 1.0 C2 0:A442 3.5 49.7 1.0 C1' 0:G41 3.6 45.1 1.0 N1 0:C40 3.8 49.3 1.0 N9 0:G41 3.8 47.1 1.0 C4' 0:G41 3.9 44.4 1.0 C2 0:C443 4.1 51.7 1.0 C6 0:A442 4.1 50.1 1.0 C5' 0:G41 4.2 43.4 1.0 C8 0:G41 4.2 47.7 1.0 N6 0:A442 4.3 51.7 1.0 N2 0:G39 4.4 51.6 1.0 C4 0:G41 4.5 47.9 1.0 N3 0:C40 4.5 49.8 1.0 O5' 0:G41 4.5 45.6 1.0 C3' 0:C40 4.5 48.1 1.0 O4' 0:C40 4.6 49.1 1.0 N3 0:C443 4.7 51.8 1.0 N3 0:A442 4.8 49.3 1.0 C2 0:G39 4.8 51.6 1.0 N1 0:G39 4.8 52.2 1.0 N1 0:C443 4.9 51.6 1.0 C1' 0:C443 4.9 51.4 1.0 N3 0:G41 4.9 47.5 1.0 C2' 0:G41 4.9 44.0 1.0 N7 0:G41 4.9 48.8 1.0

Sodium binding site 7 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8508 b:56.1 occ:1.00 O2 0:C1394 2.3 38.2 1.0 O2 0:U1724 2.4 36.5 1.0 O4 0:U1432 2.6 39.3 1.0 O6 0:G1433 3.3 41.5 1.0 C2 0:C1394 3.4 35.8 1.0 C2 0:U1724 3.5 34.6 1.0 O2' 0:C1394 3.7 34.7 1.0 C2' 0:C1394 3.7 36.2 1.0 C4 0:U1432 3.8 37.6 1.0 C6 0:G1433 4.0 40.2 1.0 C1' 0:C1394 4.1 37.4 1.0 N1 0:C1394 4.2 36.5 1.0 N3 0:C1394 4.3 34.8 1.0 N3 0:U1724 4.3 33.2 1.0 N3 0:U1432 4.4 36.2 1.0 N1 0:G1433 4.4 40.1 1.0 C1' 0:U1724 4.5 34.1 1.0 N1 0:U1724 4.5 34.6 1.0 O2' 0:U1724 4.6 33.5 1.0 OP2 0:U1722 4.7 42.9 1.0 C2' 0:U1724 4.7 35.1 1.0 C5 0:G1433 4.9 38.6 1.0

Sodium binding site 8 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8509 b:39.0 occ:1.00 O H:PRO162 2.5 52.1 1.0 O3' 0:A1133 2.7 41.4 1.0 O H:ILE160 2.8 46.3 1.0 O H:TYR157 2.8 50.8 1.0 OP1 0:G1134 2.9 42.3 1.0 O2' 0:A1133 3.3 38.8 1.0 C H:PRO162 3.4 51.9 1.0 P 0:G1134 3.5 43.6 1.0 O H:THR161 3.5 48.9 1.0 C3' 0:A1133 3.9 40.0 1.0 C H:THR161 3.9 48.4 1.0 C H:ILE160 4.0 44.6 1.0 C H:TYR157 4.1 50.0 1.0 C2' 0:A1133 4.1 39.8 1.0 N H:SER163 4.2 54.0 1.0 CA H:SER163 4.2 56.0 1.0 N H:PRO162 4.3 49.0 1.0 C5' 0:G1134 4.3 43.6 1.0 CA H:PRO162 4.3 49.7 1.0 C4' 0:A1133 4.4 39.5 1.0 O5' 0:G1134 4.4 42.0 1.0 O2' 0:G2520 4.5 41.4 1.0 OP2 0:G1134 4.6 39.5 1.0 CA H:THR161 4.6 47.2 1.0 N H:THR161 4.8 45.4 1.0 CA H:ASN158 4.8 47.8 1.0 N H:ILE160 4.9 42.5 1.0 CD1 H:TYR157 4.9 50.9 1.0 CG1 H:ILE160 4.9 41.9 1.0 N H:ASN158 4.9 49.3 1.0 CA H:TYR157 5.0 49.8 1.0

Sodium binding site 9 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8510 b:40.4 occ:1.00 O6 0:G2579 2.8 39.2 1.0 N3 0:A2577 3.0 33.9 1.0 O4' 0:A2577 3.0 40.1 1.0 N7 0:G2579 3.1 39.8 1.0 N7 0:G2578 3.3 38.9 1.0 O6 0:G2578 3.5 43.6 1.0 C6 0:G2579 3.5 39.1 1.0 C1' 0:A2577 3.6 38.2 1.0 C5 0:G2579 3.6 39.4 1.0 C5 0:G2578 3.7 40.3 1.0 C6 0:G2578 3.7 41.9 1.0 C2 0:A2577 3.8 33.3 1.0 C4 0:A2577 3.8 34.6 1.0 C4' 0:A2577 3.9 41.3 1.0 N9 0:A2577 4.1 34.6 1.0 C8 0:G2578 4.2 37.3 1.0 C8 0:G2579 4.3 39.1 1.0 C4 0:G2578 4.7 39.8 1.0 N1 0:G2578 4.8 41.6 1.0 N4 0:C2556 4.8 31.9 1.0 N1 0:G2579 4.8 38.2 1.0 O3' 0:A2577 4.8 42.6 1.0 N3 0:U2554 4.8 28.9 1.0 O6 0:G2580 4.9 40.4 1.0 C3' 0:A2577 4.9 41.6 1.0 C5' 0:A2577 4.9 41.2 1.0 C2' 0:A2577 4.9 40.2 1.0 N9 0:G2578 4.9 38.5 1.0 C4 0:G2579 5.0 38.2 1.0 N1 0:A2577 5.0 32.0 1.0

Sodium binding site 10 out of 85 in the Crystal Structure of Virginiamycin M and S Bound to the 50S 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 Crystal Structure of Virginiamycin M and S Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na8511 b:48.6 occ:1.00 N7 0:G2524 2.7 34.3 1.0 O6 0:G2525 2.7 40.6 1.0 C8 0:G2524 3.4 33.6 1.0 C6 0:G2525 3.6 39.9 1.0 C5 0:U2523 3.8 36.8 1.0 C5 0:G2524 3.8 33.5 1.0 OP2 0:G2524 3.9 39.5 1.0 C4 0:U2523 4.0 37.8 1.0 C6 0:U2523 4.2 34.9 1.0 O6 0:G2524 4.3 31.8 1.0 C5 0:G2525 4.3 38.6 1.0 N7 0:G2525 4.4 37.1 1.0 O4 0:U2523 4.4 38.7 1.0 C6 0:G2524 4.4 33.6 1.0 OP2 0:U2523 4.5 38.0 1.0 N3 0:U2523 4.6 37.8 1.0 N1 0:G2525 4.6 39.1 1.0 N9 0:G2524 4.7 33.5 1.0 N1 0:U2523 4.7 36.5 1.0 O2' 0:C2493 4.8 35.8 1.0 C4 0:G2524 4.9 34.0 1.0 C2 0:U2523 4.9 38.1 1.0 O5' 0:U2523 5.0 38.5 1.0

D.Tu, G.Blaha, P.B.Moore, T.A.Steitz. Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide A Structural Explanation For Resistance. Cell(Cambridge,Mass.) V. 121 257 2005.
ISSN: ISSN 0092-8674
PubMed: 15851032
DOI: 10.1016/J.CELL.2005.02.005