Chlorine 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
Sodium	(Na)	86 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M, PDB code: 1n8r:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8503 b:39.2 occ:1.00 N2 A:G1676 3.0 31.2 1.0 O A:HOH9815 3.3 14.7 1.0 O A:HOH6202 3.4 45.5 1.0 C1' A:G1452 3.6 36.0 1.0 CE 3:LYS2 3.9 27.0 1.0 O A:HOH3960 4.0 41.7 1.0 O2' A:G1452 4.0 35.9 1.0 C2 A:G1676 4.0 32.2 1.0 C2 A:A1486 4.1 29.5 1.0 O A:HOH7957 4.1 32.4 1.0 N3 A:A1486 4.1 29.5 1.0 N3 A:G1676 4.2 32.6 1.0 O4' A:G1452 4.3 35.9 1.0 C2' A:G1452 4.3 35.2 1.0 O A:HOH5099 4.4 57.4 1.0 O2 A:C1451 4.4 36.4 1.0 N9 A:G1452 4.4 36.8 1.0 N3 A:G1452 4.5 37.4 1.0 O A:HOH7170 4.6 44.5 1.0 CD 3:LYS2 4.7 24.6 1.0 C4 A:G1452 4.8 37.1 1.0 NZ 3:LYS2 4.9 28.5 1.0

Chlorine binding site 2 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8505 b:45.4 occ:1.00 O A:HOH5297 2.8 24.9 1.0 N2 A:G201 2.8 40.3 1.0 O A:HOH3572 3.3 22.1 1.0 O A:HOH4928 3.3 24.1 1.0 C1' A:U202 3.8 37.8 1.0 C5' A:G229 3.8 35.7 1.0 C5 A:C197 3.8 45.5 1.0 O4' A:U202 3.9 39.4 1.0 C2 A:G201 3.9 41.1 1.0 N3 A:G201 4.1 41.2 1.0 C4' A:G229 4.3 35.7 1.0 O2 A:U202 4.4 40.0 1.0 N1 A:U202 4.4 37.6 1.0 O A:HOH3142 4.4 23.7 1.0 O2 A:C195 4.4 30.2 1.0 O3' A:G229 4.4 36.1 1.0 C6 A:C197 4.5 44.5 1.0 C2 A:U202 4.6 38.5 1.0 N1 A:A199 4.6 51.1 1.0 O2' A:U202 4.6 37.3 1.0 N4 A:C197 4.8 46.3 1.0 C4 A:C197 4.8 45.7 1.0 OP1 A:G229 4.8 35.1 1.0 C2 A:A199 4.8 50.7 1.0 C2' A:U202 4.9 36.9 1.0 C4' A:U202 5.0 38.8 1.0 C3' A:G229 5.0 36.1 1.0

Chlorine binding site 3 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8511 b:52.6 occ:1.00 O A:HOH3551 2.9 18.8 1.0 N R:HIS53 3.3 31.0 1.0 O2' A:C2388 3.3 21.6 1.0 CE2 R:PHE56 3.6 22.1 1.0 CB R:PHE52 3.7 31.7 1.0 C4' A:C2388 3.7 25.3 1.0 O4' A:C2388 3.8 25.2 1.0 CA R:PHE52 3.8 32.8 1.0 CD2 R:PHE56 3.8 21.2 1.0 CG2 R:ILE84 3.9 30.2 1.0 C R:PHE52 4.0 31.8 1.0 CB R:HIS53 4.0 31.4 1.0 C1' A:C2388 4.1 24.7 1.0 C2' A:C2388 4.2 23.8 1.0 CA R:HIS53 4.3 29.8 1.0 O R:HOH3082 4.4 52.3 1.0 CG1 R:ILE84 4.4 31.6 1.0 C3' A:C2388 4.5 23.8 1.0 CB R:ILE84 4.5 30.9 1.0 CD1 R:ILE84 4.6 33.6 1.0 C5' A:C2388 4.7 26.5 1.0 CA R:ILE84 4.7 29.6 1.0 O3' A:C2388 4.8 24.3 1.0 O A:HOH3979 4.9 46.3 1.0 CZ R:PHE56 4.9 19.4 1.0 CG R:PHE52 4.9 32.0 1.0 O A:HOH3535 5.0 40.7 1.0

Chlorine binding site 4 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8513 b:46.4 occ:1.00 O A:HOH5049 2.7 91.7 1.0 N1 A:A1329 3.0 23.9 1.0 O2' A:G1300 3.3 16.9 1.0 O A:HOH5341 3.5 45.1 1.0 C2 A:A1329 3.6 23.0 1.0 N2 A:G1299 3.6 25.8 1.0 C1' A:G1300 3.6 22.2 1.0 N6 A:A1328 3.8 20.4 1.0 O4' A:G1300 3.9 22.6 1.0 O A:HOH4032 3.9 32.3 1.0 N1 A:A1330 4.0 25.9 1.0 C2' A:G1300 4.1 19.9 1.0 C6 A:A1329 4.1 24.8 1.0 O Z:HOH8536 4.2 30.5 1.0 N6 A:A1329 4.3 26.6 1.0 C2 A:A1330 4.4 24.7 1.0 N3 A:G1299 4.4 26.4 1.0 C4' A:G1300 4.4 22.1 1.0 C2 A:G1299 4.5 26.6 1.0 O A:HOH5218 4.7 49.3 1.0 N9 A:G1300 4.9 24.9 1.0 N3 A:A1329 4.9 24.6 1.0

Chlorine binding site 5 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8514 b:47.1 occ:1.00 O2' A:G644 2.8 18.4 1.0 ND1 M:HIS13 2.9 16.8 1.0 O A:HOH8209 3.3 38.6 1.0 C2' A:G644 3.5 15.6 1.0 N9 A:G644 3.7 15.7 1.0 CE1 M:HIS13 3.8 16.5 1.0 C4 A:G644 3.9 16.6 1.0 CG M:GLN7 3.9 26.9 1.0 CG M:HIS13 3.9 18.0 1.0 C1' A:G644 4.0 15.4 1.0 CB M:HIS13 4.1 17.0 1.0 C8 A:G644 4.1 17.7 1.0 N3 A:G644 4.2 17.1 1.0 CG M:LYS4 4.2 24.9 1.0 CB M:GLN7 4.3 23.2 1.0 C5 A:G644 4.3 17.9 1.0 N7 A:G644 4.5 17.2 1.0 CA M:LYS4 4.7 25.3 1.0 O A:HOH3571 4.7 33.6 1.0 CB M:LYS4 4.8 23.8 1.0 C2 A:G644 4.9 17.6 1.0 C3' A:G644 4.9 16.0 1.0 CD M:LYS4 5.0 25.7 1.0 CE M:LYS4 5.0 27.3 1.0

Chlorine binding site 6 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8515 b:66.9 occ:1.00 N6 A:A1597 3.2 33.7 1.0 N6 A:A1598 3.3 38.7 1.0 N2 A:G1646 3.3 42.1 1.0 O A:HOH7165 3.5 57.1 1.0 N7 A:A1597 3.7 34.4 1.0 C1' A:G1540 4.0 43.0 1.0 C6 A:A1598 4.1 37.4 1.0 C6 A:A1597 4.1 33.8 1.0 C1' A:G1647 4.3 41.5 1.0 C5 A:A1597 4.3 33.7 1.0 C2 A:G1646 4.3 43.6 1.0 O4' A:G1647 4.4 41.6 1.0 O4' A:G1540 4.4 41.2 1.0 N3 A:G1646 4.5 43.3 1.0 O2' A:U1596 4.6 46.0 1.0 O2' A:G1540 4.6 43.5 1.0 N9 A:G1540 4.7 45.6 1.0 N3 A:G1540 4.7 47.8 1.0 C5 A:A1598 4.7 36.7 1.0 N1 A:A1598 4.8 37.3 1.0 N7 A:A1598 4.9 37.1 1.0 C8 A:A1597 4.9 34.8 1.0 C4 A:G1540 5.0 47.6 1.0 N9 A:G1647 5.0 41.6 1.0 C2' A:G1540 5.0 41.6 1.0

Chlorine binding site 7 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8516 b:45.5 occ:1.00 O2' A:G1119 3.2 22.2 1.0 C8 A:G1119 3.4 19.2 1.0 NZ K:LYS56 3.4 31.5 1.0 CD K:LYS56 3.6 31.9 1.0 NE2 K:GLN52 3.6 39.1 1.0 N4 A:C1243 3.7 27.9 1.0 C2' A:G1119 3.8 22.3 1.0 OE1 K:GLN52 4.0 38.4 1.0 CE K:LYS56 4.0 32.1 1.0 N7 A:G1119 4.0 19.1 1.0 N9 A:G1119 4.1 20.0 1.0 CD K:GLN52 4.2 38.7 1.0 C1' A:G1119 4.4 21.3 1.0 C4 A:C1243 4.7 26.8 1.0 C5 A:C1243 4.7 26.7 1.0 CG K:LYS56 4.9 31.8 1.0 C5 A:G1119 5.0 18.9 1.0 O A:HOH3837 5.0 24.4 1.0 N6 A:A1242 5.0 22.4 1.0

Chlorine binding site 8 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl8522 b:78.2 occ:1.00 N1 A:G1072 3.1 19.2 1.0 N2 A:G1072 3.2 18.9 1.0 O2' A:G1087 3.3 24.8 1.0 N7 A:A1291 3.5 28.8 1.0 C8 A:G1087 3.6 25.2 1.0 C2 A:G1072 3.6 19.6 1.0 O A:HOH5718 3.7 40.5 1.0 C2' A:G1087 3.7 23.8 1.0 O A:HOH9546 3.8 42.1 1.0 N9 A:G1087 3.9 23.7 1.0 C5 A:A1291 3.9 27.8 1.0 N7 A:G1087 4.0 24.5 1.0 C8 A:A1291 4.1 26.6 1.0 C6 A:G1072 4.1 20.6 1.0 N6 A:A1291 4.2 27.5 1.0 O6 A:G1072 4.2 22.1 1.0 C1' A:G1087 4.3 23.6 1.0 OE2 X:GLU10 4.3 31.3 1.0 C6 A:A1291 4.3 28.1 1.0 C4 A:G1087 4.6 24.1 1.0 C5 A:G1087 4.6 24.9 1.0 O A:HOH4422 4.7 46.3 1.0 C4 A:A1291 4.7 26.2 1.0 N9 A:A1291 4.8 25.8 1.0 O A:HOH5531 4.9 52.4 1.0 N3 A:G1072 4.9 19.4 1.0

Chlorine binding site 9 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 C:Cl8509 b:77.4 occ:1.00 NZ C:LYS178 3.1 31.7 1.0 O A:HOH6783 3.5 39.0 1.0 CD C:LYS178 3.7 30.4 1.0 CE C:LYS178 3.7 30.9 1.0 CE C:LYS175 3.7 25.7 1.0 O A:HOH5618 4.0 36.3 1.0 CZ C:PHE169 4.2 22.6 1.0 CD C:LYS175 4.4 23.7 1.0 CE1 C:PHE169 4.4 23.9 1.0 O C:HOH8583 4.4 46.6 1.0 SD C:MET179 4.6 28.3 1.0 OP2 A:G1878 4.6 34.6 1.0 CE C:MET179 4.7 30.7 1.0 O A:HOH7034 4.9 44.8 1.0 O A:HOH3438 4.9 21.3 1.0 CG C:LYS178 4.9 29.7 1.0

Chlorine binding site 10 out of 22 in the Structure of Large Ribosomal Subunit in Complex with Virginiamycin M


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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 D:Cl8519 b:60.4 occ:1.00 O A:HOH3042 2.7 21.4 1.0 O A:HOH9974 3.2 29.0 1.0 N D:LYS224 3.3 26.9 1.0 O D:HOH8584 3.5 28.0 1.0 CA D:ARG223 3.5 26.7 1.0 CB D:HIS227 3.8 19.4 1.0 CD2 D:HIS227 3.8 17.7 1.0 O2' A:U2545 3.9 26.1 1.0 CD D:ARG223 3.9 31.2 1.0 C D:ARG223 3.9 28.2 1.0 CG D:HIS227 4.0 17.8 1.0 O A:HOH6539 4.0 38.2 1.0 CB D:ARG223 4.1 28.1 1.0 C4' A:U2546 4.3 21.8 1.0 O4' A:U2546 4.3 21.3 1.0 CA D:LYS224 4.4 25.5 1.0 O D:LYS224 4.4 28.2 1.0 C5' A:U2546 4.5 23.1 1.0 CG D:ARG223 4.6 31.1 1.0 CB D:LYS224 4.6 24.5 1.0 O D:LYS222 4.6 23.5 1.0 N D:ARG223 4.7 24.5 1.0 NE2 D:HIS227 4.8 18.6 1.0 N2 A:G2613 4.8 27.0 1.0 C D:LYS224 4.9 25.3 1.0 NE D:ARG223 4.9 30.5 1.0 C2' A:U2545 5.0 25.5 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