Chlorine in PDB 2qex: Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex was solved by S.J.Schroeder, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.92 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	214.620, 304.048, 578.647, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.1

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	116 atoms
Potassium	(K)	2 atoms
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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit (pdb code 2qex). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex:
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 Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8803 b:52.4 occ:1.00 N2 0:G1676 3.3 39.5 1.0 O 0:HOH3393 3.4 47.7 1.0 O 0:HOH9244 3.4 37.6 1.0 O 0:HOH5671 3.5 50.9 1.0 C1' 0:G1452 3.7 42.0 1.0 CE 2:LYS2 3.8 38.8 1.0 O2' 0:G1452 3.9 43.6 1.0 C2 0:A1486 4.1 34.5 1.0 N3 0:A1486 4.1 36.4 1.0 C2 0:G1676 4.3 39.7 1.0 C2' 0:G1452 4.4 41.8 1.0 O4' 0:G1452 4.4 41.0 1.0 N3 0:G1676 4.4 40.6 1.0 N3 0:G1452 4.5 43.3 1.0 O 0:HOH4568 4.6 44.9 1.0 N9 0:G1452 4.6 42.1 1.0 CD 2:LYS2 4.6 36.6 1.0 O2 0:C1451 4.7 45.4 1.0 NZ 2:LYS2 4.7 42.4 1.0 C4 0:G1452 4.9 43.0 1.0

Chlorine binding site 2 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8805 b:58.4 occ:1.00 O 0:HOH4394 3.3 46.5 1.0 N2 0:G201 3.4 46.5 1.0 O 0:HOH3014 3.4 33.6 1.0 O 0:HOH4764 3.4 49.9 1.0 C5' 0:G229 3.7 41.3 1.0 C1' 0:U202 3.7 48.2 1.0 O4' 0:U202 3.7 48.7 1.0 C5 0:C197 3.9 53.1 1.0 C4' 0:G229 4.1 41.4 1.0 O3' 0:G229 4.1 40.7 1.0 O2' 0:U202 4.3 49.5 1.0 C2 0:G201 4.5 46.1 1.0 O2 0:U202 4.5 48.3 1.0 N4 0:C197 4.5 51.8 1.0 N1 0:U202 4.6 47.7 1.0 N3 0:G201 4.6 47.1 1.0 C3' 0:G229 4.7 40.9 1.0 C2' 0:U202 4.7 49.3 1.0 C4' 0:U202 4.7 48.6 1.0 C4 0:C197 4.7 53.3 1.0 OP1 0:C230 4.8 44.4 1.0 C6 0:C197 4.8 51.3 1.0 C2 0:U202 4.8 47.0 1.0 O5' 0:G229 4.8 42.3 1.0 O2 0:C195 4.9 41.1 1.0 P 0:C230 5.0 42.8 1.0

Chlorine binding site 3 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8812 b:40.6 occ:1.00 O 0:HOH4953 2.6 31.0 1.0 OG K:SER33 3.1 44.9 1.0 C2 0:A2596 3.5 36.6 1.0 N2 0:G2582 3.5 34.7 1.0 NZ K:LYS14 3.6 32.5 1.0 O K:HOH7499 3.6 39.3 1.0 N3 0:A2596 3.7 35.0 1.0 CB K:SER33 3.9 41.5 1.0 O K:ILE32 3.9 38.8 1.0 CA K:SER33 4.1 39.6 1.0 CD K:LYS14 4.1 31.1 1.0 C1' 0:U2597 4.1 35.8 1.0 CG K:PRO45 4.1 32.9 1.0 CE K:LYS14 4.2 31.7 1.0 O2' 0:U2597 4.2 35.5 1.0 CB K:PRO45 4.3 31.9 1.0 O 0:HOH7193 4.5 0.1 1.0 O2 0:U2597 4.5 37.0 1.0 N1 0:A2596 4.6 35.6 1.0 N3 0:A2583 4.7 32.6 1.0 O4' 0:U2597 4.7 36.8 1.0 C2' 0:U2597 4.8 34.7 1.0 C2 0:G2582 4.8 33.2 1.0 C K:ILE32 4.9 39.0 1.0 N K:VAL34 4.9 38.3 1.0 CG K:LYS14 4.9 30.4 1.0 N K:SER33 5.0 39.3 1.0 N1 0:U2597 5.0 35.5 1.0

Chlorine binding site 4 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8813 b:55.9 occ:1.00 O 0:HOH4515 3.0 0.2 1.0 N1 0:A1329 3.0 29.9 1.0 O 0:HOH4807 3.3 47.4 1.0 C2 0:A1329 3.6 27.5 1.0 O2' 0:G1300 3.6 30.8 1.0 N6 0:A1328 3.6 24.8 1.0 O 0:HOH3461 3.6 26.7 1.0 N2 0:G1299 3.9 28.8 1.0 O Y:HOH8119 4.0 39.3 1.0 C6 0:A1329 4.1 30.4 1.0 C1' 0:G1300 4.1 31.3 1.0 O 0:HOH4688 4.3 40.1 1.0 N6 0:A1329 4.3 30.7 1.0 N1 0:A1330 4.3 28.6 1.0 O4' 0:G1300 4.3 33.0 1.0 C2' 0:G1300 4.5 31.0 1.0 C2 0:A1330 4.7 29.1 1.0 N3 0:G1299 4.8 32.9 1.0 C4' 0:G1300 4.8 32.9 1.0 C2 0:G1299 4.8 31.2 1.0 C6 0:A1328 4.9 23.1 1.0 N3 0:A1329 4.9 29.3 1.0

Chlorine binding site 5 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8814 b:46.2 occ:1.00 O L:HOH8895 2.7 55.4 1.0 ND1 L:HIS13 3.0 23.2 1.0 O2' 0:G644 3.1 26.1 1.0 C2' 0:G644 3.7 24.7 1.0 N9 0:G644 3.8 21.6 1.0 CE1 L:HIS13 3.9 22.0 1.0 C4 0:G644 3.9 21.6 1.0 CG L:GLN7 3.9 33.5 1.0 O L:HOH8888 4.0 65.8 1.0 CG L:HIS13 4.1 23.1 1.0 C8 0:G644 4.1 25.2 1.0 NZ L:LYS4 4.2 44.4 1.0 C5 0:G644 4.2 23.1 1.0 C1' 0:G644 4.2 23.6 1.0 N3 0:G644 4.3 22.6 1.0 CB L:HIS13 4.3 21.5 1.0 CG L:LYS4 4.3 33.2 1.0 N7 0:G644 4.4 24.5 1.0 CB L:GLN7 4.6 31.3 1.0 O 0:HOH3013 4.8 39.4 1.0 C2 0:G644 4.9 23.1 1.0 CE L:LYS4 4.9 39.5 1.0 CD L:GLN7 4.9 35.2 1.0 C6 0:G644 4.9 23.0 1.0

Chlorine binding site 6 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8815 b:61.3 occ:1.00 N6 0:A1598 3.3 43.6 1.0 N2 0:G1646 3.3 51.2 1.0 N6 0:A1597 3.6 45.3 1.0 O 0:HOH6634 3.8 58.3 1.0 C1' 0:G1647 4.0 48.6 1.0 O4' 0:G1647 4.1 48.3 1.0 N7 0:A1597 4.2 43.4 1.0 C1' 0:G1540 4.3 51.8 1.0 C6 0:A1598 4.3 42.0 1.0 C2 0:G1646 4.3 52.3 1.0 N3 0:G1646 4.5 51.4 1.0 C6 0:A1597 4.6 44.4 1.0 N3 0:G1540 4.6 53.0 1.0 O4' 0:G1540 4.7 51.0 1.0 O2' 0:G1540 4.8 51.7 1.0 C5 0:A1597 4.8 44.1 1.0 N9 0:G1647 4.8 48.7 1.0 O2' 0:G1647 4.9 47.8 1.0 N9 0:G1540 4.9 52.3 1.0

Chlorine binding site 7 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8816 b:57.5 occ:1.00 O2' 0:G1119 3.0 32.5 1.0 NZ J:LYS56 3.4 45.7 1.0 N4 0:C1243 3.4 34.4 1.0 C8 0:G1119 3.5 25.1 1.0 C2' 0:G1119 3.8 32.6 1.0 O 0:HOH6786 3.9 57.1 1.0 OE1 J:GLN52 3.9 41.4 1.0 NE2 J:GLN52 3.9 43.8 1.0 CD J:LYS56 4.0 44.2 1.0 N7 0:G1119 4.1 25.8 1.0 CE J:LYS56 4.2 44.2 1.0 N9 0:G1119 4.2 26.0 1.0 CD J:GLN52 4.4 42.8 1.0 C1' 0:G1119 4.5 29.8 1.0 C4 0:C1243 4.6 36.9 1.0 C5 0:C1243 4.9 36.2 1.0

Chlorine binding site 8 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8817 b:59.3 occ:1.00 O Y:HOH8137 2.7 87.1 1.0 O2' 0:C594 2.8 41.1 1.0 O Y:HOH8175 3.4 29.6 1.0 O Y:HOH8121 3.5 40.7 1.0 O4' 0:U595 3.6 44.1 1.0 C5' 0:U595 3.8 43.5 1.0 C4' 0:U595 3.8 44.2 1.0 CG Y:ARG115 3.8 41.7 1.0 NE Y:ARG115 3.9 42.9 1.0 C2' 0:C594 3.9 44.4 1.0 NH2 Y:ARG122 3.9 50.2 1.0 CD Y:ARG115 4.1 40.4 1.0 O 0:HOH6381 4.4 53.6 1.0 O2 0:C594 4.7 47.6 1.0 C1' 0:C594 4.7 45.6 1.0 C1' 0:U595 4.8 45.8 1.0 O5' 0:U595 4.9 44.0 1.0 CZ Y:ARG115 4.9 45.4 1.0 CZ Y:ARG122 4.9 48.9 1.0 NE2 Y:GLN119 5.0 32.7 1.0

Chlorine binding site 9 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8820 b:36.8 occ:1.00 O 0:HOH4792 3.2 23.4 1.0 C5' 0:G1269 3.6 34.1 1.0 O 0:HOH3200 3.6 33.8 1.0 NE Y:ARG169 3.7 37.0 1.0 O 0:HOH3461 3.8 26.7 1.0 N6 0:A1328 3.9 24.8 1.0 NH2 Y:ARG169 3.9 41.1 1.0 C4' 0:G1269 3.9 34.0 1.0 O3' 0:G1269 4.0 30.5 1.0 C6 0:A1328 4.2 23.1 1.0 CZ Y:ARG169 4.3 38.9 1.0 N1 0:A1328 4.5 22.5 1.0 MG 0:MG8075 4.5 57.6 1.0 C3' 0:G1269 4.5 32.4 1.0 CG Y:ARG169 4.6 37.5 1.0 CD Y:ARG169 4.7 37.7 1.0 O5' 0:G1269 4.8 33.3 1.0 OP1 0:U1270 4.8 29.3 1.0 C5 0:A1328 4.9 22.3 1.0 P 0:U1270 5.0 31.3 1.0 OP1 0:G1269 5.0 36.2 1.0

Chlorine binding site 10 out of 22 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:Cl8822 b:71.0 occ:1.00 N1 0:G1072 3.0 21.8 1.0 O 0:HOH5185 3.4 39.0 1.0 O2' 0:G1087 3.4 36.0 1.0 N2 0:G1072 3.5 19.3 1.0 C8 0:G1087 3.5 32.9 1.0 C2 0:G1072 3.7 22.0 1.0 N7 0:A1291 3.8 35.2 1.0 N7 0:G1087 3.9 32.4 1.0 O6 0:G1072 4.0 25.5 1.0 C6 0:G1072 4.0 22.7 1.0 C2' 0:G1087 4.0 35.6 1.0 N9 0:G1087 4.0 32.3 1.0 C5 0:A1291 4.0 34.4 1.0 O 0:HOH8964 4.2 65.1 1.0 C8 0:A1291 4.3 34.9 1.0 C6 0:A1291 4.4 34.3 1.0 N6 0:A1291 4.4 34.2 1.0 C1' 0:G1087 4.4 33.7 1.0 C5 0:G1087 4.6 31.7 1.0 O 0:HOH3868 4.6 62.5 1.0 C4 0:G1087 4.6 31.3 1.0 C4 0:A1291 4.7 33.8 1.0 N9 0:A1291 4.8 33.7 1.0

S.J.Schroeder, G.Blaha, P.B.Moore. Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit. Antimicrob.Agents Chemother. V. 51 4462 2007.
ISSN: ISSN 0066-4804
PubMed: 17664317
DOI: 10.1128/AAC.00455-07