Chlorine in PDB 1k8a: Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k8a was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.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 (%)	22.7 / 26.5

The structure of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	119 atoms
Potassium	(K)	3 atoms
Cadmium	(Cd)	5 atoms
Sodium	(Na)	83 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Chlorine atom in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1k8a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 23 binding sites of Chlorine where determined in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1k8a:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8503 b:63.6 occ:1.00 N2 A:G1676 3.1 53.4 1.0 O A:HOH5388 3.4 55.9 1.0 O A:HOH9009 3.5 96.6 1.0 C1' A:G1452 3.6 51.3 1.0 O A:HOH3156 3.9 50.6 1.0 O A:HOH7133 3.9 42.9 1.0 CE 3:LYS2 4.0 45.1 1.0 C2 A:G1676 4.2 52.3 1.0 O2' A:G1452 4.2 53.2 1.0 O4' A:G1452 4.2 51.6 1.0 C2 A:A1486 4.3 44.1 1.0 N3 A:A1486 4.3 46.1 1.0 O2 A:C1451 4.3 55.6 1.0 N3 A:G1676 4.3 52.5 1.0 O A:HOH4293 4.4 75.1 1.0 C2' A:G1452 4.4 50.9 1.0 N9 A:G1452 4.4 51.7 1.0 N3 A:G1452 4.5 50.3 1.0 O A:HOH6349 4.7 54.5 1.0 C4 A:G1452 4.8 51.2 1.0 CD 3:LYS2 4.9 42.3 1.0 NZ 3:LYS2 5.0 46.6 1.0

Chlorine binding site 2 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8505 b:95.3 occ:1.00 O A:HOH4491 3.0 62.8 1.0 N2 A:G201 3.2 70.2 1.0 O A:HOH9769 3.5 25.8 1.0 C1' A:U202 3.7 63.4 1.0 O4' A:U202 3.7 63.7 1.0 C5' A:G229 3.7 59.5 1.0 C5 A:C197 3.7 58.7 1.0 O A:HOH4122 4.0 51.0 1.0 C4' A:G229 4.1 59.5 1.0 O3' A:G229 4.1 58.6 1.0 C2 A:G201 4.3 70.1 1.0 O A:HOH9338 4.4 41.2 1.0 N3 A:G201 4.4 70.5 1.0 N1 A:U202 4.4 64.2 1.0 O2 A:U202 4.4 67.2 1.0 C6 A:C197 4.5 58.4 1.0 O2' A:U202 4.5 62.0 1.0 N4 A:C197 4.6 57.7 1.0 C4 A:C197 4.7 58.1 1.0 C2 A:U202 4.7 65.9 1.0 C3' A:G229 4.7 59.6 1.0 C4' A:U202 4.7 63.1 1.0 C2' A:U202 4.8 62.7 1.0 O2 A:C195 4.8 61.2 1.0 N1 A:A199 4.8 74.7 1.0 OP1 A:G229 4.9 57.4 1.0 OP1 A:C230 4.9 59.8 1.0 O5' A:G229 5.0 57.3 1.0 C2 A:A199 5.0 75.1 1.0

Chlorine binding site 3 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8512 b:39.1 occ:1.00 O A:HOH4679 3.2 38.4 1.0 C2 A:A2596 3.2 48.3 1.0 O A:HOH7144 3.3 36.7 1.0 NZ L:LYS14 3.3 33.1 1.0 OG L:SER33 3.3 47.5 1.0 N2 A:G2582 3.3 43.1 1.0 N3 A:A2596 3.4 48.8 1.0 O L:ILE32 3.8 42.8 1.0 CB L:SER33 3.8 45.6 1.0 C1' A:U2597 3.9 47.9 1.0 CA L:SER33 4.1 44.6 1.0 CE L:LYS14 4.1 35.0 1.0 CD L:LYS14 4.1 35.5 1.0 CG L:PRO45 4.1 42.8 1.0 CB L:PRO45 4.3 43.0 1.0 O2 A:U2597 4.3 49.5 1.0 N1 A:A2596 4.3 48.6 1.0 N3 A:A2583 4.5 39.0 1.0 C2 A:G2582 4.5 41.6 1.0 O2' A:U2597 4.5 50.3 1.0 O4' A:U2597 4.6 46.1 1.0 N1 A:U2597 4.6 49.3 1.0 O L:HOH7169 4.7 0.4 1.0 C4 A:A2596 4.7 48.8 1.0 C L:ILE32 4.8 42.6 1.0 C2 A:U2597 4.8 49.1 1.0 C2' A:U2597 4.8 46.3 1.0 C1' A:A2583 4.9 39.3 1.0 CG L:LYS14 4.9 34.1 1.0 N1 A:G2582 4.9 40.7 1.0 N L:SER33 5.0 43.3 1.0

Chlorine binding site 4 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8513 b:60.2 occ:1.00 O A:HOH4243 2.6 0.7 1.0 N1 A:A1329 2.9 34.1 1.0 C2 A:A1329 3.5 32.0 1.0 O2' A:G1300 3.5 39.6 1.0 O A:HOH4534 3.6 48.8 1.0 N2 A:G1299 3.6 34.5 1.0 N6 A:A1328 3.7 39.8 1.0 O A:HOH3227 3.8 29.3 1.0 C1' A:G1300 3.8 40.8 1.0 O4' A:G1300 4.0 38.9 1.0 C6 A:A1329 4.0 35.1 1.0 N1 A:A1330 4.1 36.8 1.0 O A:HOH9385 4.1 41.6 1.0 N6 A:A1329 4.2 37.6 1.0 C2' A:G1300 4.3 39.9 1.0 N3 A:G1299 4.4 36.3 1.0 C2 A:G1299 4.4 35.2 1.0 C2 A:A1330 4.5 35.8 1.0 C4' A:G1300 4.6 39.1 1.0 N3 A:A1329 4.9 33.1 1.0 C6 A:A1328 5.0 37.2 1.0

Chlorine binding site 5 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8514 b:57.4 occ:1.00 O A:HOH7276 3.0 48.9 1.0 ND1 M:HIS13 3.3 34.8 1.0 O2' A:G644 3.3 31.5 1.0 CG M:GLN7 3.7 37.1 1.0 O A:HOH9768 4.0 45.5 1.0 CB M:HIS13 4.1 33.2 1.0 CG M:HIS13 4.1 34.0 1.0 CG M:LYS4 4.1 32.9 1.0 C2' A:G644 4.2 29.4 1.0 CE1 M:HIS13 4.2 33.9 1.0 N9 A:G644 4.3 29.7 1.0 C4 A:G644 4.3 29.4 1.0 CB M:GLN7 4.4 35.2 1.0 C8 A:G644 4.5 30.4 1.0 C5 A:G644 4.6 30.1 1.0 O M:HIS13 4.6 34.3 1.0 C1' A:G644 4.6 29.7 1.0 CA M:LYS4 4.6 34.0 1.0 O A:HOH6654 4.7 89.9 1.0 CD M:GLN7 4.7 39.0 1.0 N7 A:G644 4.7 29.4 1.0 N3 A:G644 4.8 29.5 1.0 CB M:LYS4 4.8 32.9 1.0 OE1 M:GLN7 5.0 40.5 1.0

Chlorine binding site 6 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8515 b:92.7 occ:1.00 N6 A:A1598 3.2 61.0 1.0 N2 A:G1646 3.5 58.8 1.0 N6 A:A1597 3.7 55.7 1.0 O4' A:G1647 3.9 57.6 1.0 C1' A:G1647 3.9 56.9 1.0 O A:HOH6344 3.9 99.8 1.0 C6 A:A1598 4.2 58.9 1.0 N7 A:A1597 4.4 56.1 1.0 N3 A:G1646 4.5 60.7 1.0 C2 A:G1646 4.5 60.2 1.0 C1' A:G1540 4.6 64.3 1.0 O2' A:G1647 4.7 53.8 1.0 C6 A:A1597 4.7 55.5 1.0 N9 A:G1647 4.8 56.8 1.0 N3 A:G1540 4.8 65.5 1.0 O2' A:U1596 4.8 66.5 1.0 N1 A:A1598 4.9 58.4 1.0 C5 A:A1597 4.9 56.0 1.0 C4' A:G1647 5.0 55.9 1.0 C2' A:G1647 5.0 55.8 1.0 C5 A:A1598 5.0 57.9 1.0

Chlorine binding site 7 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8516 b:43.7 occ:1.00 O2' A:G1119 3.1 38.9 1.0 NZ K:LYS56 3.3 46.0 1.0 C8 A:G1119 3.6 34.3 1.0 N4 A:C1243 3.6 38.1 1.0 CD K:LYS56 3.7 43.6 1.0 C2' A:G1119 3.9 36.8 1.0 CE K:LYS56 4.0 44.1 1.0 NE2 K:GLN52 4.0 51.3 1.0 N7 A:G1119 4.1 33.6 1.0 OE1 K:GLN52 4.2 48.0 1.0 N9 A:G1119 4.3 34.6 1.0 CD K:GLN52 4.6 49.3 1.0 O A:HOH6496 4.6 55.9 1.0 C4 A:C1243 4.6 38.7 1.0 C1' A:G1119 4.6 35.3 1.0 C5 A:C1243 4.7 39.4 1.0 N6 A:A1242 4.7 30.6 1.0 N7 A:A1242 5.0 33.3 1.0 CG K:LYS56 5.0 41.6 1.0

Chlorine binding site 8 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8517 b:52.2 occ:1.00 O2' A:C594 2.9 48.7 1.0 O Z:HOH8556 3.0 89.1 1.0 O Z:HOH8533 3.3 49.8 1.0 O4' A:U595 3.5 58.9 1.0 CG Z:ARG115 3.6 47.9 1.0 C4' A:U595 3.7 56.6 1.0 C5' A:U595 3.7 51.8 1.0 CD Z:ARG115 3.7 48.0 1.0 C2' A:C594 3.8 49.0 1.0 O Z:HOH8600 3.8 30.8 1.0 NH2 Z:ARG122 3.8 50.0 1.0 NE Z:ARG115 3.8 48.4 1.0 O A:HOH6090 4.3 65.0 1.0 O A:HOH5846 4.4 59.8 1.0 O2 A:C594 4.5 53.6 1.0 C1' A:C594 4.7 49.8 1.0 C1' A:U595 4.7 60.5 1.0 O5' A:U595 4.9 47.3 1.0 CZ Z:ARG115 4.9 48.9 1.0 CB Z:ARG115 4.9 48.5 1.0 CZ Z:ARG122 5.0 49.3 1.0

Chlorine binding site 9 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8522 b:83.7 occ:1.00 O A:HOH4908 3.3 68.9 1.0 N1 A:G1072 3.3 26.7 1.0 O2' A:G1087 3.4 40.6 1.0 N2 A:G1072 3.5 22.7 1.0 C8 A:G1087 3.6 38.0 1.0 N7 A:A1291 3.7 43.2 1.0 C2' A:G1087 3.8 39.5 1.0 O A:HOH8743 3.9 38.5 1.0 C2 A:G1072 3.9 25.3 1.0 N9 A:G1087 4.1 38.5 1.0 N7 A:G1087 4.1 38.0 1.0 OE2 X:GLU10 4.2 44.4 1.0 C5 A:A1291 4.2 42.8 1.0 C8 A:A1291 4.3 42.1 1.0 C6 A:G1072 4.3 28.6 1.0 N6 A:A1291 4.4 45.6 1.0 O6 A:G1072 4.4 30.0 1.0 C1' A:G1087 4.4 39.5 1.0 C6 A:A1291 4.6 43.7 1.0 C5 A:G1087 4.8 38.3 1.0 C4 A:G1087 4.8 38.0 1.0 O A:HOH3613 4.9 34.5 1.0

Chlorine binding site 10 out of 23 in the Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Co-Crystal Structure of Carbomycin A Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl8523 b:56.6 occ:1.00 C2 A:CAI4000 3.2 55.0 1.0 C1' A:G2646 3.5 34.5 1.0 C4 A:CAI4000 3.7 48.9 1.0 C3 A:CAI4000 3.8 51.8 1.0 N2 A:G2099 3.8 41.8 1.0 C7 A:CAI4000 3.8 51.2 1.0 C10 A:CAI4000 3.9 57.3 1.0 N9 A:G2646 3.9 34.2 1.0 O15 A:CAI4000 4.1 59.5 1.0 C19 A:CAI4000 4.1 48.0 1.0 O4' A:G2646 4.1 33.6 1.0 C1 A:CAI4000 4.1 57.2 1.0 C4 A:G2646 4.2 34.0 1.0 N3 A:G2646 4.2 35.5 1.0 O2' A:G2646 4.3 36.2 1.0 C12 A:CAI4000 4.4 60.5 1.0 C22 A:CAI4000 4.4 53.6 1.0 C2' A:G2646 4.5 34.1 1.0 C11 A:CAI4000 4.5 59.6 1.0 O4 A:CAI4000 4.5 47.0 1.0 C8 A:CAI4000 4.6 53.8 1.0 C6 A:CAI4000 4.6 47.2 1.0 C5 A:CAI4000 4.6 47.4 1.0 C8 A:G2646 4.7 34.1 1.0 C9 A:CAI4000 4.7 56.1 1.0 C2 A:G2099 4.8 40.3 1.0 N3 A:G2099 4.8 38.2 1.0 O A:HOH9573 5.0 58.0 1.0 O1A A:CAI4000 5.0 43.6 1.0

J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz. The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit. Mol.Cell V. 10 117 2002.
ISSN: ISSN 1097-2765
PubMed: 12150912
DOI: 10.1016/S1097-2765(02)00570-1