Sodium in PDB 1kd1: Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui

The structure of Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1 was solved by J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, 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)	19.99 / 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 / 26.9

The structure of Co-Crystal Structure of Spiramycin 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
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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1kd1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 85 binding sites of Sodium where determined in the Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1kd1:
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 Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8301 b:43.5 occ:1.00 O A:HOH4974 2.1 57.4 1.0 OP2 A:C1069 2.6 26.1 1.0 O A:HOH3199 2.7 79.2 1.0 N7 A:G1072 2.8 33.8 1.0 O6 A:G1072 3.0 33.6 1.0 O A:HOH3166 3.1 30.7 1.0 O6 A:G1087 3.1 39.3 1.0 C5 A:G1072 3.4 33.4 1.0 C6 A:G1072 3.5 32.2 1.0 O A:HOH9069 3.6 23.0 1.0 C8 A:G1072 3.9 34.4 1.0 O A:HOH3532 4.0 56.3 1.0 P A:C1069 4.0 27.0 1.0 C6 A:G1087 4.1 38.8 1.0 C5' A:C1068 4.3 38.1 1.0 C3' A:C1068 4.5 33.4 1.0 O3' A:C1068 4.6 29.8 1.0 C4 A:G1072 4.6 33.2 1.0 OP1 A:C1069 4.7 26.9 1.0 O A:HOH4265 4.7 46.7 1.0 OP2 A:C1068 4.7 43.0 1.0 N1 A:G1087 4.8 37.6 1.0 N1 A:G1072 4.8 30.2 1.0 N9 A:G1072 4.8 32.9 1.0 N6 A:A1070 5.0 33.7 1.0

Sodium binding site 2 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8302 b:40.4 occ:1.00 O2' A:G1119 2.7 41.4 1.0 O A:HOH5681 2.7 54.3 1.0 OP2 A:U1120 2.9 39.0 1.0 O3' A:G1119 3.0 41.3 1.0 O A:HOH7790 3.0 70.2 1.0 O6 A:G1121 3.1 41.5 1.0 O A:HOH4162 3.2 53.5 1.0 O A:HOH4539 3.4 35.6 1.0 N7 A:G1121 3.4 40.2 1.0 P A:U1120 3.5 39.5 1.0 C2' A:G1119 3.7 41.0 1.0 MG A:MG8025 3.8 60.3 1.0 O4 A:U1122 3.8 43.6 1.0 C6 A:G1121 3.8 40.5 1.0 C3' A:G1119 3.9 42.2 1.0 C5 A:G1121 4.0 39.6 1.0 O A:HOH6929 4.3 53.1 1.0 C1' A:G1119 4.3 40.9 1.0 OP1 A:U1120 4.3 41.6 1.0 C4 A:U1122 4.6 41.5 1.0 C8 A:G1121 4.6 39.2 1.0 O5' A:U1120 4.7 37.9 1.0 O A:HOH7789 4.9 32.9 1.0 C5' A:U1120 4.9 40.2 1.0 OP1 A:C1238 4.9 39.3 1.0 C5 A:U1122 4.9 41.0 1.0

Sodium binding site 3 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8303 b:51.0 occ:1.00 OP1 A:G644 2.7 27.4 1.0 O4 A:U904 2.9 29.1 1.0 OP2 A:A643 3.0 33.6 1.0 NH2 M:ARG8 3.2 39.9 1.0 O A:HOH3259 3.2 32.2 1.0 O5' A:A643 3.3 30.9 1.0 OP1 A:G1354 3.3 36.9 1.0 P A:A643 3.5 33.0 1.0 OP1 A:A643 3.8 32.7 1.0 C4 A:U904 3.9 29.6 1.0 P A:G644 3.9 29.8 1.0 OP1 A:C1353 4.1 54.0 1.0 O A:HOH4593 4.2 82.9 1.0 C5' A:A643 4.2 30.3 1.0 N3 A:U904 4.2 29.3 1.0 O A:HOH9423 4.2 30.8 1.0 CZ M:ARG8 4.2 38.9 1.0 C3' A:A643 4.3 30.7 1.0 P A:G1354 4.4 35.5 1.0 O3' A:A643 4.4 30.2 1.0 OP2 A:G644 4.5 27.1 1.0 OP2 A:G1354 4.7 36.3 1.0 C4' A:A643 4.8 30.9 1.0 NE M:ARG8 4.9 37.9 1.0 NH1 M:ARG8 5.0 40.6 1.0 O3' A:C1353 5.0 37.5 1.0

Sodium binding site 4 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8305 b:34.2 occ:1.00 O A:HOH5784 2.1 56.2 1.0 O A:HOH4082 2.2 49.0 1.0 O2' A:A631 2.7 34.9 1.0 N3 A:A630 2.7 34.4 1.0 O A:HOH4697 2.9 50.8 1.0 O2' A:A630 3.2 35.2 1.0 OP2 A:A2074 3.4 31.5 1.0 C2' A:A631 3.5 33.9 1.0 C2 A:A630 3.6 32.5 1.0 C1' A:A630 3.6 33.6 1.0 C4 A:A630 3.8 34.7 1.0 N2 A:G2070 3.8 26.7 1.0 C2' A:A630 4.0 35.2 1.0 C3' A:A631 4.1 34.6 1.0 N9 A:A630 4.1 34.6 1.0 O3' A:A630 4.1 33.4 1.0 OP1 A:A632 4.2 36.7 1.0 OP2 A:G2072 4.4 41.1 1.0 N1 A:A629 4.4 30.3 1.0 O3' A:A631 4.5 35.7 1.0 C2 A:G2070 4.6 24.1 1.0 O A:HOH3078 4.7 64.2 1.0 C2 A:A629 4.7 31.4 1.0 O4' A:A630 4.7 33.2 1.0 C3' A:A630 4.7 33.0 1.0 P A:A2074 4.8 31.3 1.0 P A:A632 4.9 37.0 1.0 N1 A:A630 4.9 32.0 1.0 C1' A:A631 4.9 33.4 1.0 O A:HOH9401 5.0 20.0 1.0

Sodium binding site 5 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8306 b:56.8 occ:1.00 N7 A:G2094 2.6 33.6 1.0 N7 A:G2093 2.9 32.8 1.0 O6 A:G2094 2.9 34.4 1.0 N1 A:A2649 3.0 39.9 1.0 O6 A:G2093 3.2 34.3 1.0 C2 A:A2649 3.3 39.5 1.0 C5 A:G2094 3.3 34.5 1.0 C5 A:G2093 3.3 33.0 1.0 O A:HOH9126 3.3 38.6 1.0 C6 A:G2094 3.4 34.5 1.0 C6 A:G2093 3.5 34.0 1.0 N3 A:G2092 3.5 39.5 1.0 O2' A:G2092 3.5 38.6 1.0 N2 A:G2092 3.6 39.5 1.0 N6 A:A2612 3.6 29.6 1.0 C8 A:G2094 3.7 32.6 1.0 C2 A:G2092 3.8 38.9 1.0 C8 A:G2093 3.8 31.9 1.0 C6 A:A2612 4.1 31.8 1.0 C6 A:A2649 4.2 40.2 1.0 C4 A:G2093 4.4 32.0 1.0 C4 A:G2092 4.4 40.5 1.0 N6 A:A2649 4.6 40.1 1.0 N3 A:A2649 4.6 41.6 1.0 C5 A:A2612 4.6 31.4 1.0 C4 A:G2094 4.6 34.5 1.0 N1 A:A2612 4.6 33.3 1.0 N9 A:G2093 4.6 32.4 1.0 N1 A:G2093 4.6 33.7 1.0 C2' A:G2092 4.7 37.3 1.0 C1' A:G2092 4.7 38.6 1.0 N1 A:G2092 4.8 38.5 1.0 N9 A:G2094 4.8 32.6 1.0 N1 A:G2094 4.8 35.4 1.0 N7 A:A2612 4.9 31.7 1.0 N9 A:G2092 4.9 40.5 1.0

Sodium binding site 6 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8307 b:39.2 occ:1.00 O2 A:C40 2.4 59.4 1.0 O2' A:C40 2.8 56.4 1.0 O4' A:G41 2.9 53.9 1.0 N1 A:A442 3.0 57.2 1.0 C2' A:C40 3.1 56.7 1.0 O2 A:C443 3.1 64.4 1.0 C1' A:C40 3.3 57.9 1.0 C2 A:C40 3.5 60.2 1.0 C2 A:A442 3.6 56.3 1.0 C1' A:G41 3.7 53.8 1.0 N1 A:C40 3.9 59.8 1.0 C2 A:C443 3.9 63.6 1.0 C4' A:G41 4.0 53.2 1.0 C6 A:A442 4.0 57.0 1.0 N9 A:G41 4.1 54.4 1.0 N6 A:A442 4.2 58.6 1.0 C5' A:G41 4.2 52.6 1.0 N2 A:G39 4.4 57.2 1.0 C8 A:G41 4.5 55.6 1.0 N3 A:C443 4.5 64.0 1.0 O5' A:G41 4.6 52.3 1.0 O4' A:C40 4.6 57.7 1.0 O A:HOH5863 4.6 38.5 1.0 C3' A:C40 4.6 56.0 1.0 N3 A:C40 4.7 60.8 1.0 C4 A:G41 4.7 54.2 1.0 N1 A:C443 4.7 62.9 1.0 C1' A:C443 4.8 60.6 1.0 C2 A:G39 4.8 59.2 1.0 N3 A:A442 4.9 56.2 1.0 O A:HOH6972 5.0 41.1 1.0 N1 A:G39 5.0 60.4 1.0

Sodium binding site 7 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8308 b:69.6 occ:1.00 O2 A:U1724 2.2 41.1 1.0 O2 A:C1394 2.3 47.1 1.0 O4 A:U1432 2.5 39.5 1.0 O A:HOH3410 2.6 44.0 1.0 C2 A:U1724 3.4 39.8 1.0 C2 A:C1394 3.5 45.1 1.0 O6 A:G1433 3.5 40.0 1.0 C4 A:U1432 3.7 40.1 1.0 O A:HOH9292 3.8 20.9 1.0 O2' A:C1394 3.8 38.3 1.0 C2' A:C1394 4.0 41.6 1.0 O A:HOH7146 4.1 93.5 1.0 C6 A:G1433 4.2 41.3 1.0 N3 A:U1724 4.3 39.5 1.0 C1' A:C1394 4.3 42.6 1.0 O2' A:U1724 4.3 35.5 1.0 N3 A:C1394 4.3 45.7 1.0 N3 A:U1432 4.3 40.9 1.0 N1 A:C1394 4.4 44.5 1.0 C1' A:U1724 4.4 37.0 1.0 N1 A:U1724 4.4 38.6 1.0 C2' A:U1724 4.5 35.8 1.0 N1 A:G1433 4.5 42.0 1.0 O A:HOH4832 4.6 58.3 1.0 O A:HOH5464 4.8 54.5 1.0 C5 A:U1432 4.9 41.0 1.0 O2' A:C1725 4.9 38.6 1.0 OP2 A:U1722 5.0 49.4 1.0

Sodium binding site 8 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8310 b:29.1 occ:1.00 O6 A:G2579 2.7 38.5 1.0 O A:HOH4496 2.9 40.0 1.0 O4' A:A2577 3.0 45.3 1.0 N7 A:G2579 3.0 42.9 1.0 N7 A:G2578 3.0 41.6 1.0 N3 A:A2577 3.0 44.2 1.0 O6 A:G2578 3.3 42.9 1.0 C6 A:G2579 3.4 39.3 1.0 C5 A:G2578 3.5 42.3 1.0 C5 A:G2579 3.5 40.5 1.0 C6 A:G2578 3.6 42.4 1.0 C1' A:A2577 3.6 44.9 1.0 C4 A:A2577 3.9 43.5 1.0 C2 A:A2577 3.9 43.8 1.0 O A:HOH7734 3.9 86.0 1.0 C4' A:A2577 3.9 45.2 1.0 C8 A:G2578 4.0 42.0 1.0 N9 A:A2577 4.1 43.5 1.0 C8 A:G2579 4.2 42.5 1.0 O A:HOH6285 4.3 69.0 1.0 C4 A:G2578 4.6 42.3 1.0 N1 A:G2578 4.7 42.5 1.0 N4 A:C2556 4.8 47.6 1.0 N1 A:G2579 4.8 39.2 1.0 O6 A:G2580 4.8 43.1 1.0 N9 A:G2578 4.8 42.6 1.0 O A:HOH5964 4.9 50.7 1.0 C4 A:G2579 4.9 40.2 1.0 C5' A:A2577 4.9 43.4 1.0 N3 A:U2554 4.9 38.0 1.0 C3' A:A2577 4.9 46.0 1.0 O3' A:A2577 4.9 46.3 1.0 C2' A:A2577 5.0 45.7 1.0

Sodium binding site 9 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8311 b:42.9 occ:1.00 O A:HOH3570 2.0 18.1 1.0 O6 A:G2525 2.3 46.9 1.0 O A:HOH4649 2.7 33.5 1.0 N7 A:G2524 2.8 36.5 1.0 O A:HOH9180 2.9 38.8 1.0 C6 A:G2525 3.3 45.9 1.0 C8 A:G2524 3.7 36.7 1.0 C5 A:G2524 3.7 35.4 1.0 O6 A:G2524 3.7 34.8 1.0 O A:HOH3615 3.8 27.5 1.0 C5 A:U2523 3.9 37.0 1.0 O A:HOH6365 3.9 42.9 1.0 C4 A:U2523 4.1 36.8 1.0 C6 A:G2524 4.1 35.1 1.0 C5 A:G2525 4.1 45.2 1.0 N1 A:G2525 4.2 44.8 1.0 O4 A:U2523 4.2 38.1 1.0 N7 A:G2525 4.3 45.1 1.0 O2' A:C2493 4.3 42.0 1.0 C6 A:U2523 4.4 36.0 1.0 C2' A:C2493 4.6 43.1 1.0 OP2 A:G2524 4.7 38.6 1.0 N3 A:U2523 4.7 35.8 1.0 OP2 A:U2523 4.8 34.8 1.0 N9 A:G2524 4.9 36.2 1.0 C4 A:G2524 4.9 35.4 1.0

Sodium binding site 10 out of 85 in the Co-Crystal Structure of Spiramycin 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 Co-Crystal Structure of Spiramycin Bound to the 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ A:Na8313 b:63.1 occ:1.00 O A:HOH5123 1.7 46.0 1.0 O A:HOH9943 2.3 36.6 1.0 O A:HOH3830 2.5 33.9 1.0 O6 A:G2399 2.7 44.3 1.0 O A:HOH6507 3.0 75.5 1.0 O A:HOH6054 3.6 63.6 1.0 C6 A:G2399 3.6 45.3 1.0 N7 A:G2399 3.6 47.5 1.0 O A:HOH3391 3.6 39.7 1.0 O A:HOH5073 3.7 54.9 1.0 O4 A:U2389 3.8 41.6 1.0 OP2 A:A2398 3.9 50.0 1.0 C5 A:G2399 4.0 46.4 1.0 O6 A:G2400 4.2 39.3 1.0 O A:HOH6277 4.3 77.2 1.0 N3 A:U2389 4.5 43.9 1.0 C4 A:U2389 4.6 42.8 1.0 O A:HOH9735 4.7 19.1 1.0 N7 A:G2400 4.8 41.6 1.0 C8 A:G2399 4.8 47.5 1.0 N1 A:G2399 4.9 45.0 1.0 O2 A:U2390 4.9 45.3 1.0 C6 A:G2400 4.9 40.7 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