Sodium in PDB 1w2b: Trigger Factor Ribosome Binding Domain in Complex with 50S

The structure of Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b was solved by L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	210.746, 298.871, 574.173, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 26.8

The structure of Trigger Factor Ribosome Binding Domain in Complex with 50S also contains other interesting chemical elements:

Magnesium	(Mg)	117 atoms
Potassium	(K)	2 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 - 86;

Binding sites:

The binding sites of Sodium atom in the Trigger Factor Ribosome Binding Domain in Complex with 50S (pdb code 1w2b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3064 b:28.6 occ:1.00 O 0:HOH4346 2.7 23.9 1.0 O 0:HOH7412 2.7 45.8 1.0 OP2 0:C1069 2.9 15.0 1.0 O 0:HOH4718 3.2 34.2 1.0 N7 0:G1072 3.2 15.0 1.0 O6 0:G1072 3.4 15.0 1.0 O6 0:G1087 3.6 20.5 1.0 C5 0:G1072 3.9 15.0 1.0 C6 0:G1072 4.0 15.0 1.0 O 0:HOH3559 4.0 40.5 1.0 O 0:HOH6115 4.0 25.1 1.0 C5' 0:C1068 4.1 15.0 1.0 C8 0:G1072 4.3 15.0 1.0 P 0:C1069 4.4 15.0 1.0 O 0:HOH4993 4.4 21.7 1.0 OP2 0:C1068 4.5 42.3 1.0 C3' 0:C1068 4.5 15.0 1.0 N6 0:A1070 4.6 15.0 1.0 C6 0:G1087 4.6 19.0 1.0 O3' 0:C1068 4.8 15.0 1.0 C4' 0:C1068 4.9 15.0 1.0 O 0:HOH6373 4.9 20.4 1.0

Sodium binding site 2 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3065 b:39.4 occ:1.00 O 0:HOH5554 2.9 31.0 1.0 O2' 0:G1119 3.0 16.2 1.0 MG 0:MG3024 3.0 31.5 1.0 O 0:HOH5478 3.1 31.4 1.0 O3' 0:G1119 3.2 16.0 1.0 OP2 0:U1120 3.2 22.9 1.0 N7 0:G1121 3.4 18.0 1.0 O 0:HOH6502 3.5 26.3 1.0 O6 0:G1121 3.6 18.6 1.0 O4 0:U1122 3.6 18.8 1.0 P 0:U1120 3.9 19.9 1.0 O 0:HOH8573 3.9 48.3 1.0 O 0:HOH8349 4.0 62.1 1.0 C5 0:G1121 4.1 17.1 1.0 C2' 0:G1119 4.1 15.0 1.0 C6 0:G1121 4.2 16.7 1.0 C3' 0:G1119 4.3 16.5 1.0 C4 0:U1122 4.3 19.7 1.0 C8 0:G1121 4.4 17.9 1.0 OP2 0:G1121 4.5 15.1 1.0 C5 0:U1122 4.5 19.4 1.0 OP1 0:C1238 4.6 28.7 1.0 C5' 0:U1120 4.8 21.1 1.0 O5' 0:U1120 4.9 19.3 1.0 OP1 0:U1120 5.0 25.9 1.0

Sodium binding site 3 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3066 b:27.2 occ:1.00 OP1 0:C1353 2.8 36.8 1.0 O 0:HOH6155 2.9 16.4 1.0 OP1 0:G1354 3.0 22.1 1.0 OP2 0:A643 3.3 15.0 1.0 O5' 0:C1353 3.6 50.1 1.0 C5' 0:C1353 3.6 39.5 1.0 OP1 0:A643 3.7 15.4 1.0 O 0:HOH5302 3.8 23.7 1.0 P 0:C1353 3.8 56.0 1.0 P 0:A643 3.9 15.0 1.0 O 0:HOH5395 3.9 86.2 1.0 O2' 0:A1352 4.1 27.7 1.0 O 0:HOH8227 4.1 33.7 1.0 P 0:G1354 4.2 16.4 1.0 O3' 0:C1353 4.2 30.6 1.0 O5' 0:A643 4.4 15.0 1.0 C3' 0:C1353 4.4 34.3 1.0 OP1 0:G644 4.5 26.8 1.0 C4' 0:C1353 4.5 37.6 1.0 O4 0:U904 4.6 17.4 1.0 O 0:HOH6786 4.6 77.4 1.0 NH2 K:ARG8 4.7 29.1 1.0 O3' 0:A1352 4.8 27.3 1.0 OP2 0:C1353 4.9 41.3 1.0 OP2 0:G1354 4.9 16.3 1.0 O C:HOH491 5.0 33.1 1.0 N3 0:U904 5.0 18.0 1.0

Sodium binding site 4 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3067 b:26.8 occ:1.00 O2' 0:A630 2.7 15.0 1.0 O 0:HOH5073 2.8 24.6 1.0 O 0:HOH5070 2.9 24.9 1.0 O 0:HOH6920 2.9 36.4 1.0 OP2 0:A2074 3.0 15.0 1.0 N3 0:A630 3.0 22.1 1.0 C2 0:A630 3.6 23.3 1.0 N2 0:G2070 3.6 15.0 1.0 O 0:HOH3399 3.8 25.1 1.0 C2' 0:A630 3.9 15.0 1.0 C3' 0:A631 4.0 15.0 1.0 C2' 0:A631 4.1 15.0 1.0 C4 0:A630 4.1 23.1 1.0 OP2 0:G2072 4.2 31.8 1.0 C1' 0:A630 4.2 15.0 1.0 C2 0:G2070 4.3 15.0 1.0 O3' 0:A631 4.4 15.0 1.0 P 0:A2074 4.4 15.0 1.0 OP1 0:A632 4.5 15.4 1.0 N1 0:A629 4.5 16.5 1.0 N9 0:A630 4.6 21.8 1.0 OP2 0:A632 4.7 15.4 1.0 O2' 0:A631 4.7 15.0 1.0 P 0:A632 4.8 15.0 1.0 N3 0:G2070 4.8 15.0 1.0 N1 0:G2070 4.8 15.0 1.0 C2 0:A629 4.8 17.4 1.0 N1 0:A630 4.9 23.9 1.0 O5' 0:A2074 5.0 15.0 1.0

Sodium binding site 5 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3068 b:23.5 occ:1.00 N7 0:G2094 2.8 15.0 1.0 O6 0:G2094 2.8 17.6 1.0 N7 0:G2093 2.9 15.0 1.0 N1 0:A2649 3.1 15.4 1.0 N3 0:G2092 3.2 15.5 1.0 O6 0:G2093 3.2 15.0 1.0 O2' 0:G2092 3.2 15.0 1.0 N2 0:G2092 3.2 15.5 1.0 C5 0:G2093 3.2 15.0 1.0 C2 0:A2649 3.3 15.0 1.0 C6 0:G2093 3.4 15.0 1.0 C5 0:G2094 3.4 15.0 1.0 C2 0:G2092 3.4 15.5 1.0 C6 0:G2094 3.4 15.1 1.0 C8 0:G2093 3.8 15.0 1.0 O 0:HOH3277 3.9 14.6 1.0 C8 0:G2094 3.9 15.0 1.0 C4 0:G2092 4.1 15.5 1.0 C6 0:A2649 4.2 15.8 1.0 C4 0:G2093 4.3 15.0 1.0 C2' 0:G2092 4.3 15.0 1.0 N6 0:A2612 4.4 21.1 1.0 N1 0:G2092 4.4 15.5 1.0 N1 0:G2093 4.5 15.0 1.0 N3 0:A2649 4.5 15.9 1.0 N9 0:G2093 4.6 15.0 1.0 C4 0:G2094 4.7 15.0 1.0 N6 0:A2649 4.7 15.0 1.0 C6 0:A2612 4.7 21.9 1.0 N1 0:G2094 4.7 15.0 1.0 N9 0:G2092 4.8 15.5 1.0 C1' 0:G2092 4.8 15.0 1.0 N1 0:A2612 4.9 21.4 1.0 N9 0:G2094 4.9 15.0 1.0

Sodium binding site 6 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3069 b:36.9 occ:1.00 O2' 0:C40 2.8 36.1 1.0 O4' 0:G41 2.8 30.4 1.0 O2 0:C443 3.1 64.8 1.0 O2 0:C40 3.1 25.6 1.0 N1 0:A442 3.1 37.6 1.0 C2 0:A442 3.5 36.2 1.0 C2' 0:C40 3.5 35.6 1.0 C1' 0:G41 3.8 28.8 1.0 C4' 0:G41 3.8 28.7 1.0 C1' 0:C40 3.9 36.0 1.0 C2 0:C443 3.9 64.1 1.0 C5' 0:G41 4.1 28.2 1.0 C2 0:C40 4.2 24.7 1.0 C6 0:A442 4.3 36.5 1.0 N9 0:G41 4.3 15.5 1.0 N2 0:G39 4.5 28.9 1.0 O 0:HOH6797 4.5 33.6 1.0 C1' 0:C443 4.5 32.3 1.0 O5' 0:G41 4.5 27.5 1.0 N1 0:C443 4.6 64.2 1.0 N6 0:A442 4.6 37.0 1.0 N1 0:C40 4.6 24.2 1.0 N3 0:C443 4.6 63.0 1.0 C8 0:G41 4.7 15.0 1.0 N3 0:A442 4.8 36.5 1.0 C3' 0:C40 5.0 34.5 1.0

Sodium binding site 7 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3070 b:37.6 occ:1.00 O2 0:U1724 2.6 15.9 1.0 O6 0:G1433 2.9 34.6 1.0 O2 0:C1394 2.9 52.3 1.0 O4 0:U1432 3.1 38.6 1.0 C2' 0:C1394 3.2 18.6 1.0 O 0:HOH3796 3.2 18.0 1.0 O2' 0:C1394 3.2 15.6 1.0 O 0:HOH7038 3.2 42.2 1.0 C6 0:G1433 3.5 34.4 1.0 N1 0:G1433 3.5 34.9 1.0 C2 0:C1394 3.6 51.9 1.0 C2 0:U1724 3.7 15.7 1.0 O 0:HOH4567 3.7 27.4 1.0 O 0:HOH3834 3.7 22.8 1.0 C1' 0:C1394 3.9 17.8 1.0 OP2 0:C1395 4.0 20.6 1.0 N3 0:U1724 4.1 15.0 1.0 N1 0:C1394 4.1 51.5 1.0 C4 0:U1432 4.3 38.6 1.0 OP1 0:C1395 4.4 18.7 1.0 C3' 0:C1394 4.5 19.0 1.0 N3 0:C1394 4.5 50.7 1.0 P 0:C1395 4.6 17.7 1.0 C2 0:G1433 4.7 34.0 1.0 C5 0:G1433 4.7 32.9 1.0 OP2 0:U1722 4.7 30.8 1.0 N3 0:U1432 4.7 38.9 1.0 O 0:HOH4321 4.8 46.5 1.0 N1 0:U1724 4.8 15.1 1.0 O3' 0:C1394 4.9 19.5 1.0

Sodium binding site 8 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3071 b:21.8 occ:1.00 O6 0:G2579 2.9 15.0 1.0 N7 0:G2579 2.9 16.2 1.0 N7 0:G2578 3.1 15.4 1.0 N3 0:A2577 3.2 24.1 1.0 C5 0:G2578 3.5 15.4 1.0 O4' 0:A2577 3.6 19.3 1.0 C6 0:G2579 3.6 15.1 1.0 C5 0:G2579 3.6 16.7 1.0 O6 0:G2578 3.6 15.4 1.0 C1' 0:A2577 3.6 18.7 1.0 C6 0:G2578 3.7 15.5 1.0 C8 0:G2578 3.9 15.4 1.0 C4' 0:A2577 4.0 19.8 1.0 C2 0:A2577 4.0 23.5 1.0 O 0:HOH4200 4.0 31.7 1.0 C8 0:G2579 4.1 17.8 1.0 C4 0:A2577 4.1 22.3 1.0 O 0:HOH5530 4.1 63.1 1.0 O 0:HOH6333 4.2 47.1 1.0 N9 0:A2577 4.4 22.4 1.0 O2' 0:A2577 4.4 21.7 1.0 C4 0:G2578 4.5 15.8 1.0 C2' 0:A2577 4.6 19.1 1.0 O6 0:G2580 4.6 20.1 1.0 N9 0:G2578 4.7 16.8 1.0 N1 0:G2578 4.8 15.4 1.0 C3' 0:A2577 4.8 19.6 1.0 O3' 0:A2577 4.8 19.0 1.0 C4 0:G2579 4.9 16.7 1.0 N3 0:U2554 4.9 16.8 1.0 N1 0:G2579 4.9 16.0 1.0

Sodium binding site 9 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3072 b:43.5 occ:1.00 O 0:HOH6833 2.9 25.9 1.0 O 0:HOH8885 2.9 46.7 1.0 O6 0:G2525 3.0 19.2 1.0 O 0:HOH4049 3.0 37.7 1.0 O 0:HOH3761 3.1 22.9 1.0 O 0:HOH4609 3.7 18.7 1.0 N7 0:G2524 3.8 15.0 1.0 OP2 0:U2523 3.9 15.0 1.0 C5 0:U2523 4.0 15.7 1.0 C6 0:G2525 4.1 16.0 1.0 OP2 0:G2524 4.2 20.0 1.0 C8 0:G2524 4.5 15.0 1.0 C6 0:U2523 4.5 15.0 1.0 C4 0:U2523 4.6 15.0 1.0 O5' 0:U2523 4.8 15.0 1.0 O4 0:U2523 4.8 17.0 1.0 N7 0:G2525 4.8 15.5 1.0 C5 0:G2525 4.8 17.0 1.0 OP2 0:C2493 4.9 15.0 1.0 P 0:U2523 4.9 15.0 1.0 C5 0:G2524 5.0 15.0 1.0

Sodium binding site 10 out of 86 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Trigger Factor Ribosome Binding Domain in Complex with 50S within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na3073 b:43.6 occ:1.00 O 0:HOH7439 2.7 37.4 1.0 O 0:HOH4879 2.8 23.0 1.0 O 0:HOH7860 2.9 31.3 1.0 O 0:HOH8819 2.9 36.0 1.0 O6 0:G2399 3.0 37.9 1.0 O 0:HOH6172 3.0 34.3 1.0 O 0:HOH8892 3.6 41.8 1.0 O6 0:G2400 3.8 36.0 1.0 O 0:HOH5765 3.8 25.2 1.0 C6 0:G2399 4.0 36.1 1.0 O4 0:U2389 4.0 31.8 1.0 N7 0:G2399 4.0 35.6 1.0 O 0:HOH5732 4.2 31.2 1.0 N3 0:U2389 4.3 33.7 1.0 C5 0:G2399 4.4 36.1 1.0 OP2 0:A2398 4.4 29.8 1.0 C4 0:U2389 4.6 33.9 1.0 C6 0:G2400 4.7 34.5 1.0 N4 0:C2388 4.7 18.3 1.0 N7 0:G2400 5.0 38.0 1.0

L.Ferbitz, T.Maier, H.Patzelt, B.Bukau, E.Deuerling, N.Ban. Trigger Factor in Complex with the Ribosome Forms A Molecular Cradle For Nascent Proteins Nature V. 431 590 2004.
ISSN: ISSN 0028-0836
PubMed: 15334087
DOI: 10.1038/NATURE02899