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

Protein crystallography data

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

Other elements in 1w2b:

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
Sodium (Na) 86 atoms

Chlorine Binding Sites:

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 Trigger Factor Ribosome Binding Domain in Complex with 50S (pdb code 1w2b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Trigger Factor Ribosome Binding Domain in Complex with 50S, PDB code: 1w2b:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 1w2b

Go back to Chlorine Binding Sites List in 1w2b
Chlorine binding site 1 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3120

b:35.2
occ:1.00
 O 0:HOH8042 2.8 29.5 1.0
N2 0:G1676 3.0 15.1 1.0
O 0:HOH5924 3.3 19.3 1.0
C1' 0:G1452 3.6 21.0 1.0
O 0:HOH3481 3.9 20.9 1.0
O2' 0:G1452 3.9 17.6 1.0
N3 0:A1486 4.1 24.6 1.0
O4' 0:G1452 4.1 22.7 1.0
CE 1:LYS2 4.2 15.0 1.0
O 0:HOH3211 4.2 35.3 1.0
C2 0:A1486 4.2 23.1 1.0
C2 0:G1676 4.2 15.4 1.0
O2 0:C1451 4.3 34.2 1.0
C2' 0:G1452 4.4 18.3 1.0
N9 0:G1452 4.5 36.6 1.0
N3 0:G1676 4.5 15.1 1.0
N3 0:G1452 4.8 37.4 1.0
CD 1:LYS2 5.0 15.0 1.0
C4 0:G1452 5.0 37.4 1.0
O2' 0:A1486 5.0 15.8 1.0

Chlorine binding site 2 out of 22 in 1w2b

Go back to Chlorine Binding Sites List in 1w2b
Chlorine binding site 2 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3121

b:36.7
occ:1.00
 N2 0:G201 3.0 15.0 1.0
C5 0:C197 3.3 50.9 1.0
O 0:HOH8011 3.7 37.5 1.0
C5' 0:G229 3.8 15.0 1.0
O 0:HOH5176 3.9 22.6 1.0
O3' 0:G229 3.9 15.0 1.0
O4' 0:U202 4.0 26.9 1.0
C2 0:G201 4.1 17.0 1.0
C4' 0:G229 4.1 15.0 1.0
C6 0:C197 4.1 50.7 1.0
C1' 0:U202 4.2 27.2 1.0
N3 0:G201 4.3 18.4 1.0
C4 0:C197 4.3 51.2 1.0
O 0:HOH3534 4.4 21.3 1.0
N4 0:C197 4.4 50.5 1.0
O 0:HOH7027 4.6 24.6 1.0
C3' 0:G229 4.6 15.0 1.0
OP1 0:C230 4.7 18.8 1.0
O2' 0:U202 4.8 28.3 1.0
N1 0:A199 4.9 24.9 1.0
C4' 0:U202 5.0 26.5 1.0
P 0:C230 5.0 22.0 1.0
O5' 0:G229 5.0 15.8 1.0

Chlorine binding site 3 out of 22 in 1w2b

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Chlorine binding site 3 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3122

b:38.9
occ:1.00
 N1 0:A1329 2.7 15.0 1.0
O 0:HOH3868 2.9 85.4 1.0
O2' 0:G1300 3.3 15.0 1.0
O 0:HOH5740 3.4 44.2 1.0
C2 0:A1329 3.6 15.0 1.0
O 0:HOH6854 3.6 18.0 1.0
C6 0:A1329 3.6 15.0 1.0
N6 0:A1329 3.6 15.0 1.0
C1' 0:G1300 3.8 15.0 1.0
O4' 0:G1300 4.0 15.0 1.0
N6 0:A1328 4.0 15.0 1.0
O X:HOH454 4.0 26.5 1.0
N1 0:A1330 4.1 15.2 1.0
N2 0:G1299 4.1 15.3 1.0
C2' 0:G1300 4.2 15.0 1.0
C4' 0:G1300 4.4 15.0 1.0
C2 0:A1330 4.5 15.2 1.0
O 0:HOH7352 4.6 35.9 1.0
N3 0:G1299 4.8 20.8 1.0
N3 0:A1329 4.9 15.0 1.0
C2 0:G1299 4.9 20.7 1.0
C5 0:A1329 4.9 15.0 1.0
NH2 X:ARG169 5.0 21.8 1.0

Chlorine binding site 4 out of 22 in 1w2b

Go back to Chlorine Binding Sites List in 1w2b
Chlorine binding site 4 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3123

b:43.0
occ:1.00
 N6 0:A1598 3.4 17.9 1.0
O4' 0:G1647 3.6 24.0 1.0
O 0:HOH7303 3.8 50.9 1.0
C1' 0:G1647 4.0 22.7 1.0
N2 0:G1646 4.1 32.4 1.0
O2' 0:G1646 4.5 15.0 1.0
N3 0:G1646 4.5 35.4 1.0
N6 0:A1597 4.6 34.9 1.0
C6 0:A1598 4.6 19.0 1.0
N3 0:G1540 4.6 43.5 1.0
C4' 0:G1647 4.6 22.8 1.0
O 0:HOH6137 4.7 29.2 1.0
C2 0:G1646 4.8 34.3 1.0
N9 0:G1647 4.9 35.9 1.0
O2' 0:G1647 5.0 22.2 1.0

Chlorine binding site 5 out of 22 in 1w2b

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Chlorine binding site 5 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3124

b:37.1
occ:1.00
 N4 0:C1243 3.1 15.6 1.0
C8 0:G1119 3.4 16.0 1.0
NE2 I:GLN52 3.5 21.2 1.0
NZ I:LYS56 3.5 15.0 1.0
CD I:LYS56 3.9 15.0 1.0
N7 0:G1119 3.9 16.6 1.0
C2' 0:G1119 4.0 15.0 1.0
O2' 0:G1119 4.0 16.2 1.0
N9 0:G1119 4.0 16.9 1.0
O 0:HOH8083 4.1 31.5 1.0
O 0:HOH8573 4.2 48.3 1.0
C4 0:C1243 4.2 16.7 1.0
CE I:LYS56 4.3 15.0 1.0
C5 0:C1243 4.4 15.9 1.0
CD I:GLN52 4.4 20.6 1.0
C1' 0:G1119 4.5 15.0 1.0
OE1 I:GLN52 4.5 21.3 1.0
O 0:HOH8349 4.6 62.1 1.0
O I:HOH309 4.6 35.3 1.0
N6 0:A1242 4.6 15.0 1.0
C5 0:G1119 4.7 15.4 1.0
NA 0:NA3106 4.8 42.3 1.0
C4 0:G1119 4.8 15.1 1.0
N7 0:A1242 4.9 15.0 1.0

Chlorine binding site 6 out of 22 in 1w2b

Go back to Chlorine Binding Sites List in 1w2b
Chlorine binding site 6 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3125

b:45.0
occ:1.00
 O X:HOH421 2.7 77.0 1.0
O2' 0:C594 3.0 15.3 1.0
CD X:ARG115 3.3 15.0 1.0
O4' 0:U595 3.4 19.5 1.0
NE X:ARG115 3.5 16.8 1.0
O X:HOH432 3.5 26.2 1.0
CG X:ARG115 3.7 15.0 1.0
C4' 0:U595 3.8 19.2 1.0
NH2 X:ARG122 4.0 38.8 1.0
C2' 0:C594 4.0 17.6 1.0
C5' 0:U595 4.0 17.4 1.0
O X:HOH457 4.1 34.2 1.0
O2 0:C594 4.4 38.3 1.0
O 0:HOH6242 4.5 58.8 1.0
C1' 0:U595 4.5 20.4 1.0
O 0:HOH7666 4.6 38.8 1.0
CZ X:ARG115 4.7 16.9 1.0
C1' 0:C594 4.8 18.2 1.0
CB X:ARG115 4.8 15.0 1.0

Chlorine binding site 7 out of 22 in 1w2b

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Chlorine binding site 7 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl3126

b:39.4
occ:1.00
 N1 0:G1072 3.3 15.0 1.0
C8 0:G1087 3.3 17.4 1.0
N2 0:G1072 3.4 15.0 1.0
N7 0:G1087 3.7 19.6 1.0
O 0:HOH8537 3.8 48.0 1.0
C2 0:G1072 3.8 15.0 1.0
N7 0:A1291 3.9 16.9 1.0
N9 0:G1087 3.9 18.1 1.0
C2' 0:G1087 4.0 18.9 1.0
O 0:HOH8799 4.0 43.0 1.0
O 0:HOH6338 4.1 50.8 1.0
OE2 V:GLU10 4.3 0.9 1.0
C6 0:G1072 4.3 15.0 1.0
C5 0:A1291 4.3 16.9 1.0
O6 0:G1072 4.3 15.0 1.0
C8 0:A1291 4.4 16.3 1.0
C1' 0:G1087 4.5 17.4 1.0
C5 0:G1087 4.5 18.6 1.0
C4 0:G1087 4.6 17.8 1.0
O2' 0:G1087 4.7 19.5 1.0
N6 0:A1291 4.7 15.8 1.0
C6 0:A1291 4.7 17.8 1.0
C3' 0:G1087 4.9 20.0 1.0

Chlorine binding site 8 out of 22 in 1w2b

Go back to Chlorine Binding Sites List in 1w2b
Chlorine binding site 8 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
2:Cl102

b:40.5
occ:1.00
 N 2:ASP66 3.7 0.4 1.0
O 2:ASP66 3.7 0.2 1.0
CG 2:LYS24 3.8 0.0 1.0
CD2 2:LEU88 4.0 0.2 1.0
CD 2:LYS24 4.1 0.8 1.0
CE 2:LYS24 4.2 0.6 1.0
C 2:ASP66 4.2 0.8 1.0
CD2 2:LEU67 4.2 83.5 1.0
CA 2:ASP66 4.4 0.1 1.0
CA 2:THR65 4.4 0.5 1.0
CB 2:ASP66 4.5 0.1 1.0
CB 2:LYS24 4.6 0.0 1.0
C 2:THR65 4.6 0.5 1.0
O 2:LYS64 4.7 0.2 1.0
CB 2:LEU88 4.7 0.0 1.0
OG1 2:THR65 4.9 0.8 1.0
CG 2:LEU67 4.9 84.8 1.0
CG 2:LEU88 5.0 0.4 1.0

Chlorine binding site 9 out of 22 in 1w2b

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Chlorine binding site 9 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl305

b:45.0
occ:1.00
 O A:HOH527 3.1 18.8 1.0
O A:HOH473 3.7 25.1 1.0
NZ A:LYS178 3.8 22.5 1.0
CE A:LYS178 4.1 22.9 1.0
O 0:HOH8851 4.1 30.6 1.0
CE A:LYS175 4.1 17.4 1.0
CE A:MET179 4.2 29.5 1.0
O 0:HOH5940 4.2 29.5 1.0
O A:HOH535 4.2 45.2 1.0
OP2 0:G1878 4.2 19.0 1.0
CD A:LYS178 4.5 24.9 1.0
SD A:MET179 4.6 26.1 1.0
CZ A:PHE169 4.7 20.4 1.0

Chlorine binding site 10 out of 22 in 1w2b

Go back to Chlorine Binding Sites List in 1w2b
Chlorine binding site 10 out of 22 in the Trigger Factor Ribosome Binding Domain in Complex with 50S


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl404

b:28.2
occ:1.00
 O 0:HOH6150 2.9 20.3 1.0
N B:LYS224 3.1 17.8 1.0
O 0:HOH6374 3.2 12.5 1.0
CA B:ARG223 3.4 15.0 1.0
CD2 B:HIS227 3.5 15.0 1.0
O B:HOH595 3.5 24.7 1.0
CB B:HIS227 3.7 15.0 1.0
CD B:ARG223 3.7 16.9 1.0
CG B:HIS227 3.7 15.3 1.0
C B:ARG223 3.7 15.0 1.0
O B:HOH598 3.7 36.6 1.0
O2' 0:U2545 3.8 15.0 1.0
CB B:ARG223 4.0 16.9 1.0
CA B:LYS224 4.2 17.8 1.0
CB B:LYS224 4.3 17.2 1.0
O B:LYS224 4.3 19.4 1.0
C4' 0:U2546 4.4 15.0 1.0
CG B:ARG223 4.5 17.2 1.0
O4' 0:U2546 4.5 15.0 1.0
NE2 B:HIS227 4.5 16.6 1.0
C5' 0:U2546 4.5 15.0 1.0
CG B:LYS224 4.6 17.2 1.0
O B:LYS222 4.6 17.4 1.0
N B:ARG223 4.6 15.0 1.0
C B:LYS224 4.7 19.2 1.0
NE B:ARG223 4.8 15.4 1.0
ND1 B:HIS227 4.8 16.1 1.0
O B:ARG223 4.9 15.0 1.0

Reference:

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
Page generated: Sat Jul 20 03:30:56 2024

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