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Chlorine in PDB 3g4s: Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit

Protein crystallography data

The structure of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit, PDB code: 3g4s was solved by G.Gurel, G.Blaha, 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) 49.84 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.270, 299.840, 574.137, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 29

Other elements in 3g4s:

The structure of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit also contains other interesting chemical elements:

Strontium (Sr) 108 atoms
Magnesium (Mg) 93 atoms
Potassium (K) 1 atom
Cadmium (Cd) 5 atoms
Sodium (Na) 75 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 Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit (pdb code 3g4s). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit, PDB code: 3g4s:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 3g4s

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Chlorine binding site 1 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8803

b:66.5
occ:1.00
 N2 0:G1676 2.9 58.2 1.0
C1' 0:G1452 3.5 66.2 1.0
O2' 0:G1452 3.7 70.4 1.0
O 0:HOH4481 3.7 42.1 1.0
CE 2:LYS2 4.0 62.9 1.0
O 0:HOH8210 4.0 0.5 1.0
O4' 0:G1452 4.1 65.8 1.0
C2 0:G1676 4.1 59.1 1.0
N3 0:A1486 4.2 59.4 1.0
C2' 0:G1452 4.2 66.4 1.0
C2 0:A1486 4.3 59.2 1.0
O 0:HOH3526 4.3 44.6 1.0
O 0:HOH7485 4.3 66.1 1.0
N3 0:G1676 4.4 60.6 1.0
N9 0:G1452 4.4 66.7 1.0
O 0:HOH5033 4.5 63.7 1.0
N3 0:G1452 4.7 67.6 1.0
O2 0:C1451 4.7 67.5 1.0
CD 2:LYS2 4.8 62.9 1.0
C4 0:G1452 4.9 68.0 1.0
NZ 2:LYS2 5.0 61.4 1.0

Chlorine binding site 2 out of 22 in 3g4s

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Chlorine binding site 2 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8805

b:97.8
occ:1.00
 N2 0:G201 3.0 95.4 1.0
C1' 0:U202 3.3 92.5 1.0
O4' 0:U202 3.4 94.3 1.0
O 0:HOH7270 3.6 56.5 1.0
C5 0:C197 3.6 0.2 1.0
O 0:HOH3796 3.6 77.0 1.0
O2 0:U202 3.9 92.0 1.0
N4 0:C197 3.9 0.3 1.0
C2 0:G201 4.0 94.7 1.0
N1 0:U202 4.1 91.5 1.0
N3 0:G201 4.2 94.3 1.0
C5' 0:G229 4.2 71.0 1.0
O3' 0:G229 4.2 71.9 1.0
O2' 0:U202 4.2 90.2 1.0
C4 0:C197 4.2 0.6 1.0
C2 0:U202 4.3 91.9 1.0
C2' 0:U202 4.4 92.4 1.0
C4' 0:U202 4.5 94.4 1.0
C6 0:C197 4.6 0.8 1.0
C4' 0:G229 4.6 71.2 1.0
O 0:HOH3289 4.6 71.7 1.0
OP1 0:C230 4.7 75.3 1.0
OP1 0:G229 4.8 71.2 1.0
P 0:C230 5.0 73.2 1.0
C3' 0:G229 5.0 71.4 1.0

Chlorine binding site 3 out of 22 in 3g4s

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Chlorine binding site 3 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8811

b:99.1
occ:1.00
 N Q:HIS53 3.1 73.7 1.0
O2' 0:C2388 3.2 71.8 1.0
O 0:HOH7210 3.4 30.2 1.0
CE2 Q:PHE56 3.5 66.5 1.0
O 0:HOH8228 3.6 56.6 1.0
CB Q:PHE52 3.6 74.6 1.0
CA Q:PHE52 3.7 75.2 1.0
O4' 0:C2388 3.8 71.9 1.0
CB Q:HIS53 3.8 72.4 1.0
C Q:PHE52 3.8 75.1 1.0
CD2 Q:PHE56 3.8 66.4 1.0
C4' 0:C2388 3.9 71.8 1.0
C1' 0:C2388 3.9 71.7 1.0
CA Q:HIS53 4.0 71.7 1.0
C2' 0:C2388 4.1 71.5 1.0
CG2 Q:ILE84 4.2 68.0 1.0
C3' 0:C2388 4.6 71.9 1.0
CG1 Q:ILE84 4.6 67.7 1.0
CZ Q:PHE56 4.8 65.5 1.0
CB Q:ILE84 4.9 68.2 1.0
CG Q:PHE52 4.9 75.0 1.0
O Q:HOH3082 4.9 47.4 1.0
O Q:PHE52 4.9 75.0 1.0
O3' 0:C2388 5.0 72.6 1.0
C5' 0:C2388 5.0 72.5 1.0

Chlorine binding site 4 out of 22 in 3g4s

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Chlorine binding site 4 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8812

b:59.0
occ:1.00
 O 0:HOH4058 2.5 33.0 1.0
OG K:SER33 3.2 73.2 1.0
C2 0:A2596 3.2 63.0 1.0
N3 0:A2596 3.2 63.9 1.0
N2 0:G2582 3.4 57.4 1.0
O K:ILE32 3.6 70.4 1.0
CD K:LYS14 3.6 51.2 1.0
NZ K:LYS14 3.7 51.1 1.0
CE K:LYS14 3.8 51.1 1.0
CB K:SER33 4.0 73.0 1.0
CG K:PRO45 4.0 66.1 1.0
N3 0:A2583 4.1 49.3 1.0
CA K:SER33 4.2 72.3 1.0
C1' 0:U2597 4.3 69.6 1.0
O 0:HOH7499 4.3 59.4 1.0
N1 0:A2596 4.4 64.2 1.0
C K:ILE32 4.6 69.9 1.0
C2 0:A2583 4.6 49.9 1.0
C4 0:A2596 4.6 64.5 1.0
C2 0:G2582 4.6 55.7 1.0
C4 0:A2583 4.7 48.4 1.0
CB K:PRO45 4.7 67.1 1.0
O2 0:U2597 4.7 69.1 1.0
C1' 0:A2583 4.7 50.0 1.0
CG K:LYS14 4.7 51.7 1.0
O4' 0:U2597 4.8 68.2 1.0
N1 0:U2597 4.8 70.0 1.0
N K:SER33 4.9 70.7 1.0
N1 0:G2582 4.9 55.4 1.0
N9 0:A2583 4.9 47.8 1.0
C2 0:U2597 5.0 69.6 1.0

Chlorine binding site 5 out of 22 in 3g4s

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Chlorine binding site 5 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8813

b:68.3
occ:1.00
 O 0:HOH3448 2.8 0.0 1.0
N1 0:G1329 2.9 55.2 1.0
N2 0:G1329 3.0 52.4 1.0
N6 0:A1328 3.4 43.9 1.0
C2 0:G1329 3.5 52.9 1.0
N2 0:G1299 3.5 55.5 1.0
O 0:HOH3850 3.5 79.7 1.0
O2' 0:G1300 3.7 61.4 1.0
O 0:HOH5853 3.8 41.4 1.0
C6 0:G1329 4.0 56.3 1.0
O 0:HOH8283 4.0 42.7 1.0
O6 0:G1329 4.2 59.5 1.0
C1' 0:G1300 4.2 61.3 1.0
O 0:HOH3687 4.3 60.4 1.0
N1 0:A1330 4.3 57.0 1.0
O4' 0:G1300 4.4 62.0 1.0
C2 0:G1299 4.4 55.2 1.0
N3 0:G1299 4.6 57.6 1.0
C2' 0:G1300 4.6 61.4 1.0
C6 0:A1328 4.7 42.9 1.0
N3 0:G1329 4.8 53.0 1.0
C2 0:A1330 4.8 56.1 1.0
MG 0:MG8059 4.8 40.3 1.0
C4' 0:G1300 4.9 63.4 1.0

Chlorine binding site 6 out of 22 in 3g4s

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Chlorine binding site 6 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8814

b:67.5
occ:1.00
 O L:HOH7681 2.7 58.4 1.0
O2' 0:G644 3.1 49.9 1.0
ND1 L:HIS13 3.1 65.0 1.0
O 0:HOH7269 3.8 79.0 1.0
CG L:GLN7 3.8 71.8 1.0
C2' 0:G644 3.9 46.3 1.0
CG L:HIS13 4.0 65.3 1.0
CB L:HIS13 4.0 65.3 1.0
CE1 L:HIS13 4.0 65.8 1.0
N9 0:G644 4.1 41.8 1.0
CG L:LYS4 4.2 88.1 1.0
O L:HOH6828 4.2 57.8 1.0
C4 0:G644 4.3 41.4 1.0
CB L:GLN7 4.3 70.7 1.0
C8 0:G644 4.4 42.5 1.0
C1' 0:G644 4.4 44.8 1.0
O L:HIS13 4.5 65.3 1.0
C5 0:G644 4.6 42.4 1.0
O L:HOH7016 4.6 60.6 1.0
N3 0:G644 4.6 40.2 1.0
CD L:GLN7 4.7 73.5 1.0
N7 0:G644 4.7 42.9 1.0
CA L:LYS4 4.9 86.5 1.0
OE1 L:GLN7 4.9 73.2 1.0
CE L:LYS4 4.9 91.6 1.0

Chlorine binding site 7 out of 22 in 3g4s

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Chlorine binding site 7 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8815

b:90.0
occ:1.00
 O4' 0:G1647 3.1 79.9 1.0
N6 0:A1598 3.4 68.2 1.0
C1' 0:G1647 3.4 82.2 1.0
N2 0:G1646 3.6 77.6 1.0
N6 0:A1597 4.0 65.5 1.0
C4' 0:G1647 4.0 78.5 1.0
N3 0:G1646 4.1 76.7 1.0
N9 0:G1647 4.3 83.7 1.0
C2 0:G1646 4.4 76.9 1.0
O2' 0:G1646 4.4 72.8 1.0
O2' 0:G1647 4.5 82.0 1.0
N3 0:G1540 4.5 83.1 1.0
C6 0:A1598 4.5 67.8 1.0
C2' 0:G1647 4.6 81.0 1.0
O 0:HOH5804 4.7 52.1 1.0
N2 0:G1540 4.8 83.7 1.0
C5' 0:G1647 4.9 77.1 1.0

Chlorine binding site 8 out of 22 in 3g4s

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Chlorine binding site 8 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8816

b:86.6
occ:1.00
 NZ J:LYS56 3.1 64.0 1.0
N4 0:C1243 3.3 51.9 1.0
C8 0:G1119 3.4 55.1 1.0
O2' 0:G1119 3.5 61.9 1.0
CD J:LYS56 3.6 67.2 1.0
N7 0:G1119 3.8 53.4 1.0
CE J:LYS56 3.9 65.1 1.0
C2' 0:G1119 4.1 60.3 1.0
OE1 J:GLN52 4.1 84.8 1.0
N9 0:G1119 4.2 55.7 1.0
C4 0:C1243 4.4 53.3 1.0
NE2 J:GLN52 4.5 84.2 1.0
C5 0:C1243 4.5 54.1 1.0
CD J:GLN52 4.7 84.9 1.0
C1' 0:G1119 4.7 59.2 1.0
O 0:HOH8060 4.7 63.8 1.0
C5 0:G1119 4.8 51.5 1.0
O 0:HOH6604 4.9 69.6 1.0
N6 0:A1242 4.9 51.6 1.0
N7 0:A1242 4.9 51.9 1.0
CG J:LYS56 4.9 67.3 1.0

Chlorine binding site 9 out of 22 in 3g4s

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Chlorine binding site 9 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8817

b:63.4
occ:1.00
 O2' 0:C594 2.8 75.3 1.0
O Y:HOH1120 3.0 52.8 1.0
O 0:HOH3456 3.3 89.7 1.0
O4' 0:U595 3.5 84.0 1.0
NE Y:ARG115 3.5 58.8 1.0
CG Y:ARG115 3.6 59.5 1.0
O Y:HOH6413 3.6 85.0 1.0
CD Y:ARG115 3.7 58.8 1.0
C4' 0:U595 3.7 82.3 1.0
C5' 0:U595 3.9 80.1 1.0
C2' 0:C594 3.9 77.2 1.0
NH2 Y:ARG122 3.9 80.0 1.0
O 0:HOH6028 4.0 91.0 1.0
O 0:HOH5685 4.1 90.8 1.0
CZ Y:ARG115 4.6 59.5 1.0
C1' 0:C594 4.6 78.2 1.0
C1' 0:U595 4.7 85.6 1.0
O2 0:C594 4.8 80.7 1.0
O5' 0:U595 4.9 76.8 1.0
NE2 Y:GLN119 5.0 77.5 1.0
NH2 Y:ARG115 5.0 59.5 1.0
O Y:HOH3604 5.0 43.6 1.0

Chlorine binding site 10 out of 22 in 3g4s

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Chlorine binding site 10 out of 22 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


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 Tiamulin Bound to the Large Ribosomal Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Cl8822

b:94.4
occ:1.00
 N1 0:G1072 2.9 44.8 1.0
O 0:HOH4369 3.1 63.7 1.0
N2 0:G1072 3.3 44.0 1.0
C8 0:G1087 3.4 56.6 1.0
C2 0:G1072 3.6 44.6 1.0
N7 0:G1087 3.7 56.4 1.0
N6 0:A1291 3.7 54.2 1.0
N7 0:A1291 3.8 53.1 1.0
O2' 0:G1087 3.8 60.1 1.0
C6 0:G1072 3.9 47.1 1.0
O6 0:G1072 3.9 48.7 1.0
C5 0:A1291 4.0 52.0 1.0
C6 0:A1291 4.0 52.6 1.0
N9 0:G1087 4.1 56.5 1.0
O 0:HOH3877 4.2 88.1 1.0
O 0:HOH8747 4.2 0.6 1.0
C2' 0:G1087 4.3 60.4 1.0
C5 0:G1087 4.4 54.4 1.0
C8 0:A1291 4.5 51.9 1.0
C1' 0:G1087 4.6 59.0 1.0
C4 0:G1087 4.7 54.2 1.0
OE1 W:GLU10 4.7 85.2 1.0
O 0:HOH3445 4.7 55.0 1.0
C4 0:A1291 4.9 51.3 1.0
N3 0:G1072 4.9 46.4 1.0
OE2 W:GLU10 4.9 87.2 1.0
N1 0:A1291 4.9 52.7 1.0

Reference:

G.Gurel, G.Blaha, P.B.Moore, T.A.Steitz. U2504 Determines the Species Specificity of the A-Site Cleft Antibiotics: the Structures of Tiamulin, Homoharringtonine, and Bruceantin Bound to the Ribosome. J.Mol.Biol. V. 389 146 2009.
ISSN: ISSN 0022-2836
PubMed: 19362093
DOI: 10.1016/J.JMB.2009.04.005
Page generated: Sat Jul 20 19:59:18 2024

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