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Strontium 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:

Magnesium (Mg) 93 atoms
Potassium (K) 1 atom
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms
Sodium (Na) 75 atoms

Strontium Binding Sites:

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 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 108;

Binding sites:

The binding sites of Strontium 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 Strontium atom.
In total 108 binding sites of Strontium where determined in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit, PDB code: 3g4s:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 108 in 3g4s

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Strontium binding site 1 out of 108 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 Strontium with other atoms in the Sr 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:Sr8901

b:89.0
occ:1.00
 N7 0:G824 2.8 67.4 1.0
O 0:HOH8680 2.9 61.2 1.0
N7 0:G854 2.9 46.6 1.0
O 0:HOH3276 3.1 38.2 1.0
O 0:HOH3123 3.1 75.0 1.0
C8 0:G824 3.3 68.4 1.0
O 0:HOH2936 3.3 65.8 1.0
C8 0:G854 3.4 49.4 1.0
OP2 0:G824 4.0 79.2 1.0
C5 0:G824 4.0 67.7 1.0
OP2 0:U823 4.1 74.1 1.0
C5 0:G854 4.2 50.2 1.0
OP2 0:G854 4.3 61.8 1.0
OP2 0:C853 4.4 70.1 1.0
C5 0:U823 4.6 72.6 1.0
N9 0:G824 4.6 69.2 1.0
O6 0:G824 4.7 66.5 1.0
N9 0:G854 4.7 51.1 1.0
C6 0:G824 4.8 67.9 1.0
C6 0:U823 4.8 73.1 1.0
O5' 0:G824 4.9 75.1 1.0
O5' 0:U823 4.9 72.8 1.0
O6 0:G854 4.9 51.2 1.0
O 0:HOH5907 4.9 77.6 1.0
O5' 0:C853 4.9 67.5 1.0
O5' 0:G854 5.0 57.0 1.0
C6 0:G854 5.0 51.9 1.0

Strontium binding site 2 out of 108 in 3g4s

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Strontium binding site 2 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8902

b:63.5
occ:1.00
 OP1 0:G836 2.6 49.4 1.0
OP1 0:U2615 2.7 44.8 1.0
O 0:HOH4236 3.0 36.1 1.0
OE1 B:GLN230 3.0 58.5 1.0
O 0:HOH3980 3.3 36.5 1.0
O 0:HOH8488 3.3 43.3 1.0
P 0:G836 3.5 49.3 1.0
OP2 0:G836 3.5 50.3 1.0
O 0:HOH3914 3.5 45.9 1.0
O 0:HOH3694 3.9 42.5 1.0
CB B:GLN230 3.9 57.5 1.0
CD B:GLN230 4.0 59.1 1.0
P 0:U2615 4.0 45.5 1.0
C5' 0:G836 4.2 47.9 1.0
CG B:GLN230 4.2 59.0 1.0
O5' 0:G836 4.2 47.9 1.0
O 0:HOH3253 4.3 31.3 1.0
O B:GLN230 4.4 56.3 1.0
CA B:GLN230 4.5 56.3 1.0
O 0:HOH3107 4.6 29.9 1.0
OP2 0:U2615 4.6 46.6 1.0
O3' 0:C2614 4.8 42.5 1.0
O3' 0:U835 4.8 48.0 1.0
O 0:HOH6446 4.8 40.1 1.0
O 0:HOH8713 4.9 48.2 1.0
O 0:HOH4988 4.9 36.4 1.0
OP2 0:U837 4.9 54.5 1.0
C B:GLN230 5.0 56.5 1.0

Strontium binding site 3 out of 108 in 3g4s

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Strontium binding site 3 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8903

b:62.8
occ:1.00
 O6 0:G1491 2.9 88.8 1.0
O 0:HOH4367 2.9 18.8 1.0
OP2 0:G1489 2.9 68.3 1.0
O 0:HOH5539 3.0 54.5 1.0
O 0:HOH8679 3.1 59.0 1.0
O 0:HOH5697 3.1 28.8 1.0
OP1 0:G1489 3.5 69.6 1.0
O 0:HOH8278 3.6 47.2 1.0
P 0:G1489 3.7 68.2 1.0
C6 0:G1491 4.0 87.7 1.0
OP2 0:A1487 4.0 56.9 1.0
O 0:HOH5552 4.6 85.8 1.0
O5' 0:G1489 4.7 66.0 1.0
N7 0:G1491 4.7 87.7 1.0
C5 0:G1491 4.7 87.1 1.0
OP1 0:A1487 4.8 57.1 1.0
OP2 0:U1488 4.8 69.0 1.0
P 0:A1487 4.9 56.2 1.0
O3' 0:U1488 4.9 68.7 1.0

Strontium binding site 4 out of 108 in 3g4s

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Strontium binding site 4 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8904

b:64.6
occ:1.00
 OP1 0:G1354 2.8 48.8 1.0
OP2 0:A643 2.9 50.6 1.0
O 0:HOH4531 3.0 37.4 1.0
O 0:HOH7482 3.2 0.6 1.0
O 0:HOH6104 3.4 33.7 1.0
O 0:HOH7535 3.6 55.7 1.0
P 0:A643 3.8 48.3 1.0
O3' 0:C1353 3.8 51.2 1.0
P 0:G1354 3.9 46.7 1.0
OP1 0:C1353 3.9 66.7 1.0
OP1 0:A643 3.9 49.0 1.0
C5' 0:C1353 3.9 58.5 1.0
O5' 0:C1353 4.1 61.8 1.0
O4 0:U904 4.5 59.0 1.0
NH2 L:ARG8 4.5 67.7 1.0
OP1 0:G642 4.5 50.8 1.0
N3 0:U904 4.6 54.9 1.0
C3' 0:C1353 4.6 55.1 1.0
O2' 0:A1352 4.6 69.0 1.0
O5' 0:A643 4.7 45.0 1.0
P 0:C1353 4.7 66.6 1.0
C4' 0:C1353 4.7 57.5 1.0
O5' 0:G642 4.8 49.1 1.0
O5' 0:G1354 4.8 47.0 1.0
OP2 0:G642 4.9 48.7 1.0
OP2 0:G1354 4.9 47.7 1.0
P 0:G642 5.0 49.8 1.0
N6 0:A1355 5.0 49.1 1.0

Strontium binding site 5 out of 108 in 3g4s

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Strontium binding site 5 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8905

b:70.6
occ:1.00
 OP1 0:A1755 2.8 62.1 1.0
O 0:HOH7509 3.0 78.5 1.0
O 0:HOH7035 3.1 43.6 1.0
O 0:HOH6927 3.2 67.7 1.0
P 0:A1755 3.9 63.2 1.0
O3' 0:A1754 3.9 59.7 1.0
OP1 0:C1738 4.1 60.9 1.0
N2 0:G834 4.3 45.9 1.0
O 0:HOH6117 4.3 64.9 1.0
OP2 0:C1738 4.4 61.3 1.0
O2 0:C849 4.5 63.4 1.0
P 0:C1738 4.8 61.4 1.0
C5' 0:A1755 4.9 56.3 1.0
OP2 0:A1755 4.9 62.7 1.0
N3 0:G834 4.9 43.6 1.0
O5' 0:A1755 4.9 60.5 1.0

Strontium binding site 6 out of 108 in 3g4s

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Strontium binding site 6 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8906

b:65.4
occ:1.00
 O2 0:C893 2.8 39.6 1.0
O2' 0:C893 2.8 43.3 1.0
O 0:HOH5674 3.1 30.4 1.0
O 0:HOH8609 3.2 28.6 1.0
O 0:HOH7673 3.2 42.0 1.0
O 1:HOH401 3.2 23.8 1.0
O C:HOH6325 3.4 30.7 1.0
C2 0:C893 3.9 38.1 1.0
C2' 0:C893 4.0 40.7 1.0
O 0:HOH5824 4.0 53.6 1.0
C1' 0:C893 4.1 39.7 1.0
O 0:HOH3095 4.2 32.8 1.0
N7 0:G892 4.2 23.5 1.0
N1 0:C893 4.4 38.7 1.0
O3' 0:C893 4.5 40.3 1.0
O 0:HOH4776 4.5 39.3 1.0
O C:HOH4236 4.5 40.4 1.0
NZ 1:LYS53 4.6 66.9 1.0
OP2 0:G892 4.7 40.5 1.0
N3 0:C893 4.8 36.2 1.0
C8 0:G892 4.8 24.8 1.0
C3' 0:C893 4.9 40.7 1.0
OP2 0:G891 5.0 40.8 1.0

Strontium binding site 7 out of 108 in 3g4s

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Strontium binding site 7 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8907

b:63.7
occ:1.00
 O 0:HOH8478 3.0 70.3 1.0
O 0:HOH5065 3.0 0.8 1.0
O 0:HOH5761 3.1 85.4 1.0
O6 0:G1055 3.1 76.0 1.0
O 0:HOH3682 3.5 51.7 1.0
O H:ASP13 3.6 93.6 1.0
O 0:HOH8772 3.9 78.1 1.0
O 0:HOH4902 3.9 77.5 1.0
CB H:ASP13 3.9 94.3 1.0
C H:ASP13 4.1 93.4 1.0
C6 0:G1055 4.2 74.8 1.0
N7 0:G1054 4.4 69.3 1.0
OD1 H:ASP13 4.4 95.4 1.0
CG H:ASP13 4.4 94.9 1.0
N7 0:G1055 4.4 73.6 1.0
CA H:ASP13 4.6 93.8 1.0
OP2 0:G1054 4.6 70.5 1.0
C5 0:G1055 4.7 73.7 1.0
N H:LYS14 4.8 92.7 1.0
OP2 0:G1053 5.0 74.4 1.0

Strontium binding site 8 out of 108 in 3g4s

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Strontium binding site 8 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8908

b:0.8
occ:1.00
 OD2 M:ASP157 2.9 70.4 1.0
OP1 0:G147 3.0 60.4 1.0
O 0:HOH8355 3.1 73.7 1.0
O3' 0:U146 3.2 59.0 1.0
OP1 0:A183 3.3 57.8 1.0
O M:HOH7525 3.4 55.5 1.0
OD1 M:ASP157 3.5 69.0 1.0
CG M:ASP157 3.6 68.6 1.0
P 0:G147 3.7 61.0 1.0
O3' 0:G182 3.8 56.3 1.0
O2' 0:U146 4.0 55.2 1.0
C5' 0:G147 4.1 59.1 1.0
P 0:A183 4.2 57.4 1.0
O 0:HOH7006 4.4 52.5 1.0
C3' 0:U146 4.4 57.7 1.0
O5' 0:G147 4.4 60.7 1.0
C4' 0:U146 4.6 58.3 1.0
C2' 0:U146 4.8 57.1 1.0
C3' 0:G182 4.9 55.6 1.0
C5' 0:G182 4.9 56.4 1.0

Strontium binding site 9 out of 108 in 3g4s

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Strontium binding site 9 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8909

b:89.6
occ:1.00
 O 0:HOH8417 3.0 45.9 1.0
O 0:HOH7824 3.1 55.9 1.0
O 0:HOH6121 3.2 82.7 1.0
O 0:HOH4603 3.4 50.9 1.0
O 0:HOH6103 3.5 50.7 1.0
O 0:HOH5508 3.6 0.7 1.0
O 0:HOH8329 3.6 40.4 1.0
O 0:HOH7825 3.9 73.4 1.0
O 0:HOH8770 4.1 70.8 1.0
O 0:HOH9075 4.1 75.8 1.0
OP2 0:C2077 4.5 56.7 1.0
O 0:HOH6543 4.8 0.5 1.0
N7 0:G2079 4.8 57.6 1.0
O 0:HOH5546 4.8 33.3 1.0
N6 0:A536 4.9 65.3 1.0

Strontium binding site 10 out of 108 in 3g4s

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Strontium binding site 10 out of 108 in the Co-Crystal Structure of Tiamulin Bound to the Large Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr 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:Sr8910

b:0.2
occ:1.00
 OP1 0:G2585 2.7 62.7 1.0
OP2 0:U1748 2.8 62.6 1.0
O4 0:U1749 2.9 60.1 1.0
OP2 0:A1747 3.1 55.5 1.0
O 0:HOH8466 3.1 52.6 1.0
OP2 0:G2585 3.2 61.7 1.0
P 0:G2585 3.4 61.8 1.0
O 0:HOH5778 3.5 55.4 1.0
C4 0:U1749 3.6 59.9 1.0
OP2 0:U2586 3.7 60.1 1.0
C5 0:U1749 3.8 60.0 1.0
P 0:U1748 3.8 61.6 1.0
O 0:HOH5420 3.9 37.8 1.0
OP1 0:U1748 3.9 58.9 1.0
O5' 0:G2585 4.4 60.2 1.0
SR 0:SR8982 4.4 0.0 1.0
P 0:A1747 4.5 56.3 1.0
OP1 0:G1751 4.5 53.2 1.0
O3' 0:G2584 4.6 58.7 1.0
P 0:U2586 4.8 59.4 1.0
N3 0:U1749 4.8 59.6 1.0
O5' 0:U1748 4.8 59.5 1.0
C5' 0:A1747 4.9 58.8 1.0
O3' 0:A1747 4.9 60.9 1.0
C5' 0:G2585 4.9 60.9 1.0
O 0:HOH8286 5.0 30.6 1.0
O 0:HOH8113 5.0 47.7 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: Fri Oct 11 01:17:34 2024

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