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Strontium in PDB 1yhq: Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yhq was solved by D.Tu, 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) 29.96 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 212.081, 298.910, 574.815, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 22.9

Other elements in 1yhq:

The structure of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 93 atoms
Potassium (K) 2 atoms
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 Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui (pdb code 1yhq). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 108 binding sites of Strontium where determined in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yhq:
Jump to Strontium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Strontium binding site 1 out of 108 in 1yhq

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Strontium binding site 1 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8901

b:71.9
occ:1.00
 O 0:HOH4451 2.2 39.0 1.0
O 0:HOH4779 2.3 27.9 1.0
N7 0:G824 2.3 28.5 1.0
N7 0:G854 2.3 21.9 1.0
O 0:HOH4913 2.4 27.6 1.0
O 0:HOH5018 2.5 46.2 1.0
C8 0:G824 3.1 28.2 1.0
C8 0:G854 3.2 21.9 1.0
C5 0:G824 3.4 24.6 1.0
C5 0:G854 3.5 19.2 1.0
O6 0:G854 3.8 22.9 1.0
OP2 0:G854 3.9 25.1 1.0
O6 0:G824 3.9 25.6 1.0
C6 0:G854 4.0 21.7 1.0
C6 0:G824 4.1 25.3 1.0
OP2 0:G824 4.1 33.4 1.0
OP2 0:U823 4.2 26.7 1.0
N9 0:G824 4.3 26.8 1.0
N9 0:G854 4.4 21.4 1.0
O 0:HOH4080 4.4 39.2 1.0
C4 0:G824 4.5 25.6 1.0
OP2 0:C853 4.5 27.9 1.0
C4 0:G854 4.6 20.9 1.0
C5 0:U823 4.7 26.6 1.0
O5' 0:G854 4.9 27.2 1.0
C6 0:U823 4.9 26.7 1.0
O5' 0:G824 4.9 29.1 1.0
C5 0:C853 4.9 20.6 1.0

Strontium binding site 2 out of 108 in 1yhq

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Strontium binding site 2 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8902

b:49.6
occ:1.00
 OP1 0:G836 2.2 27.5 1.0
OP1 0:U2615 2.3 24.4 1.0
O B:HOH8994 2.3 32.0 1.0
O 0:HOH4333 2.5 37.4 1.0
OE1 B:GLN230 2.6 22.7 1.0
O 0:HOH9861 2.6 17.8 1.0
CD B:GLN230 3.6 22.2 1.0
P 0:G836 3.7 26.8 1.0
P 0:U2615 3.7 20.5 1.0
O 0:HOH3051 3.9 40.7 1.0
CB B:GLN230 3.9 23.6 1.0
CG B:GLN230 4.0 21.1 1.0
O 0:HOH7284 4.1 56.0 1.0
O 0:HOH5521 4.1 36.4 1.0
O 0:HOH9704 4.2 37.7 1.0
C5' 0:G836 4.3 25.3 1.0
O5' 0:G836 4.3 28.1 1.0
OP2 0:U2615 4.4 23.4 1.0
O 0:HOH4485 4.4 35.6 1.0
CA B:GLN230 4.4 23.9 1.0
O3' 0:C2614 4.4 21.8 1.0
O B:GLN230 4.5 23.5 1.0
O3' 0:U835 4.5 27.0 1.0
C3' 0:U835 4.5 25.1 1.0
OP2 0:G836 4.6 29.7 1.0
O5' 0:U2615 4.7 23.6 1.0
NE2 B:GLN230 4.8 21.1 1.0
OP2 0:G2616 4.8 22.2 1.0
N2 0:G2616 4.9 24.0 1.0
C B:GLN230 5.0 23.5 1.0
O 0:HOH9559 5.0 27.7 1.0

Strontium binding site 3 out of 108 in 1yhq

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Strontium binding site 3 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8903

b:41.7
occ:1.00
 O6 0:G1491 2.4 32.0 1.0
O 0:HOH4449 2.5 47.8 1.0
OP2 0:G1489 2.6 29.8 1.0
O 0:HOH9897 2.7 25.8 1.0
O 0:HOH6644 2.7 27.3 1.0
O 0:HOH4128 2.7 32.3 1.0
C6 0:G1491 3.6 31.6 1.0
P 0:G1489 3.8 33.8 1.0
OP1 0:G1489 4.1 34.0 1.0
O 0:HOH6758 4.2 23.1 1.0
OP2 0:A1487 4.3 28.6 1.0
C5 0:G1491 4.4 32.8 1.0
O 0:HOH9658 4.4 31.3 1.0
N7 0:G1491 4.4 33.1 1.0
N7 0:G1490 4.6 27.0 1.0
O5' 0:G1489 4.7 29.8 1.0
N1 0:G1491 4.7 29.5 1.0
OP1 0:G1453 4.7 33.0 1.0
OP2 0:G1490 4.8 28.1 1.0
O3' 0:U1488 4.9 31.8 1.0

Strontium binding site 4 out of 108 in 1yhq

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Strontium binding site 4 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8904

b:34.8
occ:1.00
 O 0:HOH9931 2.4 21.8 1.0
O 0:HOH7047 2.5 19.2 1.0
O 0:HOH8432 2.5 15.0 1.0
OP1 0:G1354 2.6 27.1 1.0
OP2 0:A643 2.8 19.1 1.0
OP1 0:C1353 3.0 35.1 1.0
O3' 0:C1353 3.6 21.2 1.0
P 0:G1354 3.6 21.6 1.0
P 0:A643 3.7 19.3 1.0
OP1 0:A643 3.8 22.6 1.0
O4 0:U904 4.3 22.9 1.0
P 0:C1353 4.3 39.1 1.0
OP1 0:G642 4.4 25.9 1.0
O5' 0:C1353 4.5 35.7 1.0
N3 0:U904 4.5 21.8 1.0
OP2 0:G1354 4.6 21.6 1.0
O5' 0:A643 4.6 19.6 1.0
OP2 0:G642 4.6 25.8 1.0
C3' 0:C1353 4.6 24.3 1.0
C5' 0:C1353 4.6 26.9 1.0
N1 0:A1355 4.6 23.2 1.0
O5' 0:G1354 4.8 20.1 1.0
P 0:G642 4.8 24.0 1.0
O2' 0:A1352 4.8 49.0 1.0
O5' 0:G642 4.9 24.9 1.0
C4 0:U904 4.9 20.9 1.0
N6 0:A1355 4.9 18.1 1.0
O 0:HOH6710 5.0 43.6 1.0

Strontium binding site 5 out of 108 in 1yhq

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Strontium binding site 5 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 5 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8905

b:48.8
occ:1.00
 O 0:HOH7055 2.5 43.0 1.0
OP1 0:A1755 2.7 25.4 1.0
O 0:HOH7625 2.7 30.3 1.0
O 0:HOH8117 2.8 26.7 1.0
O3' 0:A1754 3.5 26.7 1.0
P 0:A1755 3.7 27.0 1.0
OP1 0:C1738 4.5 35.9 1.0
C5' 0:A1755 4.6 28.6 1.0
O 0:HOH3533 4.7 52.5 1.0
O5' 0:A1755 4.7 28.2 1.0
N2 0:G834 4.7 22.5 1.0
C3' 0:A1754 4.8 25.3 1.0
OP2 0:C1738 4.8 36.6 1.0
O2' 0:G834 4.8 21.1 1.0
OP2 0:A1755 4.8 26.6 1.0
N3 0:G834 5.0 23.2 1.0
O 0:HOH3654 5.0 23.4 1.0

Strontium binding site 6 out of 108 in 1yhq

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Strontium binding site 6 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 6 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8906

b:40.7
occ:1.00
 O2 0:C893 2.6 23.0 1.0
O C:HOH8547 2.6 37.3 1.0
O2' 0:C893 2.7 22.7 1.0
O 0:HOH8431 2.8 28.5 1.0
O 0:HOH6107 2.8 15.3 1.0
O 0:HOH6741 3.6 20.7 1.0
C2 0:C893 3.7 18.4 1.0
C2' 0:C893 3.8 21.1 1.0
C1' 0:C893 3.8 20.6 1.0
O3' 0:C893 4.2 23.8 1.0
N1 0:C893 4.2 19.1 1.0
O 0:HOH5711 4.4 37.2 1.0
N7 0:G892 4.4 18.6 1.0
O C:HOH8514 4.5 17.3 1.0
C3' 0:C893 4.6 22.7 1.0
O 0:HOH4385 4.6 27.9 1.0
OP2 0:G892 4.7 18.3 1.0
OP2 0:A895 4.7 27.6 1.0
N3 0:C893 4.8 19.0 1.0
NZ 1:LYS53 4.9 28.0 1.0
O 0:HOH4896 5.0 33.2 1.0

Strontium binding site 7 out of 108 in 1yhq

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Strontium binding site 7 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 7 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8907

b:33.5
occ:1.00
 O H:ASP13 2.5 34.7 1.0
O6 0:G1055 2.6 31.1 1.0
O 0:HOH6803 2.6 28.5 1.0
O 0:HOH4321 2.7 30.0 1.0
O 0:HOH5315 2.7 24.6 1.0
O H:HOH8991 2.9 27.9 1.0
C H:ASP13 3.7 36.7 1.0
C6 0:G1055 3.7 26.1 1.0
CB H:ASP13 4.1 38.6 1.0
O 0:HOH3783 4.2 28.6 1.0
CG H:LYS14 4.3 37.4 1.0
N7 0:G1055 4.3 25.1 1.0
C5 0:G1055 4.4 24.9 1.0
CA H:ASP13 4.5 37.6 1.0
OP2 0:G1054 4.5 27.4 1.0
OD1 H:ASP13 4.5 40.3 1.0
CG H:ASP13 4.6 39.5 1.0
N7 0:G1054 4.6 31.2 1.0
CE H:LYS14 4.7 37.8 1.0
N H:LYS14 4.7 35.6 1.0
CA H:LYS14 4.8 36.0 1.0
N1 0:G1055 4.8 26.1 1.0

Strontium binding site 8 out of 108 in 1yhq

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Strontium binding site 8 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 8 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8908

b:71.4
occ:1.00
 OP1 0:A183 2.5 37.3 1.0
OP1 0:G147 2.7 29.3 1.0
OD2 M:ASP157 2.8 43.9 1.0
O M:HOH8939 3.0 45.1 1.0
O3' 0:G182 3.4 31.4 1.0
O3' 0:U146 3.5 24.1 1.0
CG M:ASP157 3.6 39.9 1.0
P 0:A183 3.6 33.6 1.0
OD1 M:ASP157 3.6 38.7 1.0
P 0:G147 3.7 25.2 1.0
O 0:HOH3609 4.3 38.5 1.0
C5' 0:G147 4.4 27.7 1.0
O 0:HOH7318 4.4 43.7 1.0
O5' 0:G147 4.5 29.0 1.0
O5' 0:A183 4.6 33.5 1.0
C3' 0:G182 4.6 32.5 1.0
C5' 0:A183 4.7 32.1 1.0
OP2 0:A183 4.7 35.7 1.0
C3' 0:U146 4.8 27.4 1.0
C5' 0:G182 4.9 34.0 1.0
OP2 0:G147 5.0 26.4 1.0
O2' 0:U146 5.0 28.0 1.0
CB M:ASP157 5.0 37.6 1.0

Strontium binding site 9 out of 108 in 1yhq

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Strontium binding site 9 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 9 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8909

b:70.1
occ:1.00
 O 0:HOH4262 2.3 52.4 1.0
O 0:HOH5986 2.5 55.2 1.0
O 0:HOH4739 2.6 74.8 1.0
O 0:HOH6625 2.8 67.3 1.0
O 0:HOH7059 2.9 64.8 1.0
O 0:HOH7353 3.0 52.1 1.0
O 0:HOH8365 3.1 46.2 1.0
O 0:HOH8364 3.1 42.2 1.0
O 0:HOH4544 3.5 51.3 1.0
OP2 0:C2077 4.3 28.1 1.0
O 0:HOH6650 4.4 77.8 1.0
O 0:HOH4180 4.4 34.2 1.0
O6 0:G2080 4.5 33.5 1.0
N6 0:A536 4.8 35.6 1.0
N7 0:G2079 4.9 27.4 1.0

Strontium binding site 10 out of 108 in 1yhq

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Strontium binding site 10 out of 108 in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 10 of Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Sr8910

b:80.9
occ:1.00
 OP1 0:G2585 2.2 27.3 1.0
OP2 0:A1747 2.3 30.1 1.0
O4 0:U1749 2.4 33.4 1.0
OP2 0:U1748 2.4 27.1 1.0
O 0:HOH3179 2.5 32.6 1.0
C4 0:U1749 3.3 30.5 1.0
P 0:G2585 3.3 28.2 1.0
OP2 0:G2585 3.6 29.4 1.0
O 0:HOH5416 3.7 43.1 1.0
P 0:U1748 3.7 26.4 1.0
C5 0:U1749 3.7 30.4 1.0
P 0:A1747 3.8 26.4 1.0
O 0:HOH3281 3.8 25.0 1.0
OP2 0:U2586 4.1 28.3 1.0
OP1 0:U1748 4.2 22.6 1.0
SR 0:SR8982 4.2 0.4 1.0
C5' 0:A1747 4.3 26.4 1.0
O 0:HOH4309 4.3 44.4 1.0
O5' 0:A1747 4.3 29.7 1.0
O5' 0:G2585 4.3 28.1 1.0
O 0:HOH8281 4.4 20.9 1.0
O3' 0:G2584 4.5 28.3 1.0
N3 0:U1749 4.5 30.7 1.0
O3' 0:A1747 4.6 26.6 1.0
OP1 0:A1747 4.7 31.2 1.0
O3' 0:A1746 4.7 27.5 1.0
C5' 0:G2585 4.7 27.4 1.0
C5 0:U1748 4.7 30.4 1.0
O5' 0:U1748 4.7 24.3 1.0
OP1 0:U2586 4.9 27.8 1.0
P 0:U2586 4.9 27.5 1.0
O 0:HOH3969 5.0 44.1 1.0

Reference:

D.Tu, G.Blaha, P.B.Moore, T.A.Steitz. Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide A Structural Explanation For Resistance. Cell(Cambridge,Mass.) V. 121 257 2005.
ISSN: ISSN 0092-8674
PubMed: 15851032
DOI: 10.1016/J.CELL.2005.02.005
Page generated: Thu Oct 10 20:56:29 2024

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