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Sodium 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:

Strontium (Sr) 108 atoms
Magnesium (Mg) 93 atoms
Potassium (K) 2 atoms
Cadmium (Cd) 5 atoms
Chlorine (Cl) 22 atoms

Sodium 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 - 75;

Binding sites:

The binding sites of Sodium 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 Sodium atom.
In total 75 binding sites of Sodium where determined in the Crystal Structure of Azithromycin Bound to the G2099A Mutant 50S Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1yhq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 1yhq

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Sodium binding site 1 out of 75 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 Sodium with other atoms in the Na 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:Na8501

b:26.8
occ:1.00
OP2 0:C1069 2.2 20.2 1.0
N7 0:G1072 2.4 22.7 1.0
O 0:HOH5452 2.4 46.9 1.0
O 0:HOH3671 2.4 28.2 1.0
O 0:HOH3702 2.7 51.3 1.0
C5 0:G1072 3.3 23.6 1.0
C8 0:G1072 3.3 21.9 1.0
O 0:HOH9566 3.4 30.3 1.0
O6 0:G1072 3.4 23.0 1.0
O6 0:G1087 3.5 26.8 1.0
P 0:C1069 3.6 23.0 1.0
C6 0:G1072 3.7 23.8 1.0
O 0:HOH4035 3.8 26.8 1.0
OP1 0:C1069 4.3 24.2 1.0
C6 0:G1087 4.4 25.1 1.0
O3' 0:C1068 4.4 23.7 1.0
C4 0:G1072 4.5 23.6 1.0
N9 0:G1072 4.5 24.1 1.0
C3' 0:C1068 4.5 24.6 1.0
O5' 0:C1069 4.6 26.5 1.0
N6 0:A1070 4.7 25.9 1.0
C5' 0:C1068 4.7 27.4 1.0
N1 0:G1087 4.8 23.3 1.0

Sodium binding site 2 out of 75 in 1yhq

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Sodium binding site 2 out of 75 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 Sodium with other atoms in the Na 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:Na8502

b:43.2
occ:1.00
O2' 0:G1119 2.8 32.6 1.0
O 0:HOH8307 2.9 41.4 1.0
O6 0:G1121 2.9 29.5 1.0
O3' 0:G1119 3.1 31.2 1.0
OP2 0:U1120 3.1 34.2 1.0
O 0:HOH5036 3.1 38.2 1.0
O 0:HOH6164 3.1 57.1 1.0
N7 0:G1121 3.3 28.6 1.0
O 0:HOH4661 3.5 23.9 1.0
O4 0:U1122 3.6 34.6 1.0
P 0:U1120 3.7 34.6 1.0
C6 0:G1121 3.7 28.7 1.0
C2' 0:G1119 3.8 30.6 1.0
C5 0:G1121 3.8 27.7 1.0
C3' 0:G1119 4.0 32.0 1.0
MG 0:MG8018 4.0 39.0 1.0
O 0:HOH7395 4.1 47.1 1.0
C1' 0:G1119 4.3 29.6 1.0
C4 0:U1122 4.3 34.4 1.0
C8 0:G1121 4.5 28.4 1.0
C5 0:U1122 4.5 33.5 1.0
OP1 0:U1120 4.6 38.0 1.0
N4 0:C1243 4.9 27.1 1.0
O5' 0:U1120 4.9 32.1 1.0

Sodium binding site 3 out of 75 in 1yhq

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Sodium binding site 3 out of 75 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 Sodium with other atoms in the Na 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:Na8504

b:26.7
occ:1.00
O 0:HOH5190 2.5 27.3 1.0
O 0:HOH4580 2.6 28.6 1.0
N3 0:A630 2.7 24.8 1.0
O 0:HOH6265 2.7 45.4 1.0
O2' 0:A630 2.7 29.1 1.0
O2' 0:A631 2.8 25.4 1.0
C2 0:A630 3.5 24.7 1.0
C2' 0:A631 3.5 25.3 1.0
OP2 0:A2074 3.5 29.4 1.0
C1' 0:A630 3.5 27.2 1.0
C4 0:A630 3.7 25.9 1.0
C2' 0:A630 3.7 29.1 1.0
C3' 0:A631 3.9 24.8 1.0
N9 0:A630 4.0 27.4 1.0
OP1 0:A632 4.0 26.4 1.0
N2 0:G2070 4.1 23.1 1.0
O3' 0:A630 4.1 29.8 1.0
O3' 0:A631 4.2 25.6 1.0
O 0:HOH9909 4.4 27.4 1.0
O 0:HOH3584 4.5 39.2 1.0
N1 0:A629 4.5 28.1 1.0
C3' 0:A630 4.6 28.0 1.0
P 0:A632 4.6 25.0 1.0
OP2 0:G2072 4.6 40.4 1.0
C2 0:A629 4.7 28.2 1.0
O4' 0:A630 4.8 28.3 1.0
C2 0:G2070 4.8 23.5 1.0
N1 0:A630 4.8 25.0 1.0
OP2 0:A632 5.0 26.9 1.0
C1' 0:A631 5.0 23.7 1.0
C5 0:A630 5.0 26.3 1.0
C2 0:1MA628 5.0 24.7 1.0
P 0:A2074 5.0 29.8 1.0

Sodium binding site 4 out of 75 in 1yhq

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Sodium binding site 4 out of 75 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 Sodium with other atoms in the Na 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:Na8505

b:33.5
occ:1.00
N7 0:G2094 2.8 24.4 1.0
N1 0:A2649 2.9 27.1 1.0
O 0:HOH9624 3.0 24.4 1.0
O6 0:G2094 3.1 31.1 1.0
N7 0:G2093 3.1 22.4 1.0
N3 0:G2092 3.3 24.9 1.0
O2' 0:G2092 3.3 23.4 1.0
C2 0:A2649 3.3 25.6 1.0
O6 0:G2093 3.5 29.4 1.0
C5 0:G2094 3.5 25.4 1.0
C5 0:G2093 3.5 23.5 1.0
N2 0:G2092 3.6 26.4 1.0
C6 0:G2094 3.6 28.2 1.0
C2 0:G2092 3.7 25.7 1.0
C6 0:G2093 3.7 23.9 1.0
N6 0:A2612 3.9 20.4 1.0
C8 0:G2094 3.9 23.1 1.0
C8 0:G2093 3.9 22.0 1.0
C6 0:A2649 4.0 26.9 1.0
C6 0:A2612 4.1 25.1 1.0
C4 0:G2092 4.2 25.9 1.0
N6 0:A2649 4.3 26.3 1.0
C2' 0:G2092 4.5 21.7 1.0
C1' 0:G2092 4.5 22.8 1.0
C4 0:G2093 4.5 22.3 1.0
N1 0:A2612 4.5 24.5 1.0
C5 0:A2612 4.5 25.2 1.0
N3 0:A2649 4.6 23.8 1.0
N9 0:G2092 4.7 23.6 1.0
N9 0:G2093 4.7 22.6 1.0
N1 0:G2092 4.8 23.2 1.0
N1 0:G2093 4.8 21.3 1.0
C4 0:G2094 4.8 25.3 1.0
N7 0:A2612 4.9 27.4 1.0
O3' 0:G2092 4.9 22.1 1.0

Sodium binding site 5 out of 75 in 1yhq

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Sodium binding site 5 out of 75 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 Sodium with other atoms in the Na 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:Na8506

b:50.6
occ:1.00
O2 0:C40 2.7 41.3 1.0
O2' 0:C40 2.7 40.0 1.0
O2 0:C443 2.8 43.1 1.0
N1 0:A442 3.0 44.7 1.0
O4' 0:G41 3.1 38.7 1.0
C2' 0:C40 3.3 40.2 1.0
C1' 0:C40 3.5 40.1 1.0
C2 0:A442 3.6 43.7 1.0
C2 0:C443 3.7 42.7 1.0
C2 0:C40 3.7 41.1 1.0
C1' 0:G41 3.9 37.4 1.0
C6 0:A442 4.0 43.6 1.0
N2 0:G39 4.0 35.6 1.0
N1 0:C40 4.1 41.0 1.0
N6 0:A442 4.2 44.2 1.0
N9 0:G41 4.3 38.2 1.0
C4' 0:G41 4.3 35.8 1.0
N3 0:C443 4.3 41.8 1.0
C5' 0:G41 4.5 35.4 1.0
N1 0:C443 4.6 43.0 1.0
C2 0:G39 4.6 36.7 1.0
C1' 0:C443 4.7 43.6 1.0
C8 0:G41 4.7 37.6 1.0
O4' 0:C40 4.7 41.8 1.0
N1 0:G39 4.7 36.9 1.0
N3 0:A442 4.8 43.5 1.0
C3' 0:C40 4.8 39.0 1.0
O 0:HOH6344 4.8 36.7 1.0
C4 0:G41 4.8 38.2 1.0
N3 0:C40 4.9 42.3 1.0
O 0:HOH7439 4.9 64.1 1.0
O5' 0:G41 5.0 37.7 1.0

Sodium binding site 6 out of 75 in 1yhq

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Sodium binding site 6 out of 75 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 Sodium with other atoms in the Na 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:Na8507

b:27.9
occ:1.00
O2 0:U1724 2.2 33.7 1.0
O2 0:C1394 2.4 33.7 1.0
O4 0:U1432 2.5 33.5 1.0
O 0:HOH3909 2.5 26.9 1.0
O6 0:G1433 3.3 41.5 1.0
C2 0:U1724 3.4 30.4 1.0
SR 0:SR8962 3.4 0.9 1.0
C2 0:C1394 3.5 33.6 1.0
C4 0:U1432 3.7 33.2 1.0
O2' 0:C1394 3.9 32.7 1.0
C6 0:G1433 4.0 38.4 1.0
C2' 0:C1394 4.0 33.6 1.0
O 0:HOH7604 4.1 60.0 1.0
N3 0:U1724 4.2 27.4 1.0
N3 0:U1432 4.3 33.5 1.0
N3 0:C1394 4.3 32.4 1.0
C1' 0:C1394 4.3 33.1 1.0
C1' 0:U1724 4.3 30.9 1.0
N1 0:C1394 4.4 33.9 1.0
N1 0:U1724 4.4 29.1 1.0
O2' 0:U1724 4.4 32.6 1.0
N1 0:G1433 4.5 38.6 1.0
O 0:HOH5321 4.5 30.8 1.0
C2' 0:U1724 4.5 32.0 1.0
O 0:HOH5943 4.6 52.8 1.0
C5 0:U1432 4.8 32.2 1.0
O2' 0:C1725 4.9 29.7 1.0
C5 0:G1433 4.9 36.7 1.0

Sodium binding site 7 out of 75 in 1yhq

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Sodium binding site 7 out of 75 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 Sodium with other atoms in the Na 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:Na8508

b:40.0
occ:1.00
O6 0:G2579 2.8 26.1 1.0
N3 0:A2577 2.9 29.8 1.0
O 0:HOH4993 3.0 38.8 1.0
N7 0:G2579 3.1 30.1 1.0
O4' 0:A2577 3.1 35.0 1.0
N7 0:G2578 3.2 30.1 1.0
O6 0:G2578 3.5 29.7 1.0
C6 0:G2579 3.5 27.9 1.0
C5 0:G2579 3.6 28.7 1.0
C5 0:G2578 3.6 30.2 1.0
O 0:HOH8253 3.7 63.7 1.0
C1' 0:A2577 3.7 33.6 1.0
C2 0:A2577 3.7 29.7 1.0
C6 0:G2578 3.7 30.2 1.0
C4 0:A2577 3.8 29.2 1.0
C4' 0:A2577 4.1 35.9 1.0
C8 0:G2578 4.1 29.0 1.0
N9 0:A2577 4.1 30.8 1.0
O 0:HOH6761 4.2 52.5 1.0
C8 0:G2579 4.2 30.6 1.0
N4 0:C2556 4.6 28.7 1.0
C4 0:G2578 4.6 28.9 1.0
N3 0:U2554 4.8 26.3 1.0
N1 0:G2579 4.8 26.8 1.0
N1 0:G2578 4.8 27.9 1.0
N9 0:G2578 4.9 29.2 1.0
N1 0:A2577 4.9 30.0 1.0
C4 0:G2579 4.9 29.1 1.0
O6 0:G2580 4.9 34.0 1.0
O3' 0:A2577 5.0 35.5 1.0
C3' 0:A2577 5.0 35.6 1.0

Sodium binding site 8 out of 75 in 1yhq

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Sodium binding site 8 out of 75 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 Sodium with other atoms in the Na 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:Na8509

b:47.3
occ:1.00
O 0:HOH4072 2.3 22.8 1.0
O 0:HOH5144 2.4 40.3 1.0
O6 0:G2525 2.5 31.6 1.0
N7 0:G2524 2.7 32.1 1.0
O 0:HOH9682 3.1 29.6 1.0
C6 0:G2525 3.5 30.3 1.0
C8 0:G2524 3.6 30.5 1.0
C5 0:G2524 3.7 28.8 1.0
O6 0:G2524 3.7 28.1 1.0
C5 0:U2523 3.8 32.9 1.0
C4 0:U2523 3.8 34.7 1.0
O 0:HOH6838 3.9 49.9 1.0
O4 0:U2523 4.0 36.5 1.0
C6 0:G2524 4.1 27.8 1.0
O 0:HOH4115 4.1 22.3 1.0
C5 0:G2525 4.3 30.8 1.0
O2' 0:C2493 4.3 30.6 1.0
N1 0:G2525 4.3 29.6 1.0
C6 0:U2523 4.4 31.9 1.0
N3 0:U2523 4.4 33.2 1.0
N7 0:G2525 4.5 32.1 1.0
OP2 0:G2524 4.5 32.2 1.0
C2' 0:C2493 4.8 31.0 1.0
N9 0:G2524 4.8 32.0 1.0
C4 0:G2524 4.9 30.6 1.0
OP2 0:U2523 4.9 36.5 1.0
N1 0:U2523 5.0 33.0 1.0

Sodium binding site 9 out of 75 in 1yhq

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Sodium binding site 9 out of 75 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 Sodium with other atoms in the Na 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:Na8511

b:59.4
occ:1.00
O 0:HOH5599 2.4 57.1 1.0
O 0:HOH4329 2.4 41.1 1.0
O 0:HOH3455 2.6 30.8 1.0
O6 0:G2399 2.6 34.9 1.0
O 0:HOH5552 2.7 49.0 1.0
N7 0:G2399 3.1 33.6 1.0
O 0:HOH6532 3.3 41.7 1.0
C6 0:G2399 3.4 34.2 1.0
C5 0:G2399 3.5 34.2 1.0
OP2 0:A2398 3.9 34.0 1.0
O6 0:G2400 3.9 36.2 1.0
O 0:HOH3889 4.0 26.5 1.0
O 0:HOH6976 4.2 70.0 1.0
O4 0:U2389 4.2 36.9 1.0
O 0:HOH6753 4.3 56.7 1.0
C8 0:G2399 4.3 32.8 1.0
N7 0:G2400 4.4 34.8 1.0
N3 0:U2389 4.5 34.0 1.0
C6 0:G2400 4.6 36.0 1.0
N1 0:G2399 4.7 33.7 1.0
C5 0:G2400 4.7 34.9 1.0
C4 0:U2389 4.9 34.7 1.0
O2 0:U2390 4.9 35.9 1.0
C4 0:G2399 4.9 33.1 1.0
O 0:HOH6617 4.9 46.0 1.0

Sodium binding site 10 out of 75 in 1yhq

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Sodium binding site 10 out of 75 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 Sodium with other atoms in the Na 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:Na8512

b:37.0
occ:1.00
O2' 0:U2607 2.4 26.3 1.0
O 0:HOH9829 2.4 28.9 1.0
O2 0:U2607 2.6 33.1 1.0
O 0:HOH3632 2.7 31.0 1.0
CZ3 B:TRP242 3.3 25.0 1.0
OP1 0:U2541 3.4 35.0 1.0
C2 0:U2607 3.5 30.1 1.0
C2' 0:U2607 3.6 26.5 1.0
C1' 0:U2607 3.8 27.9 1.0
CH2 B:TRP242 3.8 26.4 1.0
OP2 0:C2608 3.9 24.1 1.0
O 0:HOH9985 3.9 44.1 1.0
O 0:HOH5177 4.0 28.5 1.0
N1 0:U2607 4.0 30.3 1.0
OP1 0:U2610 4.1 28.4 1.0
O3' 0:U2607 4.1 24.2 1.0
CE3 B:TRP242 4.2 24.2 1.0
O 0:HOH9653 4.4 49.2 1.0
P 0:C2608 4.5 25.9 1.0
C3' 0:U2607 4.5 26.1 1.0
N3 0:U2607 4.5 29.6 1.0
P 0:U2541 4.6 35.0 1.0
O 0:HOH8308 4.6 19.8 1.0
O 0:HOH9585 4.7 36.6 1.0
O2' 0:A2488 4.7 34.3 1.0
OP2 0:U2541 4.8 32.8 1.0
CZ2 B:TRP242 5.0 24.1 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: Tue Dec 15 05:42:36 2020

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