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Sodium in PDB 2otj: 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj was solved by G.Blaha, S.J.Schroeder, J.Tirado-Rives, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.70 / 2.90
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.738, 299.519, 573.593, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.8

Other elements in 2otj:

The structure of 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium (Mg) 117 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 - 80; Page 9, Binding sites: 81 - 86;

Binding sites:

The binding sites of Sodium atom in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui (pdb code 2otj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui, PDB code: 2otj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 in 2otj

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Sodium binding site 1 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8501

b:50.2
occ:1.00
OP2 0:C1069 2.3 36.7 1.0
O 0:HOH4999 2.3 68.8 1.0
O 0:HOH3184 2.6 48.4 1.0
N7 0:G1072 2.7 30.5 1.0
O 0:HOH3217 3.0 59.3 1.0
O6 0:G1072 3.3 30.0 1.0
O6 0:G1087 3.4 39.4 1.0
C5 0:G1072 3.4 30.1 1.0
C8 0:G1072 3.7 29.8 1.0
O 0:HOH9069 3.7 42.7 1.0
P 0:C1069 3.7 37.7 1.0
C6 0:G1072 3.7 29.8 1.0
O3' 0:C1068 4.3 39.4 1.0
C6 0:G1087 4.3 38.6 1.0
C3' 0:C1068 4.3 41.1 1.0
C5' 0:C1068 4.4 43.2 1.0
OP1 0:C1069 4.4 36.0 1.0
O 0:HOH3554 4.5 35.2 1.0
C4 0:G1072 4.6 30.4 1.0
N9 0:G1072 4.7 30.8 1.0
O5' 0:C1069 4.7 36.7 1.0
N1 0:G1087 4.8 38.3 1.0
O 0:HOH5488 5.0 49.3 1.0
C4' 0:C1068 5.0 42.4 1.0

Sodium binding site 2 out of 86 in 2otj

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Sodium binding site 2 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8502

b:57.5
occ:1.00
N7 0:G1121 2.9 40.4 1.0
O3' 0:G1119 3.0 39.3 1.0
O2' 0:G1119 3.0 38.2 1.0
OP2 0:U1120 3.0 39.4 1.0
O6 0:G1121 3.0 39.5 1.0
O 0:HOH7788 3.2 58.8 1.0
O 0:HOH4576 3.3 41.7 1.0
O 0:HOH4201 3.3 32.4 1.0
O 0:HOH5720 3.4 72.3 1.0
O4 0:U1122 3.5 41.8 1.0
P 0:U1120 3.6 39.4 1.0
C5 0:G1121 3.6 39.6 1.0
C6 0:G1121 3.6 39.5 1.0
C2' 0:G1119 3.9 38.2 1.0
MG 0:MG8025 4.0 43.7 1.0
C3' 0:G1119 4.0 38.9 1.0
C8 0:G1121 4.1 40.3 1.0
C4 0:U1122 4.2 43.2 1.0
O 0:HOH6955 4.2 66.6 1.0
C1' 0:G1119 4.3 37.3 1.0
C5 0:U1122 4.4 42.5 1.0
O5' 0:U1120 4.6 39.6 1.0
OP1 0:U1120 4.7 40.2 1.0
C4 0:G1121 4.9 39.5 1.0
N1 0:G1121 5.0 39.0 1.0

Sodium binding site 3 out of 86 in 2otj

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Sodium binding site 3 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8503

b:1.6
occ:1.00
O 0:HOH6604 1.9 30.3 1.0
O 0:HOH9440 2.0 17.2 1.0
OP1 0:G1354 2.4 34.2 1.0
OP2 0:A643 2.8 34.8 1.0
OP1 0:C1353 3.4 45.6 1.0
P 0:A643 3.6 35.4 1.0
OP1 0:A643 3.7 37.2 1.0
P 0:G1354 3.8 33.8 1.0
O5' 0:C1353 3.9 43.8 1.0
P 0:C1353 4.2 45.6 1.0
O4 0:U904 4.3 40.2 1.0
O5' 0:A643 4.3 34.3 1.0
C5' 0:C1353 4.3 41.2 1.0
O 0:HOH7576 4.4 0.9 1.0
O3' 0:C1353 4.4 36.6 1.0
OP2 0:G1354 4.5 33.4 1.0
N3 0:U904 4.5 36.8 1.0
O 0:HOH3277 4.6 57.4 1.0
OP1 0:G644 4.8 34.4 1.0
NH2 L:ARG8 4.8 40.3 1.0
OP1 0:G642 4.8 36.3 1.0
N6 0:A1355 4.8 30.5 1.0
O5' 0:G1354 4.9 32.0 1.0
C3' 0:C1353 4.9 38.0 1.0
C4 0:U904 4.9 37.8 1.0
OP2 0:C1353 4.9 47.5 1.0
N1 0:A1355 5.0 29.9 1.0

Sodium binding site 4 out of 86 in 2otj

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Sodium binding site 4 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8505

b:37.2
occ:1.00
O 0:HOH4120 2.5 48.0 1.0
O 0:HOH5820 2.5 41.4 1.0
O 0:HOH4737 2.5 25.4 1.0
N3 0:A630 2.7 40.9 1.0
O2' 0:A630 2.7 39.7 1.0
O2' 0:A631 2.9 36.9 1.0
C1' 0:A630 3.5 39.9 1.0
OP2 0:A2074 3.5 39.1 1.0
C2' 0:A631 3.5 36.5 1.0
C2 0:A630 3.6 39.9 1.0
C4 0:A630 3.6 40.6 1.0
C2' 0:A630 3.6 39.8 1.0
C3' 0:A631 3.9 36.4 1.0
O3' 0:A630 3.9 38.8 1.0
N9 0:A630 3.9 40.4 1.0
N2 0:G2070 4.0 37.6 1.0
OP1 0:A632 4.2 37.3 1.0
O3' 0:A631 4.2 35.9 1.0
OP2 0:G2072 4.4 50.4 1.0
C3' 0:A630 4.5 38.8 1.0
N1 0:A629 4.5 40.1 1.0
O 0:HOH9418 4.5 37.4 1.0
C2 0:A629 4.6 40.7 1.0
O4' 0:A630 4.7 40.3 1.0
P 0:A632 4.7 38.1 1.0
C2 0:G2070 4.8 37.6 1.0
O 0:HOH3097 4.9 40.7 1.0
N1 0:A630 4.9 40.3 1.0
C5 0:A630 5.0 40.0 1.0
C2 0:1MA628 5.0 35.7 1.0

Sodium binding site 5 out of 86 in 2otj

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Sodium binding site 5 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8506

b:49.9
occ:1.00
N7 0:G2094 2.7 36.5 1.0
N1 0:A2649 3.0 39.6 1.0
N7 0:G2093 3.0 30.9 1.0
O 0:HOH9129 3.0 32.4 1.0
O6 0:G2094 3.2 37.5 1.0
N3 0:G2092 3.3 37.8 1.0
C2 0:A2649 3.3 39.2 1.0
C5 0:G2093 3.4 31.3 1.0
O2' 0:G2092 3.4 36.0 1.0
O6 0:G2093 3.4 33.4 1.0
C5 0:G2094 3.5 36.1 1.0
N2 0:G2092 3.6 39.2 1.0
C6 0:G2093 3.6 32.1 1.0
C6 0:G2094 3.7 36.0 1.0
C2 0:G2092 3.7 38.1 1.0
C8 0:G2093 3.8 31.8 1.0
C8 0:G2094 3.8 35.7 1.0
N6 0:A2612 3.9 36.6 1.0
C6 0:A2649 4.1 40.7 1.0
C4 0:G2092 4.2 37.0 1.0
C6 0:A2612 4.2 37.4 1.0
C4 0:G2093 4.4 31.2 1.0
N6 0:A2649 4.5 42.5 1.0
C2' 0:G2092 4.5 35.5 1.0
C1' 0:G2092 4.5 35.6 1.0
N9 0:G2093 4.6 31.4 1.0
N3 0:A2649 4.6 39.9 1.0
N1 0:A2612 4.7 38.1 1.0
N1 0:G2093 4.7 31.5 1.0
N9 0:G2092 4.7 36.3 1.0
C5 0:A2612 4.8 37.4 1.0
N1 0:G2092 4.8 36.7 1.0
C4 0:G2094 4.8 36.2 1.0
N9 0:G2094 5.0 35.5 1.0

Sodium binding site 6 out of 86 in 2otj

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Sodium binding site 6 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8507

b:69.9
occ:1.00
O2 0:C40 2.3 58.9 1.0
O2' 0:C40 2.9 57.0 1.0
O4' 0:G41 3.0 51.5 1.0
O2 0:C443 3.0 64.3 1.0
N1 0:A442 3.0 58.1 1.0
C2' 0:C40 3.3 56.7 1.0
C2 0:C40 3.4 58.7 1.0
C1' 0:C40 3.4 57.5 1.0
C2 0:A442 3.4 57.0 1.0
C1' 0:G41 3.8 51.1 1.0
N1 0:C40 3.8 58.4 1.0
C2 0:C443 4.0 63.6 1.0
C4' 0:G41 4.1 51.1 1.0
C6 0:A442 4.2 58.0 1.0
N9 0:G41 4.2 51.0 1.0
C5' 0:G41 4.3 52.3 1.0
N2 0:G39 4.3 56.6 1.0
N3 0:C40 4.5 58.6 1.0
N6 0:A442 4.5 57.7 1.0
C1' 0:C443 4.6 62.5 1.0
C8 0:G41 4.6 50.9 1.0
O4' 0:C40 4.7 57.4 1.0
O5' 0:G41 4.7 54.4 1.0
N3 0:A442 4.7 56.9 1.0
O 0:HOH5903 4.7 54.1 1.0
N3 0:C443 4.7 63.7 1.0
N1 0:C443 4.7 63.2 1.0
C4 0:G41 4.7 51.4 1.0
C3' 0:C40 4.8 56.8 1.0
C2 0:G39 4.8 57.1 1.0
N1 0:G39 5.0 57.6 1.0

Sodium binding site 7 out of 86 in 2otj

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Sodium binding site 7 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8508

b:58.1
occ:1.00
O2 0:U1724 2.0 41.9 1.0
O2 0:C1394 2.4 43.5 1.0
O4 0:U1432 2.4 45.1 1.0
O 0:HOH3426 2.4 39.1 1.0
O6 0:G1433 3.0 49.5 1.0
C2 0:U1724 3.2 42.2 1.0
O 0:HOH9302 3.4 36.6 1.0
C2 0:C1394 3.5 42.6 1.0
C4 0:U1432 3.6 44.5 1.0
C6 0:G1433 3.7 48.3 1.0
N3 0:U1724 3.9 43.0 1.0
O 0:HOH4867 4.0 46.6 1.0
C2' 0:C1394 4.0 43.8 1.0
O2' 0:C1394 4.1 43.2 1.0
N1 0:G1433 4.2 48.9 1.0
N3 0:U1432 4.2 44.2 1.0
N3 0:C1394 4.2 41.9 1.0
O 0:HOH7164 4.3 53.5 1.0
N1 0:U1724 4.3 41.6 1.0
C1' 0:U1724 4.4 40.9 1.0
N1 0:C1394 4.4 42.7 1.0
O2' 0:U1724 4.4 41.8 1.0
C1' 0:C1394 4.4 43.1 1.0
C2' 0:U1724 4.5 41.1 1.0
C5 0:G1433 4.6 47.2 1.0
O 0:HOH5499 4.7 65.2 1.0
C5 0:U1432 4.7 43.8 1.0
O2' 0:C1725 4.9 40.1 1.0

Sodium binding site 8 out of 86 in 2otj

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Sodium binding site 8 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8509

b:48.9
occ:1.00
O3' 0:A1133 2.3 50.0 1.0
O H:PRO159 2.6 65.2 1.0
O2' 0:A1133 2.7 48.6 1.0
O H:ILE157 3.0 60.2 1.0
OP1 0:G1134 3.1 50.0 1.0
O H:TYR154 3.2 63.8 1.0
C3' 0:A1133 3.3 49.1 1.0
O H:THR158 3.3 62.1 1.0
P 0:G1134 3.3 50.2 1.0
C H:PRO159 3.4 65.3 1.0
C2' 0:A1133 3.5 49.0 1.0
C4' 0:A1133 3.7 49.1 1.0
C H:THR158 3.8 62.2 1.0
N H:SER160 4.1 67.1 1.0
C H:ILE157 4.2 60.2 1.0
CA H:PRO159 4.2 63.9 1.0
N H:PRO159 4.2 63.0 1.0
O5' 0:G1134 4.2 50.5 1.0
C5' 0:G1134 4.3 51.1 1.0
CA H:SER160 4.3 68.9 1.0
O2' 0:G2520 4.3 53.6 1.0
C H:TYR154 4.5 63.8 1.0
OP2 0:G1134 4.5 49.6 1.0
C1' 0:A1133 4.6 49.2 1.0
O4' 0:A1133 4.7 49.4 1.0
C5' 0:A1133 4.7 49.1 1.0
CA H:THR158 4.7 61.2 1.0
N H:THR158 4.9 60.8 1.0
O 0:HOH4024 4.9 63.9 1.0

Sodium binding site 9 out of 86 in 2otj

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Sodium binding site 9 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8510

b:45.6
occ:1.00
O6 0:G2579 2.7 38.8 1.0
N7 0:G2579 2.9 40.0 1.0
O 0:HOH4534 3.0 51.5 1.0
N3 0:A2577 3.1 42.3 1.0
O4' 0:A2577 3.2 44.3 1.0
N7 0:G2578 3.3 41.9 1.0
C6 0:G2579 3.3 38.3 1.0
C5 0:G2579 3.4 39.5 1.0
O6 0:G2578 3.5 42.3 1.0
O 0:HOH7734 3.6 66.2 1.0
C5 0:G2578 3.6 41.2 1.0
C6 0:G2578 3.7 41.2 1.0
C1' 0:A2577 3.8 43.3 1.0
C2 0:A2577 3.8 42.4 1.0
O 0:HOH6316 3.9 62.7 1.0
C4 0:A2577 4.0 41.3 1.0
C4' 0:A2577 4.1 43.5 1.0
C8 0:G2579 4.1 39.7 1.0
C8 0:G2578 4.2 41.4 1.0
N9 0:A2577 4.3 41.9 1.0
N4 0:C2556 4.6 37.9 1.0
O 0:HOH6003 4.6 75.4 1.0
C4 0:G2578 4.7 41.3 1.0
N1 0:G2579 4.7 38.8 1.0
O6 0:G2580 4.8 41.7 1.0
N1 0:G2578 4.8 40.8 1.0
C4 0:G2579 4.8 38.5 1.0
N9 0:G2578 4.9 41.7 1.0
N3 0:U2554 4.9 33.8 1.0
O3' 0:A2577 5.0 43.6 1.0

Sodium binding site 10 out of 86 in 2otj

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Sodium binding site 10 out of 86 in the 13-Deoxytedanolide Bound to the Large 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 13-Deoxytedanolide Bound to the Large Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na8511

b:56.5
occ:1.00
O6 0:G2525 2.4 44.0 1.0
O 0:HOH3593 2.5 25.1 1.0
O 0:HOH4686 2.6 36.7 1.0
N7 0:G2524 2.8 43.8 1.0
O 0:HOH9187 3.0 31.6 1.0
O 0:HOH6391 3.4 50.5 1.0
C6 0:G2525 3.4 45.0 1.0
C8 0:G2524 3.7 43.2 1.0
O 0:HOH3637 3.8 26.9 1.0
C5 0:G2524 3.8 43.1 1.0
O6 0:G2524 3.9 41.2 1.0
C5 0:U2523 4.0 43.3 1.0
C4 0:U2523 4.1 43.9 1.0
C5 0:G2525 4.2 45.3 1.0
C6 0:G2524 4.2 42.9 1.0
O4 0:U2523 4.3 44.4 1.0
N7 0:G2525 4.3 45.0 1.0
OP2 0:G2524 4.4 45.1 1.0
N1 0:G2525 4.4 44.6 1.0
O2' 0:C2493 4.5 43.7 1.0
C6 0:U2523 4.5 42.6 1.0
N3 0:U2523 4.6 43.6 1.0
C2' 0:C2493 4.9 45.0 1.0
N9 0:G2524 4.9 43.6 1.0
C4 0:G2524 5.0 43.6 1.0
OP2 0:U2523 5.0 47.9 1.0

Reference:

S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, P.B.Moore. The Structures of Antibiotics Bound to the E Site Region of the 50 S Ribosomal Subunit of Haloarcula Marismortui: 13-Deoxytedanolide and Girodazole. J.Mol.Biol. V. 367 1471 2007.
ISSN: ISSN 0022-2836
PubMed: 17321546
DOI: 10.1016/J.JMB.2007.01.081
Page generated: Tue Dec 15 05:53:03 2020

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