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Sodium in PDB 1vqp: The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

Protein crystallography data

The structure of The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqp was solved by T.M.Schmeing, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.25
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 211.610, 298.189, 574.980, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 24.7

Other elements in 1vqp:

The structure of The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Strontium (Sr) 114 atoms
Magnesium (Mg) 94 atoms
Potassium (K) 3 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vqp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 75 binding sites of Sodium where determined in the The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vqp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 75 in 1vqp

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Sodium binding site 1 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9101

b:46.2
occ:1.00
OP2 0:C1069 2.5 27.1 1.0
O 0:HOH5553 2.5 70.5 1.0
N7 0:G1072 2.8 30.7 1.0
O6 0:G1087 3.0 35.0 1.0
O6 0:G1072 3.1 30.6 1.0
O 0:HOH3813 3.1 50.6 1.0
O 0:HOH3783 3.2 34.5 1.0
C5 0:G1072 3.4 29.3 1.0
C6 0:G1072 3.5 28.6 1.0
P 0:C1069 3.8 29.9 1.0
C8 0:G1072 3.8 27.3 1.0
O 0:HOH9694 3.9 37.5 1.0
C6 0:G1087 4.0 33.4 1.0
C5' 0:C1068 4.3 36.8 1.0
O 0:HOH4150 4.3 33.3 1.0
O3' 0:C1068 4.4 31.1 1.0
OP1 0:C1069 4.4 28.7 1.0
C3' 0:C1068 4.5 32.6 1.0
C4 0:G1072 4.6 30.1 1.0
N1 0:G1087 4.6 31.2 1.0
N1 0:G1072 4.8 25.2 1.0
OP2 0:C1068 4.8 40.1 1.0
N9 0:G1072 4.8 28.5 1.0
C5 0:G1087 4.9 33.6 1.0
O 0:HOH5902 4.9 64.5 1.0
O5' 0:C1069 4.9 30.9 1.0

Sodium binding site 2 out of 75 in 1vqp

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Sodium binding site 2 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9102

b:58.6
occ:1.00
O 0:HOH8341 2.6 50.4 1.0
OP2 0:U1120 2.9 42.7 1.0
N7 0:G1121 2.9 35.6 1.0
O 0:HOH5140 3.1 74.2 1.0
O3' 0:G1119 3.1 38.9 1.0
O 0:HOH4772 3.3 57.0 1.0
O6 0:G1121 3.3 38.0 1.0
O2' 0:G1119 3.4 41.2 1.0
P 0:U1120 3.6 39.6 1.0
C5 0:G1121 3.6 35.4 1.0
O4 0:U1122 3.7 37.4 1.0
C6 0:G1121 3.8 35.3 1.0
MG 0:MG8025 3.9 29.5 1.0
C8 0:G1121 3.9 35.2 1.0
O 0:HOH6249 4.1 98.2 1.0
C4 0:U1122 4.2 38.7 1.0
C3' 0:G1119 4.2 38.6 1.0
C2' 0:G1119 4.2 38.4 1.0
C5 0:U1122 4.3 37.4 1.0
O 0:HOH7450 4.4 69.4 1.0
C1' 0:G1119 4.6 37.4 1.0
OP1 0:U1120 4.7 41.7 1.0
C5' 0:U1120 4.7 40.5 1.0
O5' 0:U1120 4.7 38.9 1.0
OP2 0:G1121 4.8 32.9 1.0
C4 0:G1121 4.9 35.6 1.0

Sodium binding site 3 out of 75 in 1vqp

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Sodium binding site 3 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9105

b:38.1
occ:1.00
O 0:HOH6346 2.2 42.2 1.0
O 0:HOH4692 2.5 37.7 1.0
O 0:HOH5293 2.5 44.6 1.0
N3 0:A630 2.7 33.8 1.0
O2' 0:A630 2.7 35.4 1.0
O2' 0:A631 2.9 34.9 1.0
C2 0:A630 3.5 33.7 1.0
OP2 0:A2074 3.6 36.0 1.0
C1' 0:A630 3.6 35.4 1.0
C2' 0:A631 3.6 34.0 1.0
C4 0:A630 3.7 35.3 1.0
C2' 0:A630 3.8 37.1 1.0
C3' 0:A631 3.9 32.6 1.0
OP1 0:A632 4.0 34.9 1.0
N9 0:A630 4.1 36.2 1.0
O3' 0:A631 4.1 32.4 1.0
O3' 0:A630 4.2 36.5 1.0
N2 0:G2070 4.2 31.5 1.0
O 0:HOH3038 4.3 32.2 1.0
OP2 0:G2072 4.3 53.1 1.0
N1 0:A629 4.5 36.0 1.0
O 0:HOH3697 4.5 44.2 1.0
P 0:A632 4.5 33.9 1.0
C3' 0:A630 4.7 35.3 1.0
C2 0:A629 4.8 35.8 1.0
N1 0:A630 4.8 34.4 1.0
C2 0:1MA628 4.8 30.7 1.0
OP2 0:A632 4.9 34.8 1.0
C2 0:G2070 4.9 34.2 1.0
O4' 0:A630 4.9 36.6 1.0
C5 0:A630 5.0 34.9 1.0

Sodium binding site 4 out of 75 in 1vqp

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Sodium binding site 4 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9106

b:37.3
occ:1.00
N7 0:G2094 2.8 31.9 1.0
N1 0:A2649 2.9 32.4 1.0
O 0:HOH9752 3.0 34.6 1.0
O6 0:G2094 3.0 36.4 1.0
N7 0:G2093 3.0 29.1 1.0
O2' 0:G2092 3.2 33.3 1.0
N3 0:G2092 3.2 32.1 1.0
C2 0:A2649 3.3 29.2 1.0
O6 0:G2093 3.5 34.3 1.0
C5 0:G2093 3.5 31.7 1.0
C5 0:G2094 3.5 32.2 1.0
C6 0:G2094 3.6 33.9 1.0
N2 0:G2092 3.6 32.3 1.0
C6 0:G2093 3.7 31.4 1.0
C2 0:G2092 3.7 32.5 1.0
C8 0:G2093 3.9 30.7 1.0
C8 0:G2094 4.0 29.6 1.0
C6 0:A2649 4.0 33.0 1.0
C4 0:G2092 4.1 34.5 1.0
N6 0:A2612 4.3 34.2 1.0
N6 0:A2649 4.3 32.3 1.0
C2' 0:G2092 4.4 31.1 1.0
C6 0:A2612 4.4 36.9 1.0
C1' 0:G2092 4.4 31.1 1.0
C4 0:G2093 4.5 31.2 1.0
N3 0:A2649 4.6 30.7 1.0
N1 0:A2612 4.6 34.0 1.0
N9 0:G2092 4.6 33.1 1.0
N9 0:G2093 4.7 30.6 1.0
N1 0:G2092 4.8 30.4 1.0
N1 0:G2093 4.8 30.3 1.0
C4 0:G2094 4.8 31.3 1.0
O3' 0:G2092 4.9 29.3 1.0
N1 0:G2094 5.0 34.0 1.0
C5 0:A2612 5.0 38.1 1.0

Sodium binding site 5 out of 75 in 1vqp

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Sodium binding site 5 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9107

b:63.7
occ:1.00
O2 0:C40 2.5 56.7 1.0
O2' 0:C40 2.7 59.2 1.0
O2 0:C443 2.7 62.0 1.0
N1 0:A442 3.1 61.3 1.0
C2' 0:C40 3.2 58.9 1.0
C1' 0:C40 3.3 59.2 1.0
O4' 0:G41 3.3 50.0 1.0
C2 0:C40 3.6 59.3 1.0
C2 0:A442 3.7 60.7 1.0
C2 0:C443 3.7 62.5 1.0
N1 0:C40 3.9 59.5 1.0
N2 0:G39 4.0 51.3 1.0
C1' 0:G41 4.0 48.0 1.0
C6 0:A442 4.0 61.8 1.0
N6 0:A442 4.2 61.8 1.0
N3 0:C443 4.3 62.2 1.0
N9 0:G41 4.4 48.8 1.0
C4' 0:G41 4.5 50.5 1.0
O4' 0:C40 4.5 59.2 1.0
N1 0:C443 4.6 62.5 1.0
C2 0:G39 4.6 51.7 1.0
C1' 0:C443 4.6 63.2 1.0
O 0:HOH6424 4.7 62.5 1.0
C3' 0:C40 4.7 57.8 1.0
C5' 0:G41 4.7 51.4 1.0
N3 0:C40 4.8 60.0 1.0
C8 0:G41 4.8 48.4 1.0
N1 0:G39 4.8 53.7 1.0
N3 0:A442 4.9 60.1 1.0
C4 0:G41 4.9 48.3 1.0

Sodium binding site 6 out of 75 in 1vqp

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Sodium binding site 6 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9108

b:34.0
occ:1.00
O2 0:U1724 2.2 54.7 1.0
O2 0:C1394 2.3 33.1 1.0
O4 0:U1432 2.4 35.4 1.0
O 0:HOH4024 2.7 34.0 1.0
SR 0:SR9473 3.1 69.0 1.0
O6 0:G1433 3.3 43.8 1.0
C2 0:U1724 3.4 53.5 1.0
C2 0:C1394 3.4 35.8 1.0
C4 0:U1432 3.6 36.7 1.0
C6 0:G1433 3.9 41.3 1.0
O2' 0:C1394 4.0 40.0 1.0
C2' 0:C1394 4.0 38.9 1.0
N3 0:U1432 4.2 36.8 1.0
O 0:HOH7655 4.2 60.7 1.0
N3 0:U1724 4.2 52.4 1.0
N3 0:C1394 4.2 36.4 1.0
O2' 0:U1724 4.2 51.3 1.0
O 0:HOH5424 4.3 63.9 1.0
C1' 0:U1724 4.3 51.5 1.0
C1' 0:C1394 4.3 38.5 1.0
N1 0:G1433 4.3 41.4 1.0
N1 0:C1394 4.3 38.4 1.0
N1 0:U1724 4.3 53.5 1.0
C2' 0:U1724 4.4 51.9 1.0
C5 0:G1433 4.8 39.4 1.0
C5 0:U1432 4.8 37.4 1.0
O 0:HOH6029 4.8 73.1 1.0
O2' 0:C1725 5.0 36.2 1.0

Sodium binding site 7 out of 75 in 1vqp

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Sodium binding site 7 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9110

b:44.3
occ:1.00
O6 0:G2579 2.8 34.4 1.0
N3 0:A2577 2.9 38.6 1.0
O4' 0:A2577 3.0 40.8 1.0
O 0:HOH5098 3.0 47.1 1.0
N7 0:G2578 3.1 35.9 1.0
N7 0:G2579 3.1 36.4 1.0
O6 0:G2578 3.3 35.7 1.0
C6 0:G2579 3.5 35.5 1.0
C5 0:G2578 3.5 35.5 1.0
C5 0:G2579 3.6 35.5 1.0
C6 0:G2578 3.7 34.9 1.0
C1' 0:A2577 3.7 39.4 1.0
C2 0:A2577 3.7 37.2 1.0
O 0:HOH8289 3.8 59.7 1.0
C4 0:A2577 3.8 37.2 1.0
C4' 0:A2577 3.9 41.2 1.0
C8 0:G2578 4.0 35.0 1.0
O 0:HOH6830 4.1 63.4 1.0
N9 0:A2577 4.1 37.4 1.0
C8 0:G2579 4.3 35.0 1.0
C4 0:G2578 4.6 33.6 1.0
N4 0:C2556 4.6 36.1 1.0
N1 0:G2579 4.8 35.4 1.0
N1 0:G2578 4.8 35.5 1.0
N3 0:U2554 4.8 33.5 1.0
C5' 0:A2577 4.8 39.3 1.0
N9 0:G2578 4.9 33.5 1.0
O3' 0:A2577 4.9 41.5 1.0
C3' 0:A2577 4.9 40.2 1.0
C4 0:G2579 4.9 36.9 1.0
N1 0:A2577 5.0 36.9 1.0
C2' 0:A2577 5.0 41.2 1.0

Sodium binding site 8 out of 75 in 1vqp

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Sodium binding site 8 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9111

b:66.4
occ:1.00
O 0:HOH4188 2.4 37.2 1.0
N7 0:G2524 2.7 38.0 1.0
O6 0:G2525 3.0 43.6 1.0
O 0:HOH5246 3.1 50.1 1.0
C5 0:U2523 3.5 40.8 1.0
C8 0:G2524 3.5 36.4 1.0
O 0:HOH9811 3.6 56.2 1.0
C4 0:U2523 3.6 42.8 1.0
C5 0:G2524 3.8 36.6 1.0
C6 0:G2525 3.9 37.6 1.0
O4 0:U2523 3.9 44.5 1.0
O 0:HOH6902 3.9 72.1 1.0
C6 0:U2523 4.0 41.5 1.0
O6 0:G2524 4.0 37.0 1.0
N3 0:U2523 4.3 41.6 1.0
OP2 0:G2524 4.3 41.5 1.0
O 0:HOH4231 4.3 20.0 1.0
C6 0:G2524 4.3 35.2 1.0
OP2 0:U2523 4.5 44.7 1.0
N1 0:U2523 4.6 43.6 1.0
C5 0:G2525 4.7 38.0 1.0
N1 0:G2525 4.7 36.0 1.0
O2' 0:C2493 4.7 41.0 1.0
C2 0:U2523 4.8 42.4 1.0
N9 0:G2524 4.8 39.8 1.0
N7 0:G2525 4.9 38.8 1.0
C4 0:G2524 5.0 36.9 1.0
O5' 0:U2523 5.0 43.9 1.0

Sodium binding site 9 out of 75 in 1vqp

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Sodium binding site 9 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9113

b:61.1
occ:1.00
O 0:HOH4443 2.3 50.8 1.0
O 0:HOH5696 2.4 47.6 1.0
O 0:HOH3573 2.5 44.3 1.0
O6 0:G2399 2.5 39.6 1.0
O 0:HOH5649 2.7 57.3 1.0
N7 0:G2399 2.7 40.6 1.0
C6 0:G2399 3.1 39.8 1.0
C5 0:G2399 3.2 40.5 1.0
O 0:HOH6604 3.8 59.9 1.0
OP2 0:A2398 3.9 46.0 1.0
C8 0:G2399 3.9 40.8 1.0
O 0:HOH4002 4.2 43.7 1.0
O6 0:G2400 4.2 45.0 1.0
N7 0:G2400 4.3 44.5 1.0
O 0:HOH6822 4.4 62.7 1.0
O4 0:U2389 4.4 43.1 1.0
N1 0:G2399 4.5 39.7 1.0
C4 0:G2399 4.6 41.1 1.0
N7 0:A2398 4.7 43.6 1.0
N3 0:U2389 4.7 40.7 1.0
O2 0:U2390 4.7 44.6 1.0
C6 0:G2400 4.8 44.8 1.0
C5 0:G2400 4.8 44.0 1.0
N9 0:G2399 4.9 41.8 1.0

Sodium binding site 10 out of 75 in 1vqp

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Sodium binding site 10 out of 75 in the The Structure of the Transition State Analogue "Rap" Bound to the Large 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 The Structure of the Transition State Analogue "Rap" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range:
probe atom residue distance (Å) B Occ
0:Na9114

b:42.0
occ:1.00
O 0:HOH3745 2.3 46.7 1.0
O 0:HOH9959 2.6 39.1 1.0
O2' 0:U2607 2.6 33.3 1.0
OP1 0:U2541 2.8 56.9 1.0
O2 0:U2607 2.8 37.0 1.0
CZ3 B:TRP242 3.6 33.8 1.0
C2 0:U2607 3.7 37.1 1.0
C2' 0:U2607 3.8 33.5 1.0
OP2 0:C2608 4.0 31.2 1.0
C1' 0:U2607 4.0 33.9 1.0
P 0:U2541 4.0 51.7 1.0
CH2 B:TRP242 4.1 33.9 1.0
O 0:HOH5279 4.1 47.9 1.0
N1 0:U2607 4.2 38.0 1.0
OP1 0:U2610 4.2 31.4 1.0
O 0:HOH9782 4.2 70.9 1.0
O3' 0:U2607 4.4 34.8 1.0
OP2 0:U2541 4.4 52.9 1.0
CE3 B:TRP242 4.4 31.2 1.0
O 0:HOH8342 4.6 34.1 1.0
N3 0:U2607 4.7 38.1 1.0
P 0:C2608 4.8 35.2 1.0
C3' 0:U2607 4.8 34.4 1.0
O2' 0:A2488 4.9 37.5 1.0
O 0:HOH3115 4.9 48.0 1.0
O2 0:U2539 5.0 41.0 1.0
O5' 0:U2541 5.0 51.4 1.0

Reference:

T.M.Schmeing, K.S.Huang, D.E.Kitchen, S.A.Strobel, T.A.Steitz. Structural Insights Into the Roles of Water and the 2' Hydroxyl of the P Site Trna in the Peptidyl Transferase Reaction. Mol.Cell V. 20 437 2005.
ISSN: ISSN 1097-2765
PubMed: 16285925
DOI: 10.1016/J.MOLCEL.2005.09.006
Page generated: Thu Oct 29 04:02:09 2020

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