Sodium in PDB 1vq7: The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq7 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 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	211.150, 300.130, 573.290, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 24.5

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

Magnesium	(Mg)	118 atoms
Potassium	(K)	3 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms

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 The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1vq7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 86 binding sites of Sodium where determined in the The Structure of the Transition State Analogue "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1vq7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9101 b:46.8 occ:1.00 OP2 0:C1069 2.3 36.0 1.0 O 0:HOH5282 2.4 55.8 1.0 N7 0:G1072 2.6 33.9 1.0 O 0:HOH3492 2.8 39.4 1.0 O 0:HOH3523 2.9 56.6 1.0 O6 0:G1087 3.0 34.8 1.0 O6 0:G1072 3.1 32.9 1.0 C5 0:G1072 3.2 33.8 1.0 C6 0:G1072 3.5 33.1 1.0 C8 0:G1072 3.6 35.3 1.0 P 0:C1069 3.6 35.9 1.0 O 0:HOH9389 3.8 42.2 1.0 C6 0:G1087 3.9 35.5 1.0 C5' 0:C1068 4.2 41.2 1.0 OP1 0:C1069 4.2 34.2 1.0 O3' 0:C1068 4.3 37.9 1.0 C3' 0:C1068 4.4 39.1 1.0 C4 0:G1072 4.4 35.7 1.0 O 0:HOH3859 4.6 48.9 1.0 N9 0:G1072 4.6 35.8 1.0 N1 0:G1087 4.6 34.0 1.0 N1 0:G1072 4.8 34.4 1.0 O5' 0:C1069 4.8 38.0 1.0 C5 0:G1087 4.9 35.3 1.0 OP2 0:C1068 4.9 47.4 1.0 C4' 0:C1068 4.9 41.2 1.0 O 0:HOH5628 5.0 64.9 1.0

Sodium binding site 2 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9102 b:42.7 occ:1.00 O2' 0:G1119 2.8 41.6 1.0 O 0:HOH5978 2.9 59.4 1.0 O 0:HOH7999 3.0 52.5 1.0 O6 0:G1121 3.0 41.0 1.0 OP2 0:U1120 3.1 43.7 1.0 O3' 0:G1119 3.1 42.5 1.0 O 0:HOH4863 3.2 45.9 1.0 N7 0:G1121 3.4 43.4 1.0 O 0:HOH4496 3.5 46.9 1.0 O4 0:U1122 3.5 41.1 1.0 P 0:U1120 3.7 41.3 1.0 C6 0:G1121 3.8 39.5 1.0 C2' 0:G1119 3.8 41.7 1.0 O 0:HOH7181 3.9 74.9 1.0 C5 0:G1121 3.9 40.8 1.0 C3' 0:G1119 4.0 42.4 1.0 MG 0:MG8025 4.0 48.7 1.0 C4 0:U1122 4.2 41.6 1.0 C1' 0:G1119 4.3 39.6 1.0 C8 0:G1121 4.6 41.9 1.0 C5 0:U1122 4.6 40.4 1.0 OP1 0:U1120 4.6 45.6 1.0 OP1 0:C1238 4.9 47.8 1.0 O5' 0:U1120 4.9 41.5 1.0 CL 0:CL9316 4.9 56.4 1.0 N4 0:C1243 5.0 36.3 1.0

Sodium binding site 3 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9103 b:44.3 occ:1.00 O4 0:U904 2.9 34.3 1.0 OP1 0:G644 3.0 31.7 1.0 OP2 0:A643 3.0 29.0 1.0 OP1 0:G1354 3.1 40.1 1.0 NH2 L:ARG8 3.1 40.4 1.0 O 0:HOH3583 3.2 62.4 1.0 O5' 0:A643 3.5 28.5 1.0 P 0:A643 3.5 27.0 1.0 O 0:HOH4918 3.6 60.6 1.0 OP1 0:A643 3.8 34.1 1.0 C4 0:U904 3.9 34.8 1.0 N3 0:U904 4.0 33.9 1.0 OP1 0:C1353 4.0 53.7 1.0 P 0:G1354 4.1 35.1 1.0 CZ L:ARG8 4.2 37.7 1.0 O 0:HOH9756 4.2 36.0 1.0 P 0:G644 4.3 31.6 1.0 C5' 0:A643 4.3 29.3 1.0 OP2 0:G1354 4.3 35.1 1.0 O 0:HOH7790 4.4 95.5 1.0 C3' 0:A643 4.5 31.7 1.0 O3' 0:A643 4.6 34.0 1.0 O3' 0:C1353 4.7 37.8 1.0 NH1 L:ARG8 4.9 37.1 1.0 NE L:ARG8 4.9 36.0 1.0 OP2 0:G644 5.0 34.2 1.0

Sodium binding site 4 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9105 b:35.8 occ:1.00 O 0:HOH6073 2.3 49.8 1.0 O 0:HOH4414 2.5 39.5 1.0 O 0:HOH5020 2.6 32.0 1.0 O2' 0:A630 2.7 38.1 1.0 N3 0:A630 2.7 37.8 1.0 O2' 0:A631 2.9 35.2 1.0 C1' 0:A630 3.4 38.4 1.0 OP2 0:A2074 3.5 35.3 1.0 C2' 0:A631 3.5 32.7 1.0 C2 0:A630 3.6 37.3 1.0 C2' 0:A630 3.6 38.8 1.0 C4 0:A630 3.6 37.1 1.0 N9 0:A630 3.9 37.5 1.0 O3' 0:A630 3.9 33.6 1.0 C3' 0:A631 3.9 31.3 1.0 N2 0:G2070 3.9 36.3 1.0 OP1 0:A632 4.0 34.8 1.0 O3' 0:A631 4.3 31.0 1.0 N1 0:A629 4.4 34.8 1.0 C3' 0:A630 4.4 36.9 1.0 C2 0:A629 4.5 34.9 1.0 P 0:A632 4.6 31.4 1.0 O4' 0:A630 4.6 40.4 1.0 O 0:HOH3407 4.6 49.5 1.0 O 0:HOH9733 4.7 28.9 1.0 OP2 0:G2072 4.7 51.6 1.0 C2 0:G2070 4.7 34.9 1.0 N1 0:A630 4.9 37.5 1.0 P 0:A2074 5.0 33.9 1.0 C5 0:A630 5.0 36.3 1.0 OP2 0:A632 5.0 31.9 1.0 C1' 0:A631 5.0 33.0 1.0 C2 0:1MA628 5.0 36.5 1.0

Sodium binding site 5 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9106 b:34.0 occ:1.00 N7 0:G2094 2.7 34.8 1.0 N1 0:A2649 2.9 41.1 1.0 N7 0:G2093 3.0 33.2 1.0 O 0:HOH9453 3.0 28.3 1.0 O6 0:G2094 3.1 35.5 1.0 N3 0:G2092 3.3 38.8 1.0 O2' 0:G2092 3.3 34.9 1.0 C2 0:A2649 3.4 40.8 1.0 C5 0:G2094 3.4 35.1 1.0 C5 0:G2093 3.5 35.1 1.0 N2 0:G2092 3.5 36.6 1.0 C6 0:G2094 3.6 34.1 1.0 O6 0:G2093 3.6 37.6 1.0 C2 0:G2092 3.7 38.0 1.0 C6 0:G2093 3.7 36.0 1.0 C8 0:G2093 3.8 33.5 1.0 N6 0:A2612 3.8 30.3 1.0 C8 0:G2094 3.8 34.9 1.0 C6 0:A2612 4.1 34.6 1.0 C6 0:A2649 4.1 39.0 1.0 C4 0:G2092 4.2 37.4 1.0 N6 0:A2649 4.3 38.1 1.0 C4 0:G2093 4.4 34.7 1.0 C2' 0:G2092 4.4 35.4 1.0 C1' 0:G2092 4.5 35.7 1.0 C5 0:A2612 4.5 35.1 1.0 N1 0:A2612 4.5 34.2 1.0 N9 0:G2093 4.6 35.3 1.0 N9 0:G2092 4.7 36.2 1.0 N3 0:A2649 4.7 39.9 1.0 C4 0:G2094 4.7 34.5 1.0 N1 0:G2092 4.8 36.3 1.0 N1 0:G2093 4.8 36.5 1.0 N7 0:A2612 4.8 36.3 1.0 N9 0:G2094 4.9 34.9 1.0 O3' 0:G2092 4.9 34.7 1.0 N1 0:G2094 5.0 34.1 1.0

Sodium binding site 6 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9107 b:43.8 occ:1.00 O2 0:C40 2.7 51.1 1.0 O4' 0:G41 2.8 49.0 1.0 O2' 0:C40 2.8 52.8 1.0 N1 0:A442 3.0 60.0 1.0 O2 0:C443 3.2 56.1 1.0 C2' 0:C40 3.3 52.8 1.0 C2 0:A442 3.4 59.9 1.0 C1' 0:G41 3.7 47.6 1.0 C1' 0:C40 3.7 52.6 1.0 C2 0:C40 3.8 51.6 1.0 C4' 0:G41 3.9 47.8 1.0 C2 0:C443 4.0 55.5 1.0 N9 0:G41 4.0 48.1 1.0 C6 0:A442 4.1 58.9 1.0 C5' 0:G41 4.2 48.8 1.0 N1 0:C40 4.2 52.3 1.0 N2 0:G39 4.4 53.5 1.0 N6 0:A442 4.4 58.5 1.0 C8 0:G41 4.5 48.5 1.0 O5' 0:G41 4.6 50.8 1.0 N3 0:C443 4.7 55.5 1.0 N3 0:A442 4.7 59.3 1.0 C4 0:G41 4.7 48.9 1.0 C1' 0:C443 4.7 55.7 1.0 N1 0:C443 4.8 55.8 1.0 C3' 0:C40 4.8 52.5 1.0 N3 0:C40 4.9 52.6 1.0 C2 0:G39 5.0 54.2 1.0 O4' 0:C40 5.0 52.0 1.0

Sodium binding site 7 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9108 b:48.6 occ:1.00 O2 0:C1394 2.2 41.8 1.0 O2 0:U1724 2.3 43.7 1.0 O4 0:U1432 2.5 41.4 1.0 O 0:HOH3732 2.5 38.1 1.0 C2 0:C1394 3.4 40.3 1.0 O 0:HOH7390 3.4 75.6 1.0 C2 0:U1724 3.5 41.7 1.0 O6 0:G1433 3.5 49.8 1.0 C4 0:U1432 3.6 40.2 1.0 O 0:HOH9622 3.9 40.7 1.0 C2' 0:C1394 4.0 41.7 1.0 O2' 0:C1394 4.0 38.9 1.0 N3 0:U1432 4.1 40.7 1.0 C6 0:G1433 4.1 47.2 1.0 N3 0:C1394 4.1 39.3 1.0 C1' 0:C1394 4.2 41.5 1.0 N1 0:C1394 4.3 40.7 1.0 N3 0:U1724 4.3 40.5 1.0 O2' 0:U1724 4.4 41.2 1.0 N1 0:G1433 4.4 48.3 1.0 O 0:HOH5150 4.5 47.6 1.0 C1' 0:U1724 4.5 39.5 1.0 N1 0:U1724 4.5 40.9 1.0 C2' 0:U1724 4.6 40.0 1.0 O2' 0:C1725 4.6 38.3 1.0 O 0:HOH5758 4.6 55.4 1.0 C5 0:U1432 4.8 40.0 1.0 C5 0:G1433 4.9 45.8 1.0

Sodium binding site 8 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9110 b:37.6 occ:1.00 O6 0:G2579 2.6 38.4 1.0 O 0:HOH4825 3.0 47.7 1.0 O4' 0:A2577 3.0 46.7 1.0 N7 0:G2579 3.0 42.9 1.0 N3 0:A2577 3.1 43.0 1.0 N7 0:G2578 3.1 43.6 1.0 C6 0:G2579 3.3 41.0 1.0 O6 0:G2578 3.4 44.6 1.0 C5 0:G2579 3.5 42.6 1.0 C5 0:G2578 3.6 43.6 1.0 C1' 0:A2577 3.7 44.9 1.0 C6 0:G2578 3.7 44.5 1.0 O 0:HOH7946 3.8 56.0 1.0 C2 0:A2577 3.9 43.2 1.0 C4 0:A2577 3.9 41.0 1.0 C4' 0:A2577 3.9 47.5 1.0 O 0:HOH6557 4.0 75.4 1.0 C8 0:G2578 4.0 43.4 1.0 N9 0:A2577 4.2 42.1 1.0 C8 0:G2579 4.3 44.3 1.0 C4 0:G2578 4.6 43.2 1.0 N1 0:G2579 4.6 39.2 1.0 N4 0:C2556 4.7 42.6 1.0 N1 0:G2578 4.8 43.9 1.0 C4 0:G2579 4.8 42.6 1.0 O3' 0:A2577 4.8 49.1 1.0 N9 0:G2578 4.8 44.3 1.0 N3 0:U2554 4.9 29.7 1.0 C5' 0:A2577 4.9 46.1 1.0 O6 0:G2580 4.9 45.5 1.0 C3' 0:A2577 4.9 47.2 1.0

Sodium binding site 9 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9111 b:65.6 occ:1.00 O 0:HOH3898 2.5 28.4 1.0 O6 0:G2525 2.7 41.6 1.0 N7 0:G2524 2.9 40.0 1.0 O 0:HOH9511 3.0 36.9 1.0 O 0:HOH4973 3.0 61.8 1.0 O 0:HOH6631 3.4 70.0 1.0 C8 0:G2524 3.6 40.1 1.0 C6 0:G2525 3.6 39.6 1.0 O 0:HOH3943 3.9 40.2 1.0 OP2 0:G2524 4.0 45.0 1.0 C5 0:U2523 4.0 44.1 1.0 C5 0:G2524 4.0 39.4 1.0 C4 0:U2523 4.2 45.5 1.0 C5 0:G2525 4.4 39.2 1.0 C6 0:U2523 4.4 42.6 1.0 O6 0:G2524 4.4 38.7 1.0 N7 0:G2525 4.4 37.9 1.0 O4 0:U2523 4.5 49.0 1.0 OP2 0:U2523 4.5 46.3 1.0 C6 0:G2524 4.6 39.3 1.0 N1 0:G2525 4.6 38.3 1.0 N3 0:U2523 4.7 43.8 1.0 O2' 0:C2493 4.8 40.7 1.0 N9 0:G2524 4.9 40.2 1.0 N1 0:U2523 5.0 43.7 1.0

Sodium binding site 10 out of 86 in the The Structure of the Transition State Analogue "Dca" 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 "Dca" Bound to the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:Na9113 b:59.7 occ:1.00 O 0:HOH5426 2.5 85.7 1.0 O 0:HOH3275 2.6 66.4 1.0 O6 0:G2399 2.8 44.6 1.0 O 0:HOH4159 2.8 60.9 1.0 O 0:HOH3712 3.1 33.1 1.0 O4 0:U2389 3.4 47.1 1.0 O 0:HOH5379 3.4 56.7 1.0 O 0:HOH6768 3.7 71.7 1.0 C6 0:G2399 3.8 44.5 1.0 OP2 0:A2398 3.8 48.6 1.0 N7 0:G2399 3.9 46.2 1.0 N3 0:U2389 4.1 42.2 1.0 C5 0:G2399 4.2 45.5 1.0 C4 0:U2389 4.2 43.9 1.0 O6 0:G2400 4.3 46.7 1.0 O 0:HOH3065 4.5 40.7 1.0 O2 0:U2390 4.5 43.1 1.0 N3 0:U2390 4.6 39.8 1.0 O 0:HOH6336 4.7 58.2 1.0 C2 0:U2390 4.9 41.5 1.0 N4 0:C2388 5.0 39.5 1.0 C6 0:G2400 5.0 46.1 1.0 O 0:HOH6550 5.0 74.2 1.0

T.M.Schmeing, K.S.Huang, S.A.Strobel, T.A.Steitz. An Induced-Fit Mechanism to Promote Peptide Bond Formation and Exclude Hydrolysis of Peptidyl-Trna. Nature V. 438 520 2005.
ISSN: ISSN 0028-0836
PubMed: 16306996
DOI: 10.1038/NATURE04152