Potassium 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
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Potassium 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 Potassium atom.
In total 3 binding sites of Potassium 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 Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 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 Potassium with other atoms in the K 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:K9001 b:66.1 occ:1.00 O6 0:G2102 2.7 41.7 1.0 O6 0:G2482 2.7 41.5 1.0 O2 0:C2536 2.9 32.9 1.0 N7 0:G2482 3.0 39.0 1.0 N7 0:G2102 3.3 46.0 1.0 O4' 0:C2536 3.3 35.3 1.0 C6 0:G2482 3.4 39.8 1.0 C6 0:G2102 3.5 45.0 1.0 C2 0:C2536 3.5 35.2 1.0 C5 0:G2482 3.5 39.9 1.0 C1' 0:C2536 3.6 36.0 1.0 C5 0:G2102 3.7 45.9 1.0 N1 0:C2536 3.8 36.7 1.0 N6 0:A2486 4.1 41.3 1.0 C4' 0:C2536 4.2 35.5 1.0 C8 0:G2482 4.2 40.6 1.0 O2 0:U2535 4.3 46.2 1.0 N3 0:C2536 4.4 33.0 1.0 C2 0:U2535 4.5 44.7 1.0 C8 0:G2102 4.5 46.0 1.0 N3 0:U2535 4.7 45.3 1.0 N1 0:G2482 4.7 39.4 1.0 N1 0:G2102 4.7 45.1 1.0 OP1 0:U2539 4.8 39.0 1.0 C5' 0:C2536 4.8 36.2 1.0 C4 0:G2482 4.8 40.3 1.0 C6 0:C2536 4.9 36.5 1.0 C2' 0:U2535 4.9 41.9 1.0

Potassium binding site 2 out of 3 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 Potassium with other atoms in the K 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:K9002 b:43.1 occ:1.00 O 0:HOH9335 2.8 24.1 1.0 O 0:HOH9437 2.8 27.9 1.0 O4 0:U163 2.9 30.0 1.0 O4 0:U172 2.9 34.5 1.0 O 0:HOH9473 3.0 24.9 1.0 OP2 0:C162 3.1 25.9 1.0 O 0:HOH5237 3.2 46.1 1.0 O 0:HOH8136 3.5 24.9 1.0 C4 0:U172 3.8 35.5 1.0 N3 0:U172 3.9 33.6 1.0 CD M:ARG82 3.9 37.6 1.0 C4 0:U163 3.9 28.6 1.0 O 0:HOH9650 4.0 26.3 1.0 O 0:HOH8135 4.1 34.6 1.0 N4 0:C171 4.3 35.7 1.0 O6 0:G164 4.3 34.8 1.0 P 0:C162 4.4 23.1 1.0 C5 0:U163 4.4 29.3 1.0 OP2 0:A169 4.5 28.8 1.0 NE M:ARG82 4.7 38.3 1.0 OP1 0:C162 4.7 27.1 1.0 N3 0:C173 4.8 30.8 1.0 N4 0:C173 4.9 31.7 1.0 MG 0:MG8054 4.9 24.0 1.0 OP1 0:A169 4.9 27.5 1.0 CB M:ARG82 5.0 34.0 1.0

Potassium binding site 3 out of 3 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 Potassium with other atoms in the K 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:K9003 b:82.8 occ:1.00 O2' 4:C175 2.8 44.1 1.0 O3' 4:C175 2.9 45.8 1.0 O3' 0:C2104 3.0 46.0 1.0 OP1 0:C2105 3.2 48.2 1.0 OP2 4:A176 3.5 45.0 1.0 C3' 4:C175 3.7 45.8 1.0 O 0:HOH7968 3.7 58.7 1.0 P 0:C2105 3.7 44.0 1.0 C2' 4:C175 3.7 44.9 1.0 O2' 0:C2104 3.8 45.5 1.0 P 4:A176 3.9 41.5 1.0 C4' 4:C175 3.9 45.8 1.0 C3' 0:C2104 4.1 45.4 1.0 C4' 0:C2104 4.3 46.4 1.0 N6 0:A2474 4.4 41.3 1.0 C2' 0:C2104 4.6 44.6 1.0 O 4:HOH7924 4.6 71.0 1.0 C1' 4:C175 4.6 45.3 1.0 C5' 0:C2105 4.7 39.8 1.0 O4' 4:C175 4.7 46.1 1.0 O5' 0:C2105 4.7 44.2 1.0 OP2 0:C2105 4.8 45.4 1.0 OP1 4:A176 4.8 44.2 1.0 C4' 4:A176 4.9 46.5 1.0 O5' 4:A176 5.0 45.8 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