Potassium in PDB 1qvf: Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf was solved by T.M.Schmeing, 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)	50.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	213.522, 300.817, 574.861, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.9

The structure of Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui also contains other interesting chemical elements:

Magnesium	(Mg)	119 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Potassium atom in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui (pdb code 1qvf). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui, PDB code: 1qvf:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8201 b:89.5 occ:1.00 O6 0:G2482 2.7 38.3 1.0 O6 0:G2102 2.7 54.8 1.0 N7 0:G2482 2.9 41.3 1.0 O2 0:C2536 3.1 37.6 1.0 C6 0:G2482 3.3 37.6 1.0 O4' 0:C2536 3.4 39.6 1.0 C5 0:G2482 3.4 39.5 1.0 N7 0:G2102 3.4 53.0 1.0 C6 0:G2102 3.5 54.2 1.0 C2 0:C2536 3.7 38.5 1.0 C5 0:G2102 3.8 54.1 1.0 C1' 0:C2536 3.8 39.8 1.0 N6 0:A2486 3.9 61.6 1.0 N1 0:C2536 4.0 39.5 1.0 C8 0:G2482 4.1 40.3 1.0 O2 0:U2535 4.1 41.8 1.0 C4' 0:C2536 4.2 38.8 1.0 C2 0:U2535 4.3 41.6 1.0 N3 0:U2535 4.5 40.0 1.0 N3 0:C2536 4.5 38.0 1.0 C8 0:G2102 4.6 53.3 1.0 OP1 0:U2539 4.6 43.1 1.0 C2' 0:U2535 4.7 40.0 1.0 N1 0:G2482 4.7 36.6 1.0 C4 0:G2482 4.7 39.6 1.0 C5' 0:C2536 4.7 38.4 1.0 N1 0:G2102 4.8 54.0 1.0 N1 0:U2535 4.9 41.3 1.0

Potassium binding site 2 out of 2 in the Structure of A Deacylated Trna Minihelix Bound to the E Site of 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 Structure of A Deacylated Trna Minihelix Bound to the E Site of the Large Ribosomal Subunit of Haloarcula Marismortui within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8202 b:76.2 occ:1.00 O 0:HOH8633 2.6 38.7 1.0 O 0:HOH8535 2.8 63.1 1.0 O4 0:U172 2.9 43.3 1.0 O4 0:U163 3.0 43.2 1.0 O 0:HOH8668 3.1 71.8 1.0 O 0:HOH4419 3.1 58.8 1.0 OP2 0:C162 3.3 33.9 1.0 O 0:HOH7271 3.5 46.2 1.0 CD L:ARG82 3.6 41.9 1.0 C4 0:U172 3.8 43.1 1.0 N3 0:U172 4.0 42.6 1.0 O 0:HOH8845 4.0 38.9 1.0 C4 0:U163 4.1 43.6 1.0 N4 0:C171 4.2 45.4 1.0 NE L:ARG82 4.4 42.6 1.0 O 0:HOH7270 4.5 17.0 1.0 OP2 0:A169 4.5 37.6 1.0 O6 0:G164 4.5 40.6 1.0 C5 0:U163 4.6 43.8 1.0 P 0:C162 4.6 34.4 1.0 CB L:ARG82 4.7 39.4 1.0 CG L:ARG82 4.7 40.4 1.0 OP1 0:A169 4.8 36.9 1.0 N4 0:C173 4.9 34.8 1.0 N3 0:C173 4.9 36.1 1.0 OP1 0:C162 5.0 34.3 1.0

T.M.Schmeing, P.B.Moore, T.A.Steitz. Structures of Deacylated Trna Mimics Bound to the E Site of the Large Ribosomal Subunit Rna V. 9 1345 2003.
ISSN: ISSN 1355-8382
PubMed: 14561884
DOI: 10.1261/RNA.5120503