Potassium in PDB 2qex: Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex was solved by S.J.Schroeder, G.Blaha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.92 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	214.620, 304.048, 578.647, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.1

The structure of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit also contains other interesting chemical elements:

Magnesium	(Mg)	116 atoms
Cadmium	(Cd)	5 atoms
Chlorine	(Cl)	22 atoms
Sodium	(Na)	86 atoms

The binding sites of Potassium atom in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit (pdb code 2qex). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit, PDB code: 2qex:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8401 b:78.4 occ:1.00 O6 0:G2102 2.5 53.0 1.0 O6 0:G2482 2.6 29.1 1.0 O2 0:C2536 2.9 25.5 1.0 N7 0:G2482 3.0 28.1 1.0 C6 0:G2482 3.3 27.7 1.0 C6 0:G2102 3.4 53.8 1.0 C5 0:G2482 3.4 28.2 1.0 O4' 0:C2536 3.4 30.1 1.0 C2 0:C2536 3.5 26.0 1.0 N7 0:G2102 3.6 52.9 1.0 C1' 0:C2536 3.8 28.4 1.0 C5 0:G2102 3.8 53.5 1.0 N1 0:C2536 3.9 27.5 1.0 N6 0:A2486 3.9 51.0 1.0 O2 0:U2535 4.1 37.9 1.0 C8 0:G2482 4.2 29.7 1.0 C4' 0:C2536 4.3 31.4 1.0 N3 0:C2536 4.3 25.2 1.0 C2 0:U2535 4.4 37.0 1.0 N1 0:G2102 4.6 53.6 1.0 N3 0:U2535 4.6 35.9 1.0 N1 0:G2482 4.6 28.4 1.0 C4 0:G2482 4.8 30.0 1.0 C8 0:G2102 4.8 53.6 1.0 C5' 0:C2536 4.9 31.8 1.0 C2' 0:U2535 4.9 40.1 1.0 OP1 0:U2539 4.9 39.5 1.0 C6 0:C2536 5.0 26.0 1.0

Potassium binding site 2 out of 2 in the Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit within 5.0Å range: probe atom residue distance (Å) B Occ 0:K8402 b:49.9 occ:1.00 O4 0:U172 2.8 29.7 1.0 O4 0:U163 3.0 28.9 1.0 O 0:HOH8837 3.0 29.8 1.0 O 0:HOH8965 3.1 17.1 1.0 O 0:HOH8932 3.1 35.8 1.0 O 0:HOH4780 3.2 39.2 1.0 OP2 0:C162 3.3 25.9 1.0 CD M:ARG82 3.5 32.8 1.0 O 0:HOH7654 3.7 35.3 1.0 O 0:HOH9146 3.7 20.5 1.0 C4 0:U172 3.8 28.6 1.0 N3 0:U172 4.0 28.9 1.0 C4 0:U163 4.0 28.0 1.0 NE M:ARG82 4.2 32.5 1.0 N4 0:C171 4.5 30.8 1.0 O 0:HOH7653 4.5 39.7 1.0 P 0:C162 4.5 26.0 1.0 C5 0:U163 4.6 28.2 1.0 CG M:ARG82 4.7 32.6 1.0 O6 0:G164 4.8 25.6 1.0 CB M:ARG82 4.8 30.3 1.0 OP2 0:A169 4.8 24.3 1.0 OP1 0:C162 4.8 26.6 1.0 N4 0:C173 4.9 27.3 1.0 N3 0:C173 4.9 26.5 1.0 OP1 0:A169 5.0 24.0 1.0

S.J.Schroeder, G.Blaha, P.B.Moore. Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit. Antimicrob.Agents Chemother. V. 51 4462 2007.
ISSN: ISSN 0066-4804
PubMed: 17664317
DOI: 10.1128/AAC.00455-07