Potassium in PDB 2fcz: Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin

The structure of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin, PDB code: 2fcz was solved by E.Ennifar, J.C.Paillart, R.Marquet, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.17 / 2.01
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.125, 27.191, 106.909, 90.00, 116.72, 90.00
R / Rfree (%)	23.8 / 25.6

The structure of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin also contains other interesting chemical elements:

Bromine

(Br)

4 atoms

The binding sites of Potassium atom in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin (pdb code 2fcz). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin, PDB code: 2fcz:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K26 b:39.0 occ:1.00 OP1 A:A8 2.5 35.9 1.0 OP2 A:A9 2.7 32.7 1.0 O7 A:RIO1024 2.9 27.6 1.0 O A:HOH111 3.1 33.9 1.0 O A:HOH98 3.2 52.0 1.0 O B:HOH122 3.4 43.2 1.0 O B:HOH222 3.5 57.7 1.0 P A:A8 3.8 36.7 1.0 O D:HOH69 4.0 26.8 1.0 P A:A9 4.0 33.2 1.0 C13 A:RIO1024 4.0 25.7 1.0 C14 A:RIO1024 4.2 24.9 1.0 OP2 A:A8 4.3 39.9 1.0 O8 A:RIO1024 4.3 26.2 1.0 O5' A:A8 4.4 36.1 1.0 OP1 A:A9 4.5 36.5 1.0 C11 A:RIO1024 4.7 26.2 1.0 O B:HOH33 4.7 31.3 1.0 O A:HOH85 4.7 39.0 1.0 O D:HOH93 4.8 35.8 1.0 O3' A:A8 4.8 31.9 1.0

Potassium binding site 2 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K25 b:39.3 occ:1.00 OP1 B:A8 2.6 25.5 1.0 OP2 B:A9 2.7 25.1 1.0 O B:HOH79 2.8 46.1 1.0 O B:HOH166 2.8 41.0 1.0 O B:HOH146 3.0 44.8 1.0 O B:HOH81 3.1 31.9 1.0 O7 B:RIO2024 3.1 23.5 1.0 P B:A8 3.7 27.7 1.0 OP2 B:A8 3.9 25.3 1.0 C14 B:RIO2024 4.0 21.7 1.0 O8 B:RIO2024 4.0 22.0 1.0 C13 B:RIO2024 4.1 20.8 1.0 P B:A9 4.2 25.8 1.0 O5' B:A8 4.4 27.0 1.0 N7 B:A9 4.4 23.6 1.0 C8 B:A9 4.4 24.9 1.0 O D:HOH36 4.7 25.8 1.0 N6 D:A9 4.8 25.4 1.0 C3' B:A8 4.8 24.2 1.0 O3' B:A8 4.9 26.0 1.0 C11 B:RIO2024 4.9 22.7 1.0 O5' B:A9 4.9 26.9 1.0 O B:HOH154 4.9 39.7 1.0 C5' B:A8 5.0 25.4 1.0 O A:HOH39 5.0 29.6 1.0

Potassium binding site 3 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ C:K27 b:39.2 occ:1.00 OP2 C:A9 2.6 32.0 1.0 OP1 C:A8 2.7 41.7 1.0 O7 C:RIO3024 3.1 26.2 1.0 O C:HOH119 3.1 24.9 1.0 O D:HOH221 3.5 45.0 1.0 O C:HOH228 3.5 46.2 1.0 P C:A8 3.9 37.2 1.0 C14 C:RIO3024 4.0 26.5 1.0 O5' C:A8 4.0 39.7 1.0 P C:A9 4.0 31.1 1.0 C13 C:RIO3024 4.1 25.2 1.0 O8 C:RIO3024 4.1 25.0 1.0 O C:HOH88 4.7 37.4 1.0 C11 C:RIO3024 4.7 26.2 1.0 OP2 C:A8 4.7 41.2 1.0 OP1 C:A9 4.7 33.9 1.0 O3' C:A8 4.7 30.7 1.0 C8 C:A9 4.8 24.5 1.0 C3' C:A8 4.9 28.6 1.0 O5' C:A9 4.9 30.6 1.0 N7 C:A9 5.0 23.9 1.0

Potassium binding site 4 out of 4 in the Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Hiv-1 Dis Kissing-Loop in Complex with Ribostamycin within 5.0Å range: probe atom residue distance (Å) B Occ D:K28 b:46.4 occ:1.00 OP2 D:A9 2.6 25.1 1.0 OP1 D:A8 2.7 26.6 1.0 O D:HOH103 2.8 32.2 1.0 O D:HOH89 3.0 30.1 1.0 O7 D:RIO4024 3.2 23.2 1.0 P D:A8 3.7 26.5 1.0 C14 D:RIO4024 4.0 23.9 1.0 OP2 D:A8 4.1 30.1 1.0 O8 D:RIO4024 4.1 24.9 1.0 P D:A9 4.1 28.6 1.0 C13 D:RIO4024 4.2 23.8 1.0 O5' D:A8 4.3 24.3 1.0 N7 D:A9 4.3 26.5 1.0 C8 D:A9 4.3 27.2 1.0 C3' D:A8 4.7 23.8 1.0 O3' D:A8 4.8 27.2 1.0 O5' D:A9 4.8 28.4 1.0 C11 D:RIO4024 4.8 23.2 1.0 O C:HOH63 4.9 31.8 1.0 O B:HOH166 4.9 41.0 1.0 C5' D:A8 4.9 23.4 1.0

E.Ennifar, J.C.Paillart, A.Bodlenner, P.Walter, J.-M.Weibel, A.-M.Aubertin, P.Pale, P.Dumas, R.Marquet. Targeting the Dimerization Initiation Site of Hiv-1 Rna with Aminoglycosides: From Crystal to Cell. Nucleic Acids Res. V. 34 2328 2006.
ISSN: ISSN 0305-1048
PubMed: 16679451
DOI: 10.1093/NAR/GKL317