Potassium in PDB 3c44: Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin

The structure of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin, PDB code: 3c44 was solved by S.Freisz, E.Ennifar, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.55 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	30.818, 95.703, 47.856, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 24.7

The structure of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Potassium atom in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin (pdb code 3c44). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin, PDB code: 3c44:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ A:K25 b:62.3 occ:1.00 O A:HOH91 2.8 51.2 1.0 O4' A:A8 3.0 32.4 1.0 O5' A:A8 3.4 33.8 1.0 C1' A:A8 3.8 32.4 1.0 C4' A:A8 3.9 32.1 1.0 O A:HOH80 3.9 78.8 1.0 OP1 A:A8 4.1 33.4 1.0 C5' A:A8 4.2 33.1 1.0 P A:A8 4.5 34.0 1.0 N9 A:A8 4.5 31.8 1.0 O A:HOH27 4.5 53.2 1.0 C8 A:A8 4.7 31.9 1.0 O A:HOH71 5.0 55.3 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K25 b:51.8 occ:1.00 O6 B:G4 2.7 31.6 1.0 O4 B:U3 2.7 40.7 1.0 O B:HOH34 2.7 36.5 1.0 C4 B:U3 3.6 40.4 1.0 C6 B:G4 3.7 31.4 1.0 C5 B:U3 4.0 40.8 1.0 N7 B:G4 4.1 31.1 1.0 N4 A:C20 4.2 28.5 1.0 C5 B:G4 4.3 32.7 1.0 O B:HOH42 4.4 34.7 1.0 N6 A:A21 4.5 39.4 1.0 O6 A:G19 4.6 28.8 1.0 N3 B:U3 4.7 39.5 1.0 N4 B:C5 4.7 26.0 1.0 O A:HOH86 4.9 52.7 1.0 O4 B:U2 4.9 49.5 1.0 N1 B:G4 4.9 31.9 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K26 b:53.0 occ:1.00 O B:HOH62 2.9 36.0 1.0 N32 B:PAR24 2.9 22.5 1.0 OP1 B:A9 3.1 42.9 1.0 O11 B:PAR24 3.2 20.7 1.0 O5' B:A9 3.3 42.1 1.0 C32 B:PAR24 3.4 21.1 1.0 C51 B:PAR24 3.6 21.6 1.0 C31 B:PAR24 3.7 22.1 1.0 C2' B:A9 3.7 35.4 1.0 P B:A9 3.7 44.6 1.0 C3' B:A9 3.9 37.1 1.0 C42 B:PAR24 3.9 22.0 1.0 C41 B:PAR24 4.0 22.9 1.0 O2' B:A9 4.0 36.7 1.0 O41 B:PAR24 4.0 25.0 1.0 C11 B:PAR24 4.1 19.1 1.0 O3' B:A8 4.2 41.0 1.0 OP2 B:G10 4.2 29.7 1.0 O B:HOH69 4.2 48.9 1.0 O B:HOH61 4.2 32.9 1.0 O51 B:PAR24 4.3 19.6 1.0 C21 B:PAR24 4.4 18.5 1.0 C5' B:A9 4.4 38.5 1.0 C61 B:PAR24 4.6 24.4 1.0 O31 B:PAR24 4.7 24.1 1.0 N21 B:PAR24 4.8 14.9 1.0 C22 B:PAR24 4.8 21.6 1.0 C4' B:A9 4.8 37.1 1.0 O2' A:A9 4.9 29.6 1.0 O61 B:PAR24 5.0 25.3 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Paromomycin within 5.0Å range: probe atom residue distance (Å) B Occ B:K28 b:67.3 occ:1.00 O B:HOH66 2.9 53.7 1.0 O3' B:G10 3.0 27.5 1.0 OP1 B:U11 3.4 27.7 1.0 P B:U11 3.9 27.3 1.0 C3' B:G10 4.1 28.1 1.0 O B:HOH87 4.1 47.9 1.0 C4' B:G10 4.1 29.0 1.0 O2' B:G10 4.2 26.4 1.0 C5' B:U11 4.6 27.2 1.0 C5' B:G10 4.7 28.5 1.0 C2' B:G10 4.8 28.4 1.0 O5' B:U11 4.8 26.3 1.0

S.Freisz, K.Lang, R.Micura, P.Dumas, E.Ennifar. Binding of Aminoglycoside Antibiotics to the Duplex Form of the Hiv-1 Genomic Rna Dimerization Initiation Site. Angew.Chem.Int.Ed.Engl. V. 47 4110 2008.
ISSN: ISSN 0570-0833
PubMed: 18435520
DOI: 10.1002/ANIE.200800726