Potassium in PDB 3dvv: Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME)

The structure of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME), PDB code: 3dvv was solved by E.Ennifar, P.Dumas, V.Olieric, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.59 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.703, 30.489, 58.004, 90.00, 122.25, 90.00
R / Rfree (%)	26.8 / 27.7

The structure of Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Potassium atom in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME) (pdb code 3dvv). 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 Ribostamycin (U267OME), PDB code: 3dvv:
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 Ribostamycin (U267OME)


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 Ribostamycin (U267OME) within 5.0Å range: probe atom residue distance (Å) B Occ A:K24 b:28.3 occ:0.60 O B:HOH42 2.4 47.8 1.0 O2' B:A8 2.8 35.4 1.0 OP1 A:G10 2.8 41.6 1.0 O3' B:A8 3.2 36.9 1.0 O3' A:A9 3.5 41.7 1.0 P A:G10 3.7 43.0 1.0 C2' B:A8 3.9 36.7 1.0 C3' B:A8 4.0 38.3 1.0 OP1 B:A9 4.0 34.8 1.0 C4' B:A8 4.1 39.9 1.0 P B:A9 4.2 36.4 1.0 O2' A:A9 4.5 39.2 1.0 C5' A:G10 4.5 44.7 1.0 C5' B:A9 4.5 37.0 1.0 O5' A:G10 4.6 44.1 1.0 C1' B:A8 4.7 38.0 1.0 OP2 A:U11 4.8 47.0 1.0 O5' B:A9 4.8 38.0 1.0 C3' A:A9 4.8 40.9 1.0 O4' B:A8 4.9 39.8 1.0 OP2 A:G10 5.0 41.6 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME)


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 Ribostamycin (U267OME) within 5.0Å range: probe atom residue distance (Å) B Occ A:K25 b:43.6 occ:0.60 O6 A:G4 2.6 40.9 1.0 O4 A:OMU3 2.8 47.1 1.0 C4 A:OMU3 3.7 49.6 1.0 C6 A:G4 3.7 41.5 1.0 O6 B:G19 3.8 31.0 1.0 N4 B:C20 3.8 37.3 1.0 N4 A:C5 4.1 36.8 1.0 N7 A:G4 4.2 43.6 1.0 C5 A:OMU3 4.2 49.3 1.0 N6 B:A21 4.3 45.6 1.0 C5 A:G4 4.3 42.8 1.0 N3 A:OMU3 4.7 50.0 1.0 N1 A:G4 4.8 40.1 1.0 C6 B:G19 4.9 30.9 1.0 O4 A:U2 5.0 44.0 1.0 C4 A:C5 5.0 34.3 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME)


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 Ribostamycin (U267OME) within 5.0Å range: probe atom residue distance (Å) B Occ B:K24 b:45.3 occ:0.60 O4 B:OMU3 2.8 41.5 1.0 O6 B:G4 3.0 40.8 1.0 C4 B:OMU3 3.7 42.2 1.0 C6 B:G4 4.0 41.6 1.0 C5 B:OMU3 4.0 42.5 1.0 N7 B:G4 4.2 43.9 1.0 N4 A:C20 4.3 43.8 1.0 N6 A:A21 4.4 51.9 1.0 C5 B:G4 4.5 43.1 1.0 O6 A:G19 4.6 42.6 1.0 O4 B:U2 4.7 41.0 1.0 N3 B:OMU3 4.8 43.4 1.0 N4 B:C5 4.8 40.9 1.0 C4 B:U2 5.0 42.0 1.0 C5 B:U2 5.0 43.1 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of Hiv-1 Subtype F Dis Extended Duplex Rna Bound to Ribostamycin (U267OME)


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 Ribostamycin (U267OME) within 5.0Å range: probe atom residue distance (Å) B Occ B:K25 b:55.7 occ:0.50 O2' B:U2 3.0 41.8 1.0 O3' B:U2 3.5 42.9 1.0 C5' B:OMU3 3.8 43.9 1.0 C2' B:U2 4.1 41.5 1.0 C3' B:U2 4.3 42.7 1.0 OP1 B:OMU3 4.4 47.5 1.0 P B:OMU3 4.5 44.7 1.0 O5' B:OMU3 4.6 43.3 1.0 C4' B:U2 4.6 43.5 1.0 C4' B:OMU3 4.8 43.7 1.0

V.Olieric, U.Rieder, K.Lang, A.Serganov, C.Schulze-Brise, R.Micura, P.Dumas, E.Ennifar. A Fast Strategy For Selenium Derivatization and Phasing of Rna Structures To Be Published.