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

Protein crystallography data

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

Other elements in 2fcz:

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

Bromine (Br) 4 atoms

Potassium Binding Sites:

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 2fcz

Go back to Potassium Binding Sites List in 2fcz
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 2fcz

Go back to Potassium Binding Sites List in 2fcz
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 2fcz

Go back to Potassium Binding Sites List in 2fcz
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 2fcz

Go back to Potassium Binding Sites List in 2fcz
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

Reference:

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
Page generated: Sun Dec 13 23:09:35 2020

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