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Barium in PDB 1y6s: Hiv-1 Dis(Mal) Duplex Ba-Soaked

Protein crystallography data

The structure of Hiv-1 Dis(Mal) Duplex Ba-Soaked, PDB code: 1y6s was solved by E.Ennifar, P.Walter, P.Dumas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.99 / 2.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 58.010, 58.010, 65.420, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 27.6

Barium Binding Sites:

The binding sites of Barium atom in the Hiv-1 Dis(Mal) Duplex Ba-Soaked (pdb code 1y6s). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 6 binding sites of Barium where determined in the Hiv-1 Dis(Mal) Duplex Ba-Soaked, PDB code: 1y6s:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6;

Barium binding site 1 out of 6 in 1y6s

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Barium binding site 1 out of 6 in the Hiv-1 Dis(Mal) Duplex Ba-Soaked


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Hiv-1 Dis(Mal) Duplex Ba-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba501

b:36.4
occ:0.36
O4 A:U3 3.2 51.8 1.0
O6 A:G4 3.9 62.9 1.0
C4 A:U3 4.0 48.5 1.0
N4 B:C20 4.4 45.8 1.0
C5 A:U3 4.4 48.8 1.0
N7 A:G4 4.5 59.5 1.0
N6 B:A21 4.6 50.1 1.0
C6 A:G4 4.8 61.5 1.0
O6 B:G19 4.8 41.2 1.0
N4 A:C5 4.9 44.5 1.0
N3 A:U3 5.0 48.6 1.0

Barium binding site 2 out of 6 in 1y6s

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Barium binding site 2 out of 6 in the Hiv-1 Dis(Mal) Duplex Ba-Soaked


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Hiv-1 Dis(Mal) Duplex Ba-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba502

b:36.4
occ:0.27
O6 A:G7 3.2 51.0 1.0
O4 A:U6 3.5 47.8 1.0
N7 A:G7 4.0 50.1 1.0
C6 A:G7 4.1 49.4 1.0
C4 A:U6 4.3 46.5 1.0
C5 A:G7 4.5 48.5 1.0
N6 B:A18 4.7 43.6 1.0
C5 A:U6 4.7 44.6 1.0
N4 B:C17 4.8 46.5 1.0
N6 B:A16 4.8 50.0 1.0

Barium binding site 3 out of 6 in 1y6s

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Barium binding site 3 out of 6 in the Hiv-1 Dis(Mal) Duplex Ba-Soaked


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Hiv-1 Dis(Mal) Duplex Ba-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba503

b:36.4
occ:0.23
O6 A:G9 2.6 47.6 1.0
C6 A:G9 3.4 45.3 1.0
O6 A:G10 3.4 57.1 1.0
N7 A:G9 3.5 45.7 1.0
C5 A:G9 3.7 45.8 1.0
N7 A:G10 4.2 57.9 1.0
C6 A:G10 4.4 56.9 1.0
N1 A:G9 4.6 43.8 1.0
C5 A:G10 4.7 57.0 1.0
N4 B:C15 4.7 48.3 1.0
C8 A:G9 4.7 45.8 1.0
OP2 A:A8 4.7 46.8 1.0
N6 B:A16 4.9 50.0 1.0
N6 B:A14 5.0 44.1 1.0

Barium binding site 4 out of 6 in 1y6s

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Barium binding site 4 out of 6 in the Hiv-1 Dis(Mal) Duplex Ba-Soaked


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Hiv-1 Dis(Mal) Duplex Ba-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba504

b:36.4
occ:0.23
OP2 A:G10 4.5 50.2 1.0

Barium binding site 5 out of 6 in 1y6s

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Barium binding site 5 out of 6 in the Hiv-1 Dis(Mal) Duplex Ba-Soaked


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Hiv-1 Dis(Mal) Duplex Ba-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba505

b:36.4
occ:0.15
OP1 A:G9 2.5 61.4 1.0
OP1 B:G9 2.8 45.6 0.5
OP1 B:G9 3.5 49.7 0.5
P A:G9 3.8 58.6 1.0
O3' A:A8 3.9 55.6 1.0
C5' B:G9 3.9 40.1 0.5
O5' B:G9 4.0 43.3 0.5
P B:G9 4.0 44.7 0.5
O3' B:A8 4.0 48.1 0.5
P B:G9 4.4 49.8 0.5
C5' A:G9 4.6 54.5 1.0
O5' A:G9 4.6 56.6 1.0
O3' B:A8 4.8 45.0 0.5
OP2 A:G9 4.9 59.6 1.0
O2' A:A8 5.0 52.8 1.0

Barium binding site 6 out of 6 in 1y6s

Go back to Barium Binding Sites List in 1y6s
Barium binding site 6 out of 6 in the Hiv-1 Dis(Mal) Duplex Ba-Soaked


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Hiv-1 Dis(Mal) Duplex Ba-Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba507

b:36.4
occ:0.35
O6 B:G4 3.3 36.0 1.0
O4 B:U3 3.3 47.1 1.0
C4 B:U3 4.1 42.9 1.0
C6 B:G4 4.4 36.0 1.0
C5 B:U3 4.4 41.0 1.0
N4 A:C20 4.7 36.6 1.0
N6 A:A21 4.9 35.5 1.0
N7 B:G4 4.9 35.0 1.0

Reference:

E.Ennifar, P.Walter, P.Dumas. A Crystallographic Study of the Binding of 13 Metal Ions to Two Related Rna Duplexes Nucleic Acids Res. V. 31 2671 2003.
ISSN: ISSN 0305-1048
PubMed: 12736317
DOI: 10.1093/NAR/GKG350
Page generated: Tue Oct 27 17:00:12 2020

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