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Sodium in PDB 1duq: Crystal Structure of the Rev Binding Element of Hiv-1

Protein crystallography data

The structure of Crystal Structure of the Rev Binding Element of Hiv-1, PDB code: 1duq was solved by L.-W.Hung, E.L.Holbrook, S.R.Holbrook, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 23.993, 53.930, 64.729, 114.52, 89.88, 102.85
R / Rfree (%) 21.8 / 26.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Rev Binding Element of Hiv-1 (pdb code 1duq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Crystal Structure of the Rev Binding Element of Hiv-1, PDB code: 1duq:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 1duq

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Sodium binding site 1 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na911

b:42.3
occ:1.00
 O6 B:G124 2.3 33.9 1.0
O6 A:G106 2.5 33.4 1.0
O A:HOH603 2.5 47.0 1.0
O6 B:G123 2.9 19.8 1.0
C6 B:G124 3.3 28.8 1.0
O B:HOH531 3.4 29.2 1.0
C6 A:G106 3.4 32.1 1.0
C6 B:G123 3.7 23.9 1.0
N1 A:G106 3.7 25.0 1.0
N1 B:G124 3.8 23.5 1.0
O A:HOH508 3.8 32.9 1.0
N6 B:A126 3.9 34.2 1.0
N7 B:G123 4.2 27.1 1.0
C5 B:G123 4.2 19.9 1.0
O6 A:G105 4.3 40.8 1.0
N4 A:C107 4.4 21.2 1.0
C5 B:G124 4.6 30.3 1.0
N1 B:G123 4.7 21.6 1.0
C5 A:G106 4.8 25.7 1.0
C6 B:A126 4.9 30.3 1.0

Sodium binding site 2 out of 10 in 1duq

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Sodium binding site 2 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na904

b:44.9
occ:1.00
 O6 D:G224 2.1 48.2 1.0
O6 C:G206 2.3 43.4 1.0
O D:HOH601 2.4 30.6 1.0
O C:HOH631 2.8 42.3 1.0
O6 D:G223 3.0 31.5 1.0
C6 D:G224 3.2 29.0 1.0
C6 C:G206 3.2 33.3 1.0
N1 C:G206 3.4 37.8 1.0
N1 D:G224 3.6 38.3 1.0
C6 D:G223 3.7 33.0 1.0
N1 D:A226 3.9 39.9 1.0
C5 D:G223 4.3 31.2 1.0
N7 D:G223 4.3 38.3 1.0
C2 D:A226 4.3 51.6 1.0
O6 C:G205 4.4 28.8 1.0
C5 D:G224 4.5 38.1 1.0
O D:HOH517 4.5 40.1 1.0
C5 C:G206 4.6 30.5 1.0
O C:HOH540 4.6 48.5 1.0
C6 D:A226 4.7 46.5 1.0
N1 D:G223 4.7 39.6 1.0
C2 C:G206 4.8 47.3 1.0
N6 D:A226 4.8 34.6 1.0
N4 C:C207 4.9 50.0 1.0
C2 D:G224 4.9 43.3 1.0

Sodium binding site 3 out of 10 in 1duq

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Sodium binding site 3 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na906

b:59.2
occ:1.00
 O5' C:G201 1.9 50.1 1.0
OP2 C:C202 2.8 64.1 1.0
C5' C:G201 2.9 61.6 1.0
O3' C:G201 3.0 73.7 1.0
P C:C202 3.1 66.4 1.0
OP1 C:C202 3.3 58.4 1.0
C4' C:G201 3.4 60.3 1.0
C3' C:G201 3.5 66.0 1.0
O5' C:C202 4.6 58.5 1.0
O4' C:G201 4.8 56.4 1.0
C2' C:G201 4.9 64.5 1.0

Sodium binding site 4 out of 10 in 1duq

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Sodium binding site 4 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na913

b:42.3
occ:1.00
 N1 C:G201 2.2 44.9 1.0
O2 D:C230 2.8 47.7 1.0
N2 C:G201 3.0 69.8 1.0
C2 C:G201 3.1 54.5 1.0
C6 C:G201 3.2 37.1 1.0
O2 C:C202 3.2 35.9 1.0
O6 C:G201 3.2 44.4 1.0
C2 C:C202 3.3 50.5 1.0
O2 B:C117 3.3 46.4 1.0
C2 D:C230 3.5 57.3 1.0
N1 C:C202 3.6 28.9 1.0
N3 D:C230 3.6 50.4 1.0
N3 C:C202 3.8 32.1 1.0
C2 B:C117 3.8 37.2 1.0
C1' C:C202 3.9 57.2 1.0
N3 B:C117 4.0 35.7 1.0
O4' C:C202 4.3 68.4 1.0
N3 C:G201 4.3 38.5 1.0
C6 C:C202 4.4 31.2 1.0
N2 A:G112 4.4 29.5 1.0
C5 C:G201 4.4 33.5 1.0
C4 C:C202 4.5 36.3 1.0
N1 D:G229 4.5 42.8 1.0
N1 A:G112 4.6 25.6 1.0
N1 B:C117 4.7 45.2 1.0
C2 A:G112 4.8 40.7 1.0
C5 C:C202 4.8 42.4 1.0
C4 C:G201 4.8 47.5 1.0
N1 D:C230 4.8 56.8 1.0
N2 D:G229 4.9 66.7 1.0
C4 D:C230 4.9 54.2 1.0

Sodium binding site 5 out of 10 in 1duq

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Sodium binding site 5 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na901

b:55.3
occ:1.00
 O5' D:C222 2.1 58.6 1.0
OP2 D:A221 2.3 42.2 1.0
O2' D:G220 2.8 54.3 1.0
C5' D:A221 2.8 60.7 1.0
P D:C222 2.8 61.7 1.0
O3' D:A221 2.9 52.2 1.0
OP1 D:C222 2.9 70.7 1.0
C5' D:C222 3.0 43.7 1.0
P D:A221 3.0 70.2 1.0
C3' D:A221 3.0 40.0 1.0
O5' D:A221 3.1 55.8 1.0
C2' D:G220 3.2 44.4 1.0
O3' D:G220 3.2 56.2 1.0
C4' D:A221 3.4 48.1 1.0
C3' D:G220 3.7 45.3 1.0
C6 D:C222 3.9 28.9 1.0
O4' D:C222 4.1 45.4 1.0
C4' D:C222 4.1 42.4 1.0
OP2 D:C222 4.2 43.2 1.0
O D:HOH542 4.2 38.8 1.0
C5 D:C222 4.4 32.4 1.0
OP1 D:A221 4.5 41.9 1.0
C2' D:A221 4.5 46.6 1.0
O4' D:A221 4.6 44.9 1.0
C1' D:G220 4.7 38.5 1.0
C8 D:A221 4.9 34.5 1.0
C4' D:G220 4.9 47.9 1.0
N1 D:C222 5.0 37.5 1.0

Sodium binding site 6 out of 10 in 1duq

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Sodium binding site 6 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na912

b:42.3
occ:1.00
 O6 F:G324 2.2 36.5 1.0
O6 E:G306 2.2 34.7 1.0
O6 F:G323 3.0 26.2 1.0
C6 E:G306 3.2 22.2 1.0
C6 F:G324 3.3 24.3 1.0
N1 E:G306 3.5 20.0 1.0
N6 F:A326 3.7 28.5 1.0
O E:HOH507 3.7 33.8 1.0
C6 F:G323 3.8 23.3 1.0
N1 F:G324 3.8 22.4 1.0
O6 E:G305 4.0 38.7 1.0
N4 E:C307 4.2 18.4 1.0
C5 F:G323 4.4 28.3 1.0
N7 F:G323 4.4 27.7 1.0
C5 F:G324 4.5 22.3 1.0
C5 E:G306 4.5 29.9 1.0
C6 F:A326 4.7 26.3 1.0
N1 F:G323 4.7 22.8 1.0
C2 E:G306 4.9 35.4 1.0

Sodium binding site 7 out of 10 in 1duq

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Sodium binding site 7 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na905

b:62.6
occ:1.00
 O5' G:G401 2.1 39.8 1.0
O3' G:G401 2.8 73.2 1.0
OP2 G:C402 3.0 63.4 1.0
P G:C402 3.0 67.8 1.0
C5' G:G401 3.1 60.6 1.0
OP1 G:C402 3.2 59.0 1.0
C4' G:G401 3.4 60.0 1.0
C3' G:G401 3.6 69.0 1.0
O5' G:C402 4.6 54.3 1.0
O4' G:G401 4.9 59.0 1.0
C2' G:G401 4.9 63.8 1.0

Sodium binding site 8 out of 10 in 1duq

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Sodium binding site 8 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na914

b:42.3
occ:1.00
 N1 G:G401 2.7 37.4 1.0
O2 H:C430 2.7 67.9 1.0
N2 G:G401 3.1 59.2 1.0
O2 F:C317 3.2 45.3 1.0
O2 G:C402 3.3 51.0 1.0
C2 G:G401 3.4 44.2 1.0
C2 G:C402 3.6 56.2 1.0
C6 G:G401 3.7 35.1 1.0
C2 H:C430 3.8 62.5 1.0
O6 G:G401 3.8 40.3 1.0
C2 F:C317 3.9 32.5 1.0
N1 G:C402 3.9 40.1 1.0
C1' G:C402 4.0 66.2 1.0
N2 E:G312 4.1 31.5 1.0
N3 G:C402 4.2 40.5 1.0
N3 H:C430 4.2 51.7 1.0
N3 F:C317 4.3 30.6 1.0
O4' G:C402 4.4 73.9 1.0
C2 E:G312 4.6 31.7 1.0
N3 G:G401 4.7 34.0 1.0
N1 E:G312 4.7 20.7 1.0
C6 G:C402 4.8 37.9 1.0
N2 H:G429 4.8 65.7 1.0
N1 F:C317 4.9 41.9 1.0
N1 H:C430 4.9 63.4 1.0
C5 G:G401 5.0 25.8 1.0

Sodium binding site 9 out of 10 in 1duq

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Sodium binding site 9 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na902

b:48.9
occ:1.00
 O6 H:G424 2.2 52.3 1.0
O H:HOH602 2.2 41.0 1.0
O6 G:G406 2.3 37.7 1.0
O G:HOH635 2.8 42.4 1.0
O6 H:G423 2.8 37.1 1.0
C6 H:G424 3.1 33.7 1.0
C6 G:G406 3.3 27.4 1.0
N1 H:G424 3.4 36.8 1.0
C6 H:G423 3.6 30.1 1.0
N1 G:G406 3.6 37.9 1.0
N1 H:A426 3.9 37.6 1.0
N7 H:G423 4.0 40.3 1.0
C5 H:G423 4.1 32.7 1.0
O H:HOH515 4.1 37.4 1.0
C2 H:A426 4.4 53.7 1.0
C5 H:G424 4.5 37.8 1.0
O6 G:G405 4.5 31.6 1.0
N1 H:G423 4.6 31.4 1.0
C5 G:G406 4.7 32.2 1.0
N4 G:C407 4.7 41.3 1.0
C6 H:A426 4.7 46.3 1.0
C2 H:G424 4.8 44.4 1.0
N6 H:A426 4.9 39.2 1.0
C2 G:G406 5.0 42.1 1.0

Sodium binding site 10 out of 10 in 1duq

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Sodium binding site 10 out of 10 in the Crystal Structure of the Rev Binding Element of Hiv-1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of the Rev Binding Element of Hiv-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na903

b:55.4
occ:1.00
 OP2 H:A421 1.9 55.2 1.0
O5' H:C422 2.8 59.0 1.0
C2' H:G420 2.8 50.2 1.0
O2' H:G420 2.9 51.2 1.0
P H:A421 2.9 71.2 1.0
O3' H:G420 3.1 63.4 1.0
C5' H:A421 3.3 60.5 1.0
C3' H:G420 3.3 54.3 1.0
O5' H:A421 3.4 59.6 1.0
C6 H:C422 3.4 27.1 1.0
OP1 H:C422 3.5 74.4 1.0
P H:C422 3.5 66.2 1.0
C5 H:C422 3.6 19.1 1.0
O3' H:A421 3.6 57.5 1.0
C3' H:A421 3.7 45.3 1.0
C5' H:C422 3.8 49.5 1.0
C4' H:A421 4.1 48.1 1.0
OP1 H:A421 4.3 48.9 1.0
O4' H:C422 4.3 36.1 1.0
C1' H:G420 4.3 48.1 1.0
O H:HOH615 4.5 46.4 1.0
N1 H:C422 4.6 37.1 1.0
C4' H:C422 4.7 43.1 1.0
C4' H:G420 4.7 55.2 1.0
N9 H:G420 4.9 48.5 1.0
O H:HOH515 4.9 37.4 1.0
OP2 H:C422 4.9 45.7 1.0
C4 H:C422 5.0 34.4 1.0

Reference:

L.W.Hung, E.L.Holbrook, S.R.Holbrook. The Crystal Structure of the Rev Binding Element of Hiv-1 Reveals Novel Base Pairing and Conformational Variability. Proc.Natl.Acad.Sci.Usa V. 97 5107 2000.
ISSN: ISSN 0027-8424
PubMed: 10792052
DOI: 10.1073/PNAS.090588197
Page generated: Sun Oct 6 18:19:15 2024

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