Sodium in PDB 1jtw: Structure of SL4 Rna From the Hiv-1 Packaging Signal

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Sodium atom in the Structure of SL4 Rna From the Hiv-1 Packaging Signal (pdb code 1jtw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 15 binding sites of Sodium where determined in the Structure of SL4 Rna From the Hiv-1 Packaging Signal, PDB code: 1jtw:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na17 b:0.0 occ:1.00 OP1 A:G2 2.5 0.0 1.0 P A:G2 3.9 0.0 1.0 H5'' A:G2 3.9 0.0 1.0 O3' A:G1 4.2 0.0 1.0 H5' A:G2 4.4 0.0 1.0 C5' A:G2 4.6 0.0 1.0 O5' A:G2 4.7 0.0 1.0 OP2 A:G2 4.9 0.0 1.0

Sodium binding site 2 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na18 b:0.0 occ:1.00 O6 A:G13 2.6 0.0 1.0 O6 A:G3 2.6 0.0 1.0 O4 A:U4 2.7 0.0 1.0 O4 A:U14 2.9 0.0 1.0 H3 A:U14 3.4 0.0 1.0 H3 A:U4 3.4 0.0 1.0 C4 A:U4 3.6 0.0 1.0 H42 A:C12 3.6 0.0 1.0 C6 A:G13 3.7 0.0 1.0 C4 A:U14 3.8 0.0 1.0 C6 A:G3 3.8 0.0 1.0 H41 A:C12 3.8 0.0 1.0 N3 A:U4 3.9 0.0 1.0 N4 A:C12 3.9 0.0 1.0 N3 A:U14 3.9 0.0 1.0 H41 A:C15 4.2 0.0 1.0 O6 A:G5 4.4 0.0 1.0 H1 A:G3 4.5 0.0 1.0 C5 A:G13 4.6 0.0 1.0 N1 A:G3 4.7 0.0 1.0 N7 A:G13 4.7 0.0 1.0 N4 A:C15 4.7 0.0 1.0 C5 A:G3 4.7 0.0 1.0 H1 A:G13 4.7 0.0 1.0 N1 A:G13 4.7 0.0 1.0 C5 A:U4 4.8 0.0 1.0 O6 A:G2 4.8 0.0 1.0 N7 A:G3 4.9 0.0 1.0 H42 A:C15 4.9 0.0 1.0 C4 A:C12 5.0 0.0 1.0

Sodium binding site 3 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na19 b:0.0 occ:1.00 OP2 A:U4 2.5 0.0 1.0 OP1 A:G3 2.6 0.0 1.0 H5'' A:G3 2.9 0.0 1.0 O5' A:G3 3.1 0.0 1.0 P A:G3 3.2 0.0 1.0 H3' A:G3 3.3 0.0 1.0 C5' A:G3 3.5 0.0 1.0 P A:U4 3.6 0.0 1.0 OP2 A:G3 3.7 0.0 1.0 O3' A:G3 3.7 0.0 1.0 C3' A:G3 3.9 0.0 1.0 C4' A:G3 4.3 0.0 1.0 H5' A:G3 4.3 0.0 1.0 OP1 A:U4 4.3 0.0 1.0 O3' A:G2 4.7 0.0 1.0 O5' A:U4 4.9 0.0 1.0 H8 A:G3 4.9 0.0 1.0 H4' A:G3 5.0 0.0 1.0

Sodium binding site 4 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na20 b:0.0 occ:1.00 OP1 A:U4 2.6 0.0 1.0 OP2 A:G5 2.7 0.0 1.0 H5'' A:U4 2.9 0.0 1.0 O5' A:U4 3.0 0.0 1.0 P A:U4 3.1 0.0 1.0 H3' A:U4 3.2 0.0 1.0 C5' A:U4 3.4 0.0 1.0 P A:G5 3.4 0.0 1.0 O3' A:U4 3.5 0.0 1.0 OP2 A:U4 3.5 0.0 1.0 C3' A:U4 3.7 0.0 1.0 OP1 A:G5 3.9 0.0 1.0 C4' A:U4 4.2 0.0 1.0 H5' A:U4 4.3 0.0 1.0 O3' A:G3 4.7 0.0 1.0 H6 A:U4 4.8 0.0 1.0 H4' A:U4 4.8 0.0 1.0 O5' A:G5 4.9 0.0 1.0

Sodium binding site 5 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na21 b:0.0 occ:1.00 OP1 A:U14 2.6 0.0 1.0 P A:U14 3.2 0.0 1.0 O3' A:G13 3.2 0.0 1.0 OP2 A:U14 3.6 0.0 1.0 H5' A:G13 3.8 0.0 1.0 H4' A:G13 4.1 0.0 1.0 C3' A:G13 4.4 0.0 1.0 C4' A:G13 4.6 0.0 1.0 C5' A:G13 4.6 0.0 1.0 O5' A:U14 4.7 0.0 1.0 H3' A:G13 4.9 0.0 1.0

Sodium binding site 6 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na22 b:0.0 occ:1.00 OP1 A:A8 2.7 0.0 1.0 OP2 A:G7 2.8 0.0 1.0 OP1 A:G7 3.0 0.0 1.0 P A:G7 3.1 0.0 1.0 P A:A8 3.1 0.0 1.0 O5' A:G7 3.2 0.0 1.0 OP2 A:A8 3.2 0.0 1.0 O3' A:G7 3.3 0.0 1.0 H5'' A:G7 3.5 0.0 1.0 H3' A:G7 3.6 0.0 1.0 C5' A:G7 3.9 0.0 1.0 C3' A:G7 4.0 0.0 1.0 C4' A:G7 4.5 0.0 1.0 O3' A:C6 4.7 0.0 1.0 O5' A:A8 4.7 0.0 1.0 H5' A:G7 4.8 0.0 1.0

Sodium binding site 7 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na23 b:0.0 occ:1.00 OP1 A:C6 2.5 0.0 1.0 H5'' A:C6 3.5 0.0 1.0 P A:C6 3.7 0.0 1.0 O5' A:C6 4.1 0.0 1.0 OP2 A:C6 4.2 0.0 1.0 C5' A:C6 4.3 0.0 1.0 OP2 A:G7 4.4 0.0 1.0 H5' A:C6 4.8 0.0 1.0 O3' A:G5 5.0 0.0 1.0

Sodium binding site 8 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na24 b:0.0 occ:1.00 OP2 A:G9 2.6 0.0 1.0 OP2 A:A8 2.6 0.0 1.0 H2' A:G7 2.8 0.0 1.0 H3' A:G7 3.3 0.0 1.0 N7 A:G7 3.3 0.0 1.0 C8 A:G7 3.3 0.0 1.0 H5'' A:A8 3.5 0.0 1.0 H8 A:G7 3.6 0.0 1.0 P A:G9 3.6 0.0 1.0 C5 A:G7 3.7 0.0 1.0 C2' A:G7 3.7 0.0 1.0 P A:A8 3.8 0.0 1.0 N9 A:G7 3.8 0.0 1.0 H3' A:A8 3.9 0.0 1.0 O5' A:A8 3.9 0.0 1.0 C3' A:G7 3.9 0.0 1.0 C4 A:G7 4.0 0.0 1.0 O3' A:A8 4.1 0.0 1.0 OP1 A:G9 4.1 0.0 1.0 C5' A:A8 4.2 0.0 1.0 O3' A:G7 4.3 0.0 1.0 C1' A:G7 4.4 0.0 1.0 C3' A:A8 4.4 0.0 1.0 C6 A:G7 4.5 0.0 1.0 O2' A:G7 4.8 0.0 1.0 O6 A:G7 4.9 0.0 1.0 C4' A:A8 4.9 0.0 1.0 N3 A:G7 5.0 0.0 1.0

Sodium binding site 9 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na25 b:0.0 occ:1.00 OP2 A:A10 2.6 0.0 1.0 H5'' A:G9 2.7 0.0 1.0 OP1 A:G9 2.9 0.0 1.0 O5' A:G9 2.9 0.0 1.0 H3' A:G9 3.1 0.0 1.0 P A:G9 3.3 0.0 1.0 C5' A:G9 3.3 0.0 1.0 H1 A:G7 3.4 0.0 1.0 O3' A:G9 3.5 0.0 1.0 P A:A10 3.5 0.0 1.0 N1 A:G7 3.6 0.0 1.0 C3' A:G9 3.7 0.0 1.0 H21 A:G7 3.7 0.0 1.0 OP2 A:G9 3.7 0.0 1.0 C2 A:G7 4.0 0.0 1.0 N2 A:G7 4.0 0.0 1.0 C4' A:G9 4.1 0.0 1.0 OP1 A:A10 4.1 0.0 1.0 H5' A:G9 4.2 0.0 1.0 C6 A:G7 4.2 0.0 1.0 H8 A:G9 4.4 0.0 1.0 O6 A:G7 4.5 0.0 1.0 H22 A:G7 4.7 0.0 1.0 H4' A:G9 4.7 0.0 1.0 O3' A:A8 4.8 0.0 1.0 N3 A:G7 4.8 0.0 1.0 O5' A:A10 4.9 0.0 1.0

Sodium binding site 10 out of 15 in the Structure of SL4 Rna From the Hiv-1 Packaging Signal


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Structure of SL4 Rna From the Hiv-1 Packaging Signal within 5.0Å range: probe atom residue distance (Å) B Occ A:Na26 b:0.0 occ:1.00 OP2 A:G11 2.6 0.0 1.0 OP1 A:G11 2.7 0.0 1.0 P A:G11 3.0 0.0 1.0 O3' A:A10 3.6 0.0 1.0 O2' A:A10 4.1 0.0 1.0 HO2' A:A10 4.2 0.0 1.0 O5' A:G11 4.5 0.0 1.0 C3' A:A10 4.7 0.0 1.0 C2' A:A10 4.8 0.0 1.0 H5' A:G11 4.9 0.0 1.0 H2' A:A10 5.0 0.0 1.0

D.J.Kerwood, M.J.Cavaluzzi, P.N.Borer. Structure of SL4 Rna From the Hiv-1 Packaging Signal. Biochemistry V. 40 14518 2001.
ISSN: ISSN 0006-2960
PubMed: 11724565
DOI: 10.1021/BI0111909