Calcium in PDB 397d: A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation

The structure of A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation, PDB code: 397d was solved by J.A.Ippolito, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.100, 27.100, 31.600, 69.20, 77.50, 63.00
R / Rfree (%)	12.6 / 17.7

The binding sites of Calcium atom in the A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation (pdb code 397d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation, PDB code: 397d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca48 b:14.7 occ:1.00 OP1 A:U23 2.3 14.5 1.0 OP2 A:C24 2.3 15.3 1.0 OP2 A:G26 2.3 15.0 1.0 O A:HOH54 2.4 18.4 1.0 O A:HOH53 2.4 18.5 1.0 O A:HOH52 2.4 19.6 1.0 P A:C24 3.7 15.3 1.0 P A:U23 3.7 14.5 1.0 P A:G26 3.8 15.5 1.0 O5' A:U23 4.2 13.9 1.0 C5' A:U23 4.3 14.4 1.0 C5' A:G26 4.3 14.9 1.0 OP1 A:C24 4.3 18.0 1.0 O A:HOH101 4.4 25.6 1.0 O5' A:G26 4.4 16.0 1.0 O A:HOH74 4.4 32.4 1.0 O A:HOH164 4.5 38.4 1.0 OP2 A:A22 4.6 18.6 1.0 C3' A:U25 4.6 15.8 1.0 O3' A:U23 4.6 15.8 1.0 OP1 A:A22 4.6 19.1 1.0 OP2 A:U23 4.6 14.7 1.0 O A:HOH104 4.6 22.7 1.0 O3' A:U25 4.6 15.3 1.0 O5' A:C24 4.6 16.0 1.0 O A:HOH113 4.7 27.5 1.0 O3' A:A22 4.7 13.8 1.0 OP1 A:G26 4.7 16.1 1.0 O5' A:A22 4.8 17.3 1.0 P A:A22 4.8 18.3 1.0 C3' A:A22 4.9 15.1 1.0 C3' A:U23 4.9 14.6 1.0

Calcium binding site 2 out of 4 in the A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca49 b:15.8 occ:1.00 O A:HOH136 2.3 18.9 1.0 OP1 A:G26 2.4 16.1 1.0 O A:HOH58 2.4 17.5 1.0 O A:HOH56 2.4 20.7 1.0 O A:HOH55 2.4 21.2 1.0 O A:HOH60 2.5 18.7 1.0 O A:HOH59 2.5 18.0 1.0 P A:G26 3.6 15.5 1.0 O3' A:U25 3.8 15.3 1.0 O5' A:G26 4.2 16.0 1.0 N7 A:A27 4.3 14.2 1.0 O A:HOH91 4.4 23.2 1.0 C4' A:U25 4.4 16.8 1.0 O B:HOH151 4.4 37.1 1.0 O A:HOH113 4.5 27.5 1.0 O4' A:U25 4.5 17.9 1.0 O A:HOH101 4.7 25.6 1.0 O6 A:G28 4.8 15.9 1.0 C3' A:U25 4.8 15.8 1.0 N7 A:G28 4.8 15.1 1.0 OP2 A:G26 4.8 15.0 1.0 C1' A:U25 4.8 17.3 1.0 OP2 A:A27 4.9 14.4 1.0 N6 A:A27 4.9 14.3 1.0

Calcium binding site 3 out of 4 in the A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca51 b:23.8 occ:1.00 O A:HOH210 2.2 39.0 1.0 O A:HOH68 2.4 34.4 1.0 O A:HOH67 2.4 29.7 1.0 O A:HOH69 2.4 25.7 1.0 O A:HOH71 2.5 25.3 1.0 O A:HOH189 2.5 25.0 1.0 O A:HOH70 2.5 20.2 1.0 O B:HOH162 2.7 38.5 1.0 O B:HOH102 4.3 26.4 1.0 O A:HOH217 4.4 38.7 1.0 O A:HOH159 4.4 26.0 1.0 O A:HOH77 4.5 25.3 1.0 O B:HOH90 4.5 25.2 1.0 O B:HOH160 4.6 27.8 1.0 O6 A:G21 4.7 17.7 1.0 N7 A:G21 4.7 18.5 1.0 N6 A:A22 4.8 14.8 1.0 O6 A:G26 4.9 15.2 1.0

Calcium binding site 4 out of 4 in the A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A 1.3 A Resolution Crystal Structure of the Hiv-1 Trans- Activation Response Region Rna Stem Reveals A Metal Ion- Dependent Bulge Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca50 b:17.8 occ:1.00 OP1 A:A27 2.3 16.3 1.0 O A:HOH61 2.3 25.1 1.0 O A:HOH62 2.4 19.1 1.0 O A:HOH64 2.4 19.1 1.0 O A:HOH66 2.4 20.6 1.0 O A:HOH63 2.4 17.5 1.0 O A:HOH65 2.5 21.3 1.0 P A:A27 3.6 14.8 1.0 O5' A:A27 4.1 14.1 1.0 C5' A:A27 4.1 15.1 1.0 OP2 A:A27 4.2 14.4 1.0 O2' A:U25 4.4 16.7 1.0 O A:HOH76 4.4 32.3 1.0 O A:HOH111 4.5 27.9 1.0 N3 A:C24 4.6 16.4 1.0 O A:HOH82 4.6 27.9 1.0 O2 A:U25 4.7 17.7 1.0 O3' A:G26 4.8 14.7 1.0

J.A.Ippolito, T.A.Steitz. A 1.3-A Resolution Crystal Structure of the Hiv-1 Trans-Activation Response Region Rna Stem Reveals A Metal Ion-Dependent Bulge Conformation. Proc.Natl.Acad.Sci.Usa V. 95 9819 1998.
ISSN: ISSN 0027-8424
PubMed: 9707559
DOI: 10.1073/PNAS.95.17.9819