Calcium in PDB 6bsi: Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence

Protein crystallography data

The structure of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence, PDB code: 6bsi was solved by L.Tian, M.Kim, W.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 3.25
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 163.850, 163.850, 129.570, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / 24.1

Other elements in 6bsi:

The structure of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence (pdb code 6bsi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence, PDB code: 6bsi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6bsi

Go back to Calcium Binding Sites List in 6bsi
Calcium binding site 1 out of 2 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:0.1
occ:1.00
OD1 A:ASP443 2.9 0.6 1.0
OE1 A:GLU478 3.1 0.1 1.0
OD2 A:ASP498 3.1 0.9 1.0
O A:GLY444 3.3 0.4 1.0
OP1 R:A26 3.5 0.2 1.0
OD2 A:ASP443 3.7 0.3 1.0
CG A:ASP443 3.7 0.1 1.0
OD1 A:ASP498 3.8 0.7 1.0
CG A:ASP498 3.9 0.8 1.0
CD A:GLU478 4.0 0.1 1.0
OE2 A:GLU478 4.4 0.9 1.0
C A:GLY444 4.4 0.8 1.0
N A:GLY444 4.8 0.4 1.0
P R:A26 4.9 0.5 1.0

Calcium binding site 2 out of 2 in 6bsi

Go back to Calcium Binding Sites List in 6bsi
Calcium binding site 2 out of 2 in the Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Hiv-1 Rt Complexed with An Rna/Dna Hybrid Containing the Polypurine-Tract Sequence within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:0.8
occ:1.00
N7 D:DG21 3.5 0.6 1.0
N7 D:DG22 3.6 0.3 1.0
O1 D:GOL102 3.9 0.9 1.0
C7 D:DT20 4.0 0.5 1.0
O6 D:DG21 4.1 0.6 1.0
C5 D:DG21 4.3 0.0 1.0
C8 D:DG21 4.4 0.7 1.0
C8 D:DG22 4.4 0.1 1.0
C6 D:DG21 4.5 0.1 1.0
C5 D:DT20 4.6 1.0 1.0
O6 D:DG22 4.7 0.6 1.0
C5 D:DG22 4.8 0.2 1.0
OP2 D:DG21 4.8 99.5 1.0
OP2 D:DT20 4.9 97.1 1.0

Reference:

L.Tian, M.S.Kim, H.Li, J.Wang, W.Yang. Structure of Hiv-1 Reverse Transcriptase Cleaving Rna in An Rna/Dna Hybrid. Proc. Natl. Acad. Sci. V. 115 507 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29295939
DOI: 10.1073/PNAS.1719746115
Page generated: Sat Dec 12 06:00:01 2020

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