Calcium in PDB 6bsh: Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode

Enzymatic activity of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode

All present enzymatic activity of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode:
2.7.7.7;

Protein crystallography data

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode, PDB code: 6bsh 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) 37.20 / 2.65
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.792, 161.792, 128.773, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 22.7

Other elements in 6bsh:

The structure of Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode 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 Rna/Dna Hybrid in the Rna Hydrolysis Mode (pdb code 6bsh). 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 Rna/Dna Hybrid in the Rna Hydrolysis Mode, PDB code: 6bsh:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 6bsh

Go back to Calcium Binding Sites List in 6bsh
Calcium binding site 1 out of 2 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode


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 Rna/Dna Hybrid in the Rna Hydrolysis Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:69.6
occ:1.00
O A:HOH741 2.3 63.2 1.0
O R:HOH205 2.4 59.3 1.0
OP1 R:A25 2.5 64.5 1.0
OD2 A:ASP443 2.5 69.7 1.0
O A:HOH721 2.5 63.7 1.0
OD1 A:ASP549 2.8 72.1 1.0
OD1 A:ASP443 3.1 68.2 1.0
CG A:ASP443 3.1 66.9 1.0
CG A:ASP549 3.4 68.7 1.0
P R:A25 3.6 68.2 1.0
CB A:ASP549 3.8 60.3 1.0
OP2 R:A25 4.0 61.7 1.0
CA A:CA603 4.0 64.0 1.0
O A:GLY444 4.2 62.3 1.0
OD2 A:ASP549 4.3 77.4 1.0
OD2 A:ASP498 4.3 62.8 1.0
NH2 A:ARG557 4.3 82.5 1.0
O5' R:A25 4.3 68.1 1.0
CA A:ASP549 4.4 56.7 1.0
CB A:ASP443 4.6 61.4 1.0
OP1 R:U26 4.6 82.5 1.0
C5' R:A25 4.6 62.9 1.0
O3' R:C24 4.8 72.8 1.0
CE1 A:HIS539 4.9 82.7 1.0

Calcium binding site 2 out of 2 in 6bsh

Go back to Calcium Binding Sites List in 6bsh
Calcium binding site 2 out of 2 in the Structure of Hiv-1 Rt Complexed with Rna/Dna Hybrid in the Rna Hydrolysis Mode


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 Rna/Dna Hybrid in the Rna Hydrolysis Mode within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:64.0
occ:1.00
OD1 A:ASP498 2.2 75.0 1.0
OE2 A:GLU478 2.3 61.7 1.0
OP1 R:A25 2.4 64.5 1.0
OD1 A:ASP443 2.5 68.2 1.0
OD2 A:ASP498 2.6 62.8 1.0
CG A:ASP498 2.7 64.2 1.0
O3' R:C24 2.9 72.8 1.0
CD A:GLU478 2.9 67.0 1.0
OE1 A:GLU478 3.0 70.5 1.0
P R:A25 3.3 68.2 1.0
CG A:ASP443 3.7 66.9 1.0
O A:HOH721 4.0 63.7 1.0
CA A:CA602 4.0 69.6 1.0
CB A:ASP498 4.1 56.6 1.0
C3' R:C24 4.2 60.8 1.0
C5' R:A25 4.3 62.9 1.0
O5' R:A25 4.3 68.1 1.0
O A:GLY444 4.3 62.3 1.0
CG A:GLU478 4.4 68.0 1.0
N A:GLY444 4.4 59.0 1.0
O2' R:C24 4.4 65.2 1.0
OP2 R:A25 4.4 61.7 1.0
OD2 A:ASP443 4.4 69.7 1.0
CA A:ASP443 4.4 52.6 1.0
C4' R:C24 4.5 63.2 1.0
CB A:ASP443 4.5 61.4 1.0
N A:ASP498 4.8 54.9 1.0
CA A:ASP498 4.8 59.4 1.0
C A:ASP498 4.8 61.6 1.0
N A:SER499 4.8 60.8 1.0
C2' R:C24 4.9 64.4 1.0
C5' R:C24 5.0 59.9 1.0
C A:ASP443 5.0 58.4 1.0
O R:HOH205 5.0 59.3 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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