Atomistry » Calcium » PDB 6bia-6bxu » 6bsh
Atomistry »
  Calcium »
    PDB 6bia-6bxu »
      6bsh »

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: Mon Jul 15 17:05:53 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy