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Magnesium in PDB 5j2p: Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2p was solved by Z.L.Salie, K.A.Kirby, S.G.Sarafianos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.78 / 2.53
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.977, 170.183, 99.695, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.6

Other elements in 5j2p:

The structure of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site (pdb code 5j2p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site, PDB code: 5j2p:

Magnesium binding site 1 out of 1 in 5j2p

Go back to Magnesium Binding Sites List in 5j2p
Magnesium binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hiv-1 Reverse Transcriptase in Complex with Dna That Has Incorporated Efda-Mp at the P-(Post-Translocation) Site and A Second Efda-Mp at the N-(Pre-Translocation) Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:31.9
occ:1.00
OD2 A:ASP443 2.0 35.1 1.0
OE2 A:GLU478 2.0 31.9 1.0
O A:HOH848 2.0 32.5 1.0
O A:HOH748 2.0 88.2 1.0
OD1 A:ASP498 2.1 67.3 1.0
OD2 A:ASP498 2.1 41.6 1.0
CG A:ASP498 2.3 37.5 1.0
CD A:GLU478 2.9 46.9 1.0
CG A:ASP443 3.1 45.4 1.0
OE1 A:GLU478 3.1 51.7 1.0
O A:HOH701 3.5 31.1 1.0
OD1 A:ASP443 3.6 51.8 1.0
O A:HOH820 3.7 32.8 1.0
O A:GLY444 3.8 33.8 1.0
CB A:ASP498 3.8 30.6 1.0
O A:HOH842 3.9 46.3 1.0
O A:HOH716 4.1 68.1 1.0
N A:GLY444 4.1 39.9 1.0
CB A:ASP443 4.2 48.5 1.0
CG A:GLU478 4.3 47.4 1.0
CA A:ASP443 4.4 32.7 1.0
C A:ASP498 4.6 38.9 1.0
O A:HOH736 4.6 51.5 1.0
CA A:ASP498 4.6 36.0 1.0
CB A:ALA538 4.8 31.5 1.0
N A:SER499 4.8 29.9 1.0
C A:GLY444 4.8 43.5 1.0
C A:ASP443 4.8 42.0 1.0
N A:ASP498 4.8 34.7 1.0
O A:ASP498 4.9 35.5 1.0

Reference:

Z.L.Salie, K.A.Kirby, E.Michailidis, B.Marchand, K.Singh, L.C.Rohan, E.N.Kodama, H.Mitsuya, M.A.Parniak, S.G.Sarafianos. Structural Basis of Hiv Inhibition By Translocation-Defective Rt Inhibitor 4'-Ethynyl-2-Fluoro-2'-Deoxyadenosine (Efda). Proc.Natl.Acad.Sci.Usa V. 113 9274 2016.
ISSN: ESSN 1091-6490
PubMed: 27489345
DOI: 10.1073/PNAS.1605223113
Page generated: Sun Sep 29 17:35:24 2024

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