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Magnesium in PDB 7adu: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)

Enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)

All present enzymatic activity of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J):
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J), PDB code: 7adu was solved by V.E.Pye, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.32 / 2.62
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.469, 159.469, 123.499, 90, 90, 90
R / Rfree (%) 20.2 / 23.2

Other elements in 7adu:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) (pdb code 7adu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J), PDB code: 7adu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 7adu

Go back to Magnesium Binding Sites List in 7adu
Magnesium binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:55.4
occ:1.00
 N31 A:R7K403 1.9 74.4 1.0
OD1 A:ASP128 2.1 60.2 1.0
OD2 A:ASP185 2.1 72.2 1.0
O A:HOH509 2.1 59.7 1.0
O32 A:R7K403 2.1 64.8 1.0
O A:HOH527 2.2 51.3 1.0
C17 A:R7K403 2.7 74.7 1.0
N26 A:R7K403 2.8 76.0 1.0
C30 A:R7K403 2.9 68.5 1.0
CG A:ASP128 2.9 48.4 1.0
CG A:ASP185 3.1 64.3 1.0
OD2 A:ASP128 3.2 55.2 1.0
O A:HOH506 3.6 66.9 1.0
OD1 A:ASP185 3.6 61.0 1.0
MG A:MG402 3.6 45.8 1.0
C18 A:R7K403 4.0 74.6 1.0
C15 A:R7K403 4.1 71.7 1.0
OE2 A:GLU221 4.1 57.9 1.0
C29 A:R7K403 4.1 84.7 1.0
O A:HOH533 4.2 52.8 1.0
CB A:ASP128 4.2 42.0 1.0
CB A:ASP185 4.4 57.3 1.0
N A:TYR129 4.5 39.4 1.0
O A:TYR129 4.5 53.7 1.0
C28 A:R7K403 4.6 87.8 1.0
O D:HOH203 4.6 50.1 1.0
N1 D:DA17 4.6 92.3 1.0
O33 A:R7K403 4.7 63.6 1.0
CA A:ASP128 4.7 47.0 1.0

Magnesium binding site 2 out of 2 in 7adu

Go back to Magnesium Binding Sites List in 7adu
Magnesium binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and the Insti XZ440 (Compound 5J) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:45.8
occ:1.00
 O32 A:R7K403 1.8 64.8 1.0
OE1 A:GLU221 2.1 46.2 1.0
OE2 A:GLU221 2.1 57.9 1.0
OD2 A:ASP128 2.1 55.2 1.0
O D:HOH203 2.2 50.1 1.0
O33 A:R7K403 2.3 63.6 1.0
CD A:GLU221 2.3 43.2 1.0
N26 A:R7K403 2.7 76.0 1.0
C15 A:R7K403 2.9 71.7 1.0
CG A:ASP128 3.2 48.4 1.0
MG A:MG401 3.6 55.4 1.0
OD1 A:ASP128 3.7 60.2 1.0
ND2 A:ASN224 3.7 43.6 1.0
CG A:GLU221 3.9 41.4 1.0
O D:HOH201 3.9 59.6 1.0
O A:HOH506 3.9 66.9 1.0
C17 A:R7K403 4.0 74.7 1.0
F10 A:R7K403 4.1 61.4 1.0
C14 A:R7K403 4.2 74.7 1.0
O A:HOH509 4.4 59.7 1.0
OP1 D:DA17 4.4 56.8 1.0
N31 A:R7K403 4.4 74.4 1.0
CB A:ASP128 4.4 42.0 1.0
O A:TYR129 4.5 53.7 1.0
C2 D:DA17 4.6 82.3 1.0
N11 A:R7K403 4.6 42.8 1.0
CB A:GLU221 4.7 38.3 1.0
OD2 A:ASP185 4.8 72.2 1.0
O3' D:DC16 4.9 56.2 1.0
CA A:GLU221 4.9 36.7 1.0
C12 A:R7K403 5.0 70.8 1.0

Reference:

S.J.Smith, X.Z.Zhao, D.O.Passos, V.E.Pye, P.Cherepanov, D.Lyumkis, T.R.Burke Jr., S.H.Hughes. Hiv-1 Integrase Inhibitors with Modifications That Affect Their Potencies Against Drug Resistant Integrase Mutants. Acs Infect Dis. 2021.
ISSN: ESSN 2373-8227
PubMed: 33686850
DOI: 10.1021/ACSINFECDIS.0C00819
Page generated: Wed Oct 2 09:37:43 2024

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