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Magnesium in PDB 3s3n: Crystal Structure of the Prototype Foamy Virus (Pfv) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)

Protein crystallography data

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572), PDB code: 3s3n was solved by S.Hare, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.16 / 2.49
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 160.050, 160.050, 123.610, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.2

Other elements in 3s3n:

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) (pdb code 3s3n). 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) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572), PDB code: 3s3n:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3s3n

Go back to Magnesium Binding Sites List in 3s3n
Magnesium binding site 1 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)


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) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg396

b:41.1
occ:1.00
OD1 A:ASP128 2.0 45.5 1.0
OD1 A:ASP185 2.0 40.9 1.0
O A:HOH527 2.0 30.2 1.0
OAE A:DLU398 2.0 46.2 1.0
OAC A:DLU398 2.1 45.8 1.0
O A:HOH400 2.2 32.7 1.0
CG A:ASP128 3.0 44.6 1.0
CAS A:DLU398 3.1 47.5 1.0
CG A:ASP185 3.1 43.2 1.0
CAW A:DLU398 3.1 46.8 1.0
OD2 A:ASP128 3.4 47.1 1.0
CAY A:DLU398 3.5 47.1 1.0
OD2 A:ASP185 3.5 44.0 1.0
MG A:MG397 3.7 46.3 1.0
O A:HOH521 3.8 43.9 1.0
O A:HOH433 4.1 40.4 1.0
O A:HOH528 4.2 43.8 1.0
OE2 A:GLU221 4.2 38.9 1.0
NBC A:DLU398 4.3 46.8 1.0
CB A:ASP128 4.3 42.8 1.0
CAZ A:DLU398 4.3 48.0 1.0
N A:TYR129 4.3 41.9 1.0
O A:TYR129 4.4 43.2 1.0
CB A:ASP185 4.4 45.1 1.0
O A:HOH518 4.5 41.0 1.0
OAD A:DLU398 4.6 49.1 1.0
CA A:ASP128 4.7 42.1 1.0
CBA A:DLU398 4.7 46.2 1.0
O D:HOH289 4.9 51.9 1.0
NBD A:DLU398 4.9 46.5 1.0

Magnesium binding site 2 out of 2 in 3s3n

Go back to Magnesium Binding Sites List in 3s3n
Magnesium binding site 2 out of 2 in the Crystal Structure of the Prototype Foamy Virus (Pfv) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572)


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) S217H Mutant Intasome in Complex with Magnesium and Dolutegravir (S/GSK1349572) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg397

b:46.3
occ:1.00
O A:HOH528 2.0 43.8 1.0
OE2 A:GLU221 2.0 38.9 1.0
OE1 A:GLU221 2.1 38.3 1.0
OAD A:DLU398 2.1 49.1 1.0
OD2 A:ASP128 2.2 47.1 1.0
OAE A:DLU398 2.3 46.2 1.0
CD A:GLU221 2.4 38.0 1.0
CAZ A:DLU398 2.9 48.0 1.0
CAW A:DLU398 3.0 46.8 1.0
CG A:ASP128 3.3 44.6 1.0
OD1 A:ASP128 3.7 45.5 1.0
MG A:MG396 3.7 41.1 1.0
ND2 A:ASN224 3.8 38.8 1.0
CG A:GLU221 3.9 38.7 1.0
O A:HOH521 4.0 43.9 1.0
O A:HOH527 4.1 30.2 1.0
OP1 D:DA17 4.2 52.7 0.5
CAX A:DLU398 4.2 45.8 1.0
O A:TYR129 4.3 43.2 1.0
CAY A:DLU398 4.4 47.1 1.0
C5' D:DA17 4.4 55.1 0.5
OP1 D:DA17 4.4 53.4 0.5
NAP A:DLU398 4.5 43.1 1.0
CB A:ASP128 4.5 42.8 1.0
OD1 A:ASP185 4.8 40.9 1.0
CB A:GLU221 4.8 40.0 1.0
FAG A:DLU398 4.9 44.8 1.0
CA A:GLU221 4.9 40.2 1.0
CAR A:DLU398 4.9 45.9 1.0
OAC A:DLU398 4.9 45.8 1.0
O5' D:DA17 4.9 54.0 0.5
NE2 A:HIS217 5.0 46.5 1.0
O3' D:DC16 5.0 50.1 1.0

Reference:

S.Hare, S.J.Smith, M.Metifiot, A.Jaxa-Chamiec, Y.Pommier, S.H.Hughes, P.Cherepanov. Structural and Functional Analyses of the Second-Generation Integrase Strand Transfer Inhibitor Dolutegravir (S/GSK1349572). Mol.Pharmacol. V. 80 565 2011.
ISSN: ISSN 0026-895X
PubMed: 21719464
DOI: 10.1124/MOL.111.073189
Page generated: Mon Dec 14 08:49:11 2020

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