Magnesium in PDB 3l2u: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir)

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir), PDB code: 3l2u was solved by S.Hare, S.S.Gupta, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.44 / 3.15
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	157.100, 157.100, 124.530, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 21.8

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir) also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir) (pdb code 3l2u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir), PDB code: 3l2u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir)


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 GS9137 (Elvitegravir) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg394 b:70.3 occ:1.00 OD1 A:ASP128 2.0 88.2 1.0 OAG A:ELV397 2.4 75.6 1.0 OD1 A:ASP185 2.4 91.4 1.0 OAD A:ELV397 2.6 74.5 1.0 CAS A:ELV397 2.9 74.8 1.0 CG A:ASP128 3.1 86.7 1.0 OD2 A:ASP185 3.2 90.8 1.0 CG A:ASP185 3.2 90.7 1.0 OD2 A:ASP128 3.7 86.8 1.0 N A:TYR129 3.9 88.1 1.0 O A:TYR129 3.9 89.5 1.0 CB A:ASP128 4.4 86.0 1.0 CAY A:ELV397 4.4 74.4 1.0 MG A:MG395 4.5 80.0 1.0 CA A:ASP128 4.5 87.0 1.0 CB A:ASP185 4.7 89.9 1.0 CA A:TYR129 4.7 88.6 1.0 CE2 A:PHE190 4.7 94.0 1.0 CB A:TYR129 4.7 89.8 1.0 C A:ASP128 4.7 87.5 1.0 C A:TYR129 4.7 88.8 1.0 CAO A:ELV397 5.0 74.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir)


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 GS9137 (Elvitegravir) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg395 b:80.0 occ:1.00 OD2 A:ASP128 2.2 86.8 1.0 OE1 A:GLU221 2.3 78.6 1.0 OAD A:ELV397 2.4 74.5 1.0 OAE A:ELV397 2.5 69.5 1.0 OE2 A:GLU221 2.9 80.6 1.0 CD A:GLU221 3.0 80.3 1.0 CAS A:ELV397 3.3 74.8 1.0 CG A:ASP128 3.3 86.7 1.0 CAZ A:ELV397 3.5 73.8 1.0 ND2 A:ASN224 3.5 85.3 1.0 CAY A:ELV397 3.7 74.4 1.0 OP1 D:DA17 3.7 97.4 1.0 O A:TYR129 3.8 89.5 1.0 OD1 A:ASP128 3.8 88.2 1.0 O3' D:DC16 3.9 90.8 1.0 OAG A:ELV397 4.3 75.6 1.0 P D:DA17 4.4 94.5 1.0 MG A:MG394 4.5 70.3 1.0 CG A:GLU221 4.5 83.3 1.0 CB A:ASP128 4.6 86.0 1.0 CG A:ASN224 4.7 84.8 1.0 CBA A:ELV397 4.7 74.5 1.0 C A:TYR129 4.8 88.8 1.0 C2' D:DC16 4.9 84.4 1.0 C3' D:DC16 4.9 87.9 1.0 O5' D:DA17 4.9 98.6 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Magnesium and GS9137 (Elvitegravir) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg393 b:0.9 occ:1.00 OD1 B:ASP128 2.8 0.3 1.0 OD1 B:ASP185 3.0 0.5 1.0 OD2 B:ASP185 3.3 0.1 1.0 CG B:ASP185 3.6 0.6 1.0 CG B:ASP128 3.8 0.7 1.0 N B:TYR129 4.1 0.8 1.0 CE2 B:PHE190 4.1 0.2 1.0 OD2 B:ASP128 4.2 0.1 1.0 CB B:TYR129 4.4 0.9 1.0 O B:TYR129 4.6 0.5 1.0 CA B:TYR129 4.7 0.7 1.0 CZ B:PHE190 4.8 0.3 1.0 CA B:GLY187 5.0 0.6 1.0

S.Hare, S.S.Gupta, E.Valkov, A.Engelman, P.Cherepanov. Retroviral Intasome Assembly and Inhibition of Dna Strand Transfer Nature V. 464 232 2010.
ISSN: ISSN 0028-0836
PubMed: 20118915
DOI: 10.1038/NATURE08784