Manganese in PDB 3oy9: Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution, PDB code: 3oy9 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)	39.21 / 2.55
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	160.090, 160.090, 123.940, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.2

The structure of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution (pdb code 3oy9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution, PDB code: 3oy9:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn394 b:79.0 occ:1.00 OD1 A:ASP128 2.3 47.4 1.0 OD1 A:ASP185 2.5 56.5 1.0 O A:HOH400 2.7 49.1 1.0 O A:HOH399 2.7 42.5 1.0 MN A:MN395 3.1 58.2 1.0 O A:HOH546 3.1 65.1 1.0 CG A:ASP128 3.3 45.0 1.0 O A:HOH461 3.5 59.4 1.0 OD2 A:ASP128 3.5 46.6 1.0 CG A:ASP185 3.7 52.3 1.0 O3' D:DA17 4.0 43.2 1.0 OE2 A:GLU221 4.1 44.0 1.0 O A:HOH398 4.2 44.8 1.0 OD2 A:ASP185 4.3 55.9 1.0 O A:TYR129 4.3 44.5 1.0 O D:HOH19 4.5 52.3 1.0 N A:TYR129 4.6 43.6 1.0 O A:HOH561 4.6 51.8 1.0 CB A:ASP128 4.6 43.6 1.0 O A:HOH436 4.7 52.0 1.0 CB A:ASP185 4.8 49.9 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn395 b:58.2 occ:1.00 OE2 A:GLU221 2.1 44.0 1.0 O A:HOH398 2.2 44.8 1.0 OD2 A:ASP128 2.4 46.6 1.0 OE1 A:GLU221 2.5 42.3 1.0 O3' D:DA17 2.6 43.2 1.0 CD A:GLU221 2.6 41.3 1.0 MN A:MN394 3.1 79.0 1.0 CG A:ASP128 3.3 45.0 1.0 OD1 A:ASP128 3.5 47.4 1.0 C3' D:DA17 3.5 41.5 1.0 O A:HOH461 3.7 59.4 1.0 C4' D:DA17 3.7 41.1 1.0 C2' D:DA17 3.8 38.6 1.0 ND2 A:ASN224 4.1 39.2 1.0 O A:TYR129 4.1 44.5 1.0 CG A:GLU221 4.2 40.3 1.0 C1' D:DA17 4.3 39.0 1.0 O D:HOH19 4.5 52.3 1.0 CB A:ASP128 4.6 43.6 1.0 O4' D:DA17 4.6 39.1 1.0 OP1 D:DA17 4.7 44.1 1.0 O A:HOH546 4.7 65.1 1.0 C5' D:DA17 4.8 41.1 1.0 OD1 A:ASP185 5.0 56.5 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Prototype Foamy Virus (Pfv) Intasome in Complex with Manganese at 2.55 Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn393 b:56.4 occ:1.00 OD1 B:ASP185 2.0 47.3 1.0 O B:HOH395 2.0 35.8 1.0 O B:HOH396 2.1 55.4 1.0 OD1 B:ASP128 2.4 56.5 1.0 O B:HOH439 2.7 58.8 1.0 CG B:ASP185 3.0 48.7 1.0 CG B:ASP128 3.2 54.4 1.0 OD2 B:ASP185 3.3 51.0 1.0 OD2 B:ASP128 3.4 56.0 1.0 O B:HOH409 3.9 50.1 1.0 CB B:ASP185 4.3 47.5 1.0 O B:TYR129 4.4 54.7 1.0 N B:TYR129 4.5 52.7 1.0 O B:HOH415 4.5 59.5 1.0 CB B:ASP128 4.6 52.5 1.0 O B:HOH416 4.8 63.3 1.0 CA B:ASP128 5.0 52.1 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