Manganese in PDB 3oym: Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese

The structure of Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese, PDB code: 3oym 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)	39.89 / 2.02
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	158.050, 158.050, 122.160, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.8

The structure of Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Manganese atom in the Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese (pdb code 3oym). 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 Pfv N224H Mutant Intasome Bound to Manganese, PDB code: 3oym:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese


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 Pfv N224H Mutant Intasome Bound to Manganese within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn394 b:36.5 occ:1.00 O A:HOH589 2.1 35.5 1.0 OD1 A:ASP128 2.1 31.0 1.0 OD1 A:ASP185 2.2 31.9 1.0 O A:HOH588 2.3 35.3 1.0 O A:HOH399 2.3 35.9 1.0 O A:HOH400 2.3 35.8 1.0 CG A:ASP128 3.1 30.3 1.0 CG A:ASP185 3.2 31.5 1.0 OD2 A:ASP128 3.4 30.8 1.0 OD2 A:ASP185 3.5 31.4 1.0 O A:HOH441 3.9 33.4 1.0 O D:HOH345 3.9 49.7 1.0 O A:HOH590 4.0 57.2 1.0 O A:HOH477 4.1 38.9 1.0 O A:HOH587 4.2 37.5 1.0 OE2 A:GLU221 4.4 32.8 1.0 N A:TYR129 4.5 28.7 1.0 O A:TYR129 4.5 29.9 1.0 CB A:ASP128 4.5 28.5 1.0 CB A:ASP185 4.5 30.6 1.0 O D:HOH26 4.6 48.7 1.0 O3' D:DA17 4.7 34.7 1.0 O D:HOH346 4.8 42.3 1.0 CA A:ASP128 4.9 28.5 1.0 O A:HOH572 4.9 39.2 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese


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 Pfv N224H Mutant Intasome Bound to Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn393 b:39.0 occ:1.00 O B:HOH511 2.0 33.9 1.0 OD1 B:ASP185 2.1 29.2 1.0 O B:HOH415 2.2 35.9 1.0 OD1 B:ASP128 2.2 27.0 1.0 O B:HOH514 2.4 32.7 1.0 CG B:ASP185 3.1 29.9 1.0 CG B:ASP128 3.2 29.8 1.0 OD2 B:ASP185 3.5 32.1 1.0 OD2 B:ASP128 3.6 31.6 1.0 O B:HOH423 3.8 37.5 1.0 O B:HOH529 3.9 30.2 1.0 O B:HOH425 4.2 38.9 1.0 O B:HOH536 4.3 46.5 1.0 O B:TYR129 4.5 31.2 1.0 N B:TYR129 4.5 29.0 1.0 CB B:ASP185 4.5 28.6 1.0 CB B:ASP128 4.6 27.6 1.0 CA B:ASP128 4.9 27.9 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of the Pfv N224H Mutant Intasome Bound to Manganese


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 Pfv N224H Mutant Intasome Bound to Manganese within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn394 b:36.0 occ:1.00 OE1 B:GLU221 2.1 31.3 1.0 O B:HOH417 2.3 37.8 1.0 O B:HOH416 2.3 36.1 1.0 ND1 B:HIS224 2.4 32.0 1.0 O B:HOH418 2.5 47.4 1.0 CD B:GLU221 3.2 34.9 1.0 CG B:HIS224 3.3 32.0 1.0 CE1 B:HIS224 3.4 32.6 1.0 OE2 B:GLU221 3.5 35.8 1.0 CB B:HIS224 3.5 31.1 1.0 OD2 B:ASP128 4.2 31.6 1.0 NE2 B:GLN215 4.2 48.5 1.0 O B:HOH422 4.3 38.7 1.0 NE2 B:HIS224 4.5 31.0 1.0 CD2 B:HIS224 4.5 32.1 1.0 CG B:GLU221 4.5 33.1 1.0 NZ B:LYS228 4.7 37.2 1.0 O B:HOH429 4.7 55.2 1.0 O B:HOH423 4.8 37.5 1.0 CA B:GLU221 4.8 32.1 1.0 CB B:GLU221 4.8 32.4 1.0 CG B:GLN215 4.9 47.6 1.0 O B:HOH514 5.0 32.7 1.0

S.Hare, A.M.Vos, R.F.Clayton, J.W.Thuring, M.D.Cummings, P.Cherepanov. Molecular Mechanisms of Retroviral Integrase Inhibition and the Evolution of Viral Resistance. Proc.Natl.Acad.Sci.Usa V. 107 20057 2010.
ISSN: ISSN 0027-8424
PubMed: 21030679
DOI: 10.1073/PNAS.1010246107