Manganese in PDB 5mlu: Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome

The structure of Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome, PDB code: 5mlu was solved by V.E.Pye, D.P.Maskell, P.Lesbats, P.Cherepanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.61 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.260, 109.450, 175.820, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.2

The binding sites of Manganese atom in the Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome (pdb code 5mlu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome, PDB code: 5mlu:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome


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 Gag Cbs Bound to A Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:78.4 occ:1.00 O A:HOH326 1.8 92.3 1.0 O B:HOH226 1.8 81.3 1.0 O A:HOH314 2.3 55.8 1.0 OD1 A:ASP77 2.4 86.5 1.0 CG A:ASP77 3.3 81.8 1.0 OD2 A:ASP77 3.7 85.6 1.0 O A:GLU73 4.4 80.3 1.0 O B:HOH208 4.4 82.2 1.0 O B:LEU22 4.6 67.8 1.0 CB A:ASP77 4.7 73.0 1.0 N A:ASP77 4.7 73.6 1.0 CG A:GLU73 4.8 78.2 1.0 CB A:GLN76 4.8 71.0 1.0 CA A:ASP77 4.9 73.8 1.0 OE1 A:GLN76 4.9 87.0 1.0 CD A:GLN76 4.9 85.5 1.0 CG A:GLN76 5.0 77.1 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome


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 Gag Cbs Bound to A Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:0.6 occ:1.00 N7 I:DA-34 2.6 1.0 1.0 N6 I:DA-34 3.3 0.6 1.0 C5 I:DA-34 3.4 0.1 1.0 C8 I:DA-34 3.6 0.1 1.0 C6 I:DA-34 3.8 0.9 1.0 C4 I:DA-34 4.6 0.6 1.0 N9 I:DA-34 4.7 0.9 1.0 N7 I:DG-35 4.9 0.1 1.0 C8 I:DG-35 4.9 0.1 1.0 O6 I:DG-33 5.0 0.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome


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 Gag Cbs Bound to A Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:0.8 occ:1.00 N7 I:DA-72 2.4 0.3 1.0 C8 I:DA-72 2.9 0.4 1.0 C5 I:DA-72 3.7 0.8 1.0 OP2 I:DA-72 4.1 0.2 1.0 N9 I:DA-72 4.2 0.5 1.0 N6 I:DA-72 4.5 0.5 1.0 C6 I:DA-72 4.6 0.5 1.0 P I:DA-72 4.6 0.8 1.0 C4 I:DA-72 4.6 0.2 1.0 O5' I:DA-72 4.8 0.1 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Pfv Gag Cbs Bound to A Mononucleosome within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn101 b:0.1 occ:1.00 N7 J:DG27 2.9 0.1 1.0 O6 J:DG27 3.1 1.0 1.0 C8 J:DG26 3.3 0.6 1.0 C5 J:DG27 3.5 0.1 1.0 C6 J:DG27 3.6 0.4 1.0 N7 J:DG26 3.7 0.9 1.0 C8 J:DG27 4.0 0.1 1.0 C2' J:DG26 4.0 0.9 1.0 N9 J:DG26 4.1 0.2 1.0 C1' J:DG26 4.7 0.1 1.0 C5 J:DG26 4.7 0.8 1.0 C4 J:DG27 4.8 0.4 1.0 C4 J:DG26 4.9 0.4 1.0 N1 J:DG27 5.0 0.4 1.0

P.Lesbats, E.Serrao, D.P.Maskell, V.E.Pye, N.O'reilly, D.Lindemann, A.N.Engelman, P.Cherepanov. Structural Basis For Spumavirus Gag Tethering to Chromatin. Proc. Natl. Acad. Sci. V. 114 5509 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28490494
DOI: 10.1073/PNAS.1621159114