Manganese in PDB 3w96: Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region

The structure of Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region, PDB code: 3w96 was solved by W.Iwasaki, Y.Miya, N.Horikoshi, A.Osakabe, H.Tachiwana, T.Shibata, W.Kagawa, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.44 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.515, 109.319, 175.658, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 29.6

The structure of Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Manganese atom in the Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region (pdb code 3w96). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region, PDB code: 3w96:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region


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 Human Nucleosome Core Particle Lacking H2A N- Terminal Region within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1001 b:83.9 occ:1.00 OD1 E:ASP77 2.1 78.9 1.0 CG E:ASP77 3.0 80.4 1.0 OD2 E:ASP77 3.1 77.2 1.0 O F:LEU22 4.3 70.6 1.0 CB E:ASP77 4.4 76.0 1.0 NE2 E:GLN76 4.6 93.7 1.0 O E:GLU73 4.8 77.0 1.0 CG E:GLU73 4.9 51.1 1.0 CA E:ASP77 4.9 80.6 1.0 N E:ASP77 4.9 79.3 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Human Nucleosome Core Particle Lacking H2A N- Terminal Region


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 Human Nucleosome Core Particle Lacking H2A N- Terminal Region within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1001 b:0.9 occ:1.00 N7 I:DA133 2.3 0.5 1.0 C5 I:DA133 3.2 0.1 1.0 N6 I:DA133 3.3 1.0 1.0 C5 I:DC132 3.3 0.7 1.0 C8 I:DA133 3.3 0.2 1.0 C6 I:DA133 3.6 0.3 1.0 C6 I:DC132 3.6 0.2 1.0 C4 I:DC132 4.3 0.5 1.0 OP2 I:DC132 4.3 0.3 1.0 C4 I:DA133 4.4 0.8 1.0 N9 I:DA133 4.5 0.6 1.0 N4 I:DC132 4.6 0.1 1.0 N1 I:DC132 4.8 0.6 1.0 O6 I:DG134 4.9 0.6 1.0 N1 I:DA133 5.0 0.0 1.0

W.Iwasaki, Y.Miya, N.Horikoshi, A.Osakabe, H.Taguchi, H.Tachiwana, T.Shibata, W.Kagawa, H.Kurumizaka. Contribution of Histone N-Terminal Tails to the Structure and Stability of Nucleosomes Febs Open Bio V. 3 363 2013.
ISSN: ESSN 2211-5463
PubMed: 24251097
DOI: 10.1016/J.FOB.2013.08.007