Manganese in PDB 5z30: The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant

The structure of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant, PDB code: 5z30 was solved by N.Horikoshi, Y.Arimura, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.70 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.399, 108.332, 170.902, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 24.4

The structure of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Manganese atom in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant (pdb code 5z30). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant, PDB code: 5z30:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn301 b:47.6 occ:1.00 OD1 E:ASP77 2.1 36.5 1.0 CG E:ASP77 3.2 39.5 1.0 OD2 E:ASP77 3.5 43.5 1.0 O E:GLU73 4.3 36.6 1.0 O F:LEU22 4.3 42.5 1.0 CB E:ASP77 4.6 36.0 1.0 CG E:GLU73 4.8 33.1 1.0 N E:ASP77 4.8 37.7 1.0 CA E:ASP77 4.9 37.4 1.0

Manganese binding site 2 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn301 b:70.7 occ:1.00 N7 I:DG121 2.4 53.7 1.0 C8 I:DG121 3.3 58.6 1.0 C5 I:DG121 3.3 52.8 1.0 O6 I:DG121 3.5 53.5 1.0 C6 I:DG121 3.8 50.5 1.0 C2' I:DT120 4.3 57.5 1.0 N9 I:DG121 4.5 49.1 1.0 O6 I:DG122 4.5 52.9 1.0 C4 I:DG121 4.5 51.3 1.0 N4 J:DC171 4.8 56.6 1.0

Manganese binding site 3 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn302 b:87.7 occ:1.00 O6 I:DG68 2.7 63.0 1.0 C6 I:DG68 3.7 63.1 1.0 N4 J:DC225 4.0 65.0 1.0 N7 J:DG224 4.0 71.1 1.0 N7 I:DG68 4.1 63.9 1.0 C5 I:DG68 4.3 60.6 1.0 O6 J:DG224 4.3 64.7 1.0 C5 J:DG224 4.8 64.8 1.0 N7 I:DA67 4.9 69.3 1.0 C6 J:DG224 4.9 60.7 1.0 N1 I:DG68 4.9 59.9 1.0 C8 J:DG224 5.0 69.8 1.0

Manganese binding site 4 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn303 b:82.6 occ:1.00 N7 I:DG134 2.5 73.4 1.0 C8 I:DG134 3.3 75.7 1.0 C5 I:DG134 3.6 72.7 1.0 O6 I:DG134 3.8 77.7 1.0 C6 I:DG134 4.1 75.0 1.0 C8 I:DA133 4.1 80.4 1.0 N7 I:DA133 4.2 78.7 1.0 O6 I:DG135 4.5 73.4 1.0 N9 I:DG134 4.6 73.8 1.0 OP2 I:DA133 4.7 88.9 1.0 C4 I:DG134 4.7 73.1 1.0 N9 I:DA133 5.0 77.6 1.0 C2' I:DA133 5.0 84.1 1.0

Manganese binding site 5 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn304 b:87.2 occ:1.00 N7 I:DG131 2.4 78.8 1.0 O6 I:DG131 2.6 83.2 1.0 C5 I:DG131 3.0 73.7 1.0 C6 I:DG131 3.1 79.6 1.0 C8 I:DG131 3.6 83.9 1.0 C2' I:DT130 3.9 82.2 1.0 N4 I:DC132 4.2 76.4 1.0 C4 I:DG131 4.4 76.5 1.0 N1 I:DG131 4.5 72.5 1.0 O6 J:DG161 4.5 80.5 1.0 N9 I:DG131 4.6 76.9 1.0 C6 I:DT130 4.9 70.8 1.0 C3' I:DT130 4.9 82.5 1.0

Manganese binding site 6 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:68.9 occ:1.00 O2 I:DT86 4.0 54.8 1.0 C2 J:DA207 4.2 50.0 1.0 O2 J:DT208 4.2 49.5 1.0 O4' J:DT208 4.3 47.7 1.0 O4' I:DG87 4.4 49.7 1.0 N3 J:DA207 4.4 48.8 1.0 C4' I:DG87 4.7 51.6 1.0 C1' J:DT208 4.7 49.6 1.0 C4' J:DT208 4.9 47.1 1.0 C2 J:DT208 4.9 47.6 1.0 N3 I:DG87 4.9 49.4 1.0 O4' I:DC88 5.0 57.8 1.0

Manganese binding site 7 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn302 b:65.3 occ:1.00 N7 J:DG185 2.4 51.4 1.0 O6 J:DG186 3.1 53.0 1.0 C8 J:DG185 3.2 51.1 1.0 C5 J:DG185 3.6 52.1 1.0 C6 J:DG186 4.0 53.3 1.0 O6 J:DG185 4.0 57.9 1.0 OP2 J:DG185 4.2 56.3 1.0 C6 J:DG185 4.2 52.4 1.0 C2' J:DT184 4.3 45.7 1.0 N7 J:DG186 4.4 51.0 1.0 N9 J:DG185 4.5 53.4 1.0 C5 J:DG186 4.5 49.0 1.0 N4 I:DC107 4.6 54.8 1.0 C4 J:DG185 4.7 50.7 1.0 O3' J:DT184 4.7 55.0 1.0 C3' J:DT184 4.8 54.1 1.0

Manganese binding site 8 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn303 b:83.7 occ:1.00 N7 J:DG217 2.6 46.6 1.0 C8 J:DG217 3.4 54.2 1.0 C5 J:DG217 3.7 50.3 1.0 O6 J:DG217 4.0 46.9 1.0 C2' J:DT216 4.3 54.2 1.0 OP2 J:DG217 4.3 50.1 1.0 C6 J:DG217 4.3 49.5 1.0 N6 J:DA218 4.3 43.2 1.0 N9 J:DG217 4.6 52.3 1.0 C4 J:DG217 4.8 51.5 1.0 C6 J:DT216 5.0 51.6 1.0

Manganese binding site 9 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn304 b:79.4 occ:1.00 N7 J:DG280 2.4 66.8 1.0 C5 J:DG280 3.4 73.0 1.0 C8 J:DG280 3.4 74.3 1.0 O6 J:DG280 3.5 70.4 1.0 C6 J:DG280 3.8 72.7 1.0 N7 J:DA279 4.2 66.3 1.0 C8 J:DA279 4.2 66.7 1.0 C4 J:DG280 4.6 73.8 1.0 N9 J:DG280 4.6 75.7 1.0 O6 J:DG281 4.7 80.7 1.0 OP2 J:DA279 4.8 65.1 1.0

Manganese binding site 10 out of 11 in the The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Crystal Structure of the Nucleosome Containing A Cancer-Associated Histone H2A.Z R80C Mutant within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn305 b:75.3 occ:1.00 OP1 J:DT183 2.4 56.9 1.0 P J:DT183 3.3 55.5 1.0 O5' J:DT183 3.7 59.9 1.0 OP2 J:DT183 3.8 42.7 1.0 O3' J:DT182 4.7 56.5 1.0

Y.Arimura, M.Ikura, R.Fujita, M.Noda, W.Kobayashi, N.Horikoshi, J.Sun, L.Shi, M.Kusakabe, M.Harata, Y.Ohkawa, S.Tashiro, H.Kimura, T.Ikura, H.Kurumizaka. Cancer-Associated Mutations of Histones H2B, H3.1 and H2A.Z.1 Affect the Structure and Stability of the Nucleosome. Nucleic Acids Res. V. 46 10007 2018.
ISSN: ESSN 1362-4962
PubMed: 30053102
DOI: 10.1093/NAR/GKY661