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Manganese in PDB 5y0d: Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Protein crystallography data
The structure of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant, PDB code: 5y0d
was solved by
H.Kurumizaka,
Y.Arimura,
R.Fujita,
M.Noda,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
| Resolution Low / High (Å) | 49.58 / 1.99 |
| Space group | P 21 21 21 |
| Cell size a, b, c (Å), α, β, γ (°) | 98.992, 107.316, 167.719, 90.00, 90.00, 90.00 |
| R / Rfree (%) | 21.1 / 25.2 |
Other elements in 5y0d:
The structure of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant also contains other interesting chemical elements:
| Chlorine | (Cl) | 4 atoms |
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
(pdb code 5y0d). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant, PDB code: 5y0d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;
In total 10 binding sites of Manganese where determined in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant, PDB code: 5y0d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;
Manganese binding site 1 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 1 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 2 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 2 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 3 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 3 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 4 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 4 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
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 Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 5 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 5 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 6 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 6 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 7 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 7 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 8 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 8 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 9 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 9 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Manganese with other atoms in the Mn binding
site number 9 of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Manganese binding site 10 out of 10 in 5y0d
Go back to
Manganese Binding Sites List in 5y0d
Manganese binding site 10 out
of 10 in the Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant
Mono view
Stereo pair view
Mono view
Stereo pair view
A full contact list of Manganese with other atoms in the Mn binding
site number 10 of Crystal Structure of the Human Nucleosome Containing the H2B E76K Mutant within 5.0Å range:
|
Reference:
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
Page generated: Sun Oct 6 03:31:26 2024
ISSN: ESSN 1362-4962
PubMed: 30053102
DOI: 10.1093/NAR/GKY661
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