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Manganese in PDB 5zbx: The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)

Protein crystallography data

The structure of The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D), PDB code: 5zbx was solved by Y.Arimura, H.Takagi, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.28 / 2.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.543, 109.003, 170.136, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.9

Other elements in 5zbx:

The structure of The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D) (pdb code 5zbx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D), PDB code: 5zbx:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5zbx

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Manganese binding site 1 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1001

b:42.7
occ:1.00
 OD1 E:ASP77 1.9 59.6 1.0
O F:HOH201 2.0 39.4 1.0
O E:HOH3003 2.1 48.6 1.0
O E:HOH3001 2.2 34.4 1.0
O E:HOH3002 2.5 49.3 1.0
CG E:ASP77 2.6 55.3 1.0
OD2 E:ASP77 3.0 58.9 1.0
CB E:ASP77 3.9 44.0 1.0
CA E:ASP77 4.1 48.4 1.0
N E:ASP77 4.2 50.6 1.0
O F:LEU22 4.4 52.2 1.0
NE2 E:GLN76 4.4 56.6 1.0
O E:GLU73 4.5 49.0 1.0
CB E:GLN76 4.7 42.8 1.0
C E:GLN76 4.8 51.5 1.0
CG E:GLU73 4.9 48.2 1.0

Manganese binding site 2 out of 8 in 5zbx

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Manganese binding site 2 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1001

b:94.0
occ:1.00
 O6 I:DG68 2.6 83.5 1.0
C6 I:DG68 3.7 79.8 1.0
N4 J:DC225 4.1 84.5 1.0
N7 I:DG68 4.2 77.8 1.0
C5 I:DG68 4.3 75.6 1.0
O6 J:DG224 4.4 80.8 1.0
N7 I:DA67 4.8 84.5 1.0
N7 J:DG224 4.8 88.2 1.0
N1 I:DG68 4.8 77.2 1.0

Manganese binding site 3 out of 8 in 5zbx

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Manganese binding site 3 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1002

b:72.5
occ:1.00
 N7 I:DG121 2.5 53.5 1.0
C8 I:DG121 3.4 59.6 1.0
C5 I:DG121 3.5 53.2 1.0
O6 I:DG121 3.7 57.0 1.0
C6 I:DG121 4.0 56.3 1.0
O6 I:DG122 4.2 53.7 1.0
C2' I:DT120 4.4 67.8 1.0
N9 I:DG121 4.6 60.7 1.0
C4 I:DG121 4.7 55.6 1.0

Manganese binding site 4 out of 8 in 5zbx

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Manganese binding site 4 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1003

b:0.3
occ:1.00
 N7 I:DG134 2.8 0.2 1.0
O6 I:DG134 3.6 96.7 1.0
C5 I:DG134 3.7 97.8 1.0
C8 I:DG134 3.7 98.2 1.0
C6 I:DG134 4.0 97.9 1.0
O6 I:DG135 4.2 98.3 1.0
N7 I:DA133 4.3 0.1 1.0
C8 I:DA133 4.4 1.0 1.0
OP2 I:DA133 4.8 0.2 1.0
C4 I:DG134 4.9 98.5 1.0
N9 I:DG134 4.9 98.9 1.0

Manganese binding site 5 out of 8 in 5zbx

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Manganese binding site 5 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1001

b:71.0
occ:1.00
 N7 J:DG185 2.2 55.0 1.0
O6 J:DG186 2.8 58.1 1.0
C8 J:DG185 3.1 49.9 1.0
C5 J:DG185 3.3 52.4 1.0
C6 J:DG186 3.6 52.2 1.0
O6 J:DG185 3.8 60.5 1.0
C6 J:DG185 3.9 55.9 1.0
OP2 J:DG185 4.1 65.7 1.0
N4 I:DC107 4.2 56.2 1.0
N7 J:DG186 4.2 48.7 1.0
C5 J:DG186 4.2 49.6 1.0
N9 J:DG185 4.3 52.0 1.0
C4 J:DG185 4.4 49.0 1.0
C2' J:DT184 4.5 51.9 1.0
N1 J:DG186 4.7 50.8 1.0
O3' J:DT184 4.7 55.8 1.0

Manganese binding site 6 out of 8 in 5zbx

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Manganese binding site 6 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1002

b:86.9
occ:1.00
 N7 J:DG267 2.5 71.7 1.0
C8 J:DG267 3.3 67.2 1.0
C5 J:DG267 3.5 68.5 1.0
O6 J:DG267 3.8 71.9 1.0
OP2 J:DG267 3.8 71.8 1.0
O6 J:DG268 4.0 68.1 1.0
C6 J:DG267 4.0 72.6 1.0
C2' J:DT266 4.4 66.4 1.0
N9 J:DG267 4.6 72.0 1.0
C4 J:DG267 4.7 67.7 1.0
N4 I:DC25 4.8 68.2 1.0
C6 J:DG268 4.9 67.6 1.0

Manganese binding site 7 out of 8 in 5zbx

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Manganese binding site 7 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1003

b:88.2
occ:1.00
 N7 J:DG217 2.4 60.4 1.0
C8 J:DG217 3.3 68.4 1.0
C5 J:DG217 3.4 64.0 1.0
O6 J:DG217 3.7 67.1 1.0
N6 J:DA218 3.9 58.7 1.0
C6 J:DG217 3.9 65.6 1.0
C2' J:DT216 4.2 71.0 1.0
OP2 J:DG217 4.3 68.4 1.0
N9 J:DG217 4.5 67.4 1.0
C4 J:DG217 4.5 65.8 1.0
C6 J:DT216 4.7 68.3 1.0
N7 J:DA218 4.8 62.5 1.0
C6 J:DA218 4.8 65.7 1.0

Manganese binding site 8 out of 8 in 5zbx

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Manganese binding site 8 out of 8 in the The Crystal Structure of the Nucleosome Containing Histone H3.1 Catd(V76Q, K77D)


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 Histone H3.1 Catd(V76Q, K77D) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1004

b:90.2
occ:1.00
 N7 J:DG280 2.7 91.1 1.0
C8 J:DG280 3.5 94.0 1.0
C5 J:DG280 3.6 94.3 1.0
O6 J:DG280 3.8 93.0 1.0
C6 J:DG280 4.0 95.2 1.0
O6 J:DG281 4.2 0.3 1.0
C8 J:DA279 4.7 84.7 1.0
N7 J:DA279 4.7 88.4 1.0
N9 J:DG280 4.7 94.7 1.0
C4 J:DG280 4.7 95.0 1.0
OP2 J:DA279 4.9 78.8 1.0

Reference:

Y.Arimura, H.Tachiwana, H.Takagi, T.Hori, H.Kimura, T.Fukagawa, H.Kurumizaka. The Cenp-A Centromere Targeting Domain Facilitates H4K20 Monomethylation in the Nucleosome By Structural Polymorphism. Nat Commun V. 10 576 2019.
ISSN: ESSN 2041-1723
PubMed: 30718488
DOI: 10.1038/S41467-019-08314-X
Page generated: Sun Oct 6 03:38:47 2024

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