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Manganese in PDB 6v2k: The Nucleosome Structure After H2A-H2B Exchange

Protein crystallography data

The structure of The Nucleosome Structure After H2A-H2B Exchange, PDB code: 6v2k was solved by Y.Arimura, R.Hirano, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.72 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.561, 107.711, 168.158, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.9

Other elements in 6v2k:

The structure of The Nucleosome Structure After H2A-H2B Exchange also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Nucleosome Structure After H2A-H2B Exchange (pdb code 6v2k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the The Nucleosome Structure After H2A-H2B Exchange, PDB code: 6v2k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 6v2k

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Manganese binding site 1 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn201

b:63.0
occ:1.00
 OD1 E:ASP77 2.0 55.7 1.0
CG E:ASP77 3.0 46.7 1.0
NE2 E:GLN76 3.2 75.7 1.0
OD2 E:ASP77 3.4 56.6 1.0
CG E:GLN76 3.7 59.7 1.0
CD E:GLN76 3.9 67.5 1.0
O F:LEU22 4.0 52.9 1.0
O E:GLU73 4.2 41.7 1.0
CB E:ASP77 4.4 32.2 1.0
N E:ASP77 4.6 42.4 1.0
CG E:GLU73 4.6 40.9 1.0
CA E:ASP77 4.7 42.0 1.0

Manganese binding site 2 out of 10 in 6v2k

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Manganese binding site 2 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn201

b:0.4
occ:1.00
 OP2 I:DA27 2.7 91.8 1.0
O3' I:DC26 3.7 67.5 1.0
N7 I:DA27 3.7 53.9 1.0
P I:DA27 3.8 80.5 1.0
C3' I:DC26 3.8 68.8 1.0
C2' I:DC26 3.9 68.0 1.0
C8 I:DA27 3.9 67.0 1.0
OP1 I:DA27 4.7 81.6 1.0
O5' I:DA27 4.9 83.9 1.0

Manganese binding site 3 out of 10 in 6v2k

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Manganese binding site 3 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn202

b:0.2
occ:1.00
 N7 I:DG134 3.8 95.3 1.0
O6 I:DG134 4.3 88.7 1.0
C5 I:DG134 4.7 0.1 1.0
N7 I:DA133 4.7 0.2 1.0
C8 I:DG134 4.8 0.3 1.0
C6 I:DG134 4.9 93.7 1.0

Manganese binding site 4 out of 10 in 6v2k

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Manganese binding site 4 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn203

b:76.5
occ:1.00
 O6 I:DG68 2.6 67.1 1.0
C6 I:DG68 3.6 63.5 1.0
O6 J:DG224 3.9 61.1 1.0
N7 I:DG68 4.0 62.4 1.0
C5 I:DG68 4.1 57.4 1.0
N7 J:DG224 4.2 64.5 1.0
N4 J:DC225 4.3 56.9 1.0
C6 J:DG224 4.7 57.5 1.0
N1 I:DG68 4.7 70.9 1.0
C5 J:DG224 4.8 62.2 1.0

Manganese binding site 5 out of 10 in 6v2k

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Manganese binding site 5 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn204

b:77.4
occ:1.00
 N3 I:DA113 4.1 53.1 1.0
N3 J:DA181 4.3 55.8 1.0
O4' J:DT182 4.5 63.9 1.0
C5' J:DT182 4.5 60.9 1.0
O4' I:DC114 4.6 56.4 1.0
C4' J:DT182 4.6 67.7 1.0
C2 I:DA113 4.6 48.6 1.0
C5' I:DC114 4.7 54.0 1.0
C1' J:DA181 4.9 63.1 1.0
C4' I:DC114 4.9 51.2 1.0
O4' J:DA181 4.9 65.9 1.0
C1' I:DA113 5.0 57.1 1.0
C2 J:DA181 5.0 48.7 1.0
O4' I:DA113 5.0 64.4 1.0

Manganese binding site 6 out of 10 in 6v2k

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Manganese binding site 6 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn205

b:0.1
occ:1.00
 N7 I:DG121 2.4 69.5 1.0
C8 I:DG121 3.3 66.7 1.0
C5 I:DG121 3.4 57.0 1.0
O6 I:DG121 3.6 47.4 1.0
C6 I:DG121 3.9 47.2 1.0
C2' I:DT120 4.1 68.4 1.0
O6 I:DG122 4.2 52.7 1.0
OP2 I:DG121 4.5 50.1 1.0
N9 I:DG121 4.5 55.9 1.0
C4 I:DG121 4.5 53.2 1.0

Manganese binding site 7 out of 10 in 6v2k

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Manganese binding site 7 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3001

b:83.6
occ:1.00
 N7 J:DG280 2.4 72.7 1.0
C8 J:DG280 3.0 74.0 1.0
C5 J:DG280 3.5 74.8 1.0
O6 J:DG280 4.1 75.1 1.0
C6 J:DG280 4.2 72.7 1.0
O6 J:DG281 4.2 86.4 1.0
N9 J:DG280 4.3 74.9 1.0
N7 J:DG281 4.4 68.2 1.0
C4 J:DG280 4.6 71.2 1.0
C8 J:DA279 4.6 72.5 1.0
N7 J:DA279 4.6 76.0 1.0

Manganese binding site 8 out of 10 in 6v2k

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Manganese binding site 8 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3002

b:80.9
occ:1.00
 N7 J:DG267 2.6 66.1 1.0
C8 J:DG267 3.4 55.7 1.0
C5 J:DG267 3.6 57.1 1.0
O6 J:DG267 3.9 53.3 1.0
OP2 J:DG267 3.9 68.1 1.0
C6 J:DG267 4.1 55.0 1.0
O6 J:DG268 4.3 56.2 1.0
C2' J:DT266 4.4 64.3 1.0
N9 J:DG267 4.7 56.4 1.0
C4 J:DG267 4.8 48.2 1.0

Manganese binding site 9 out of 10 in 6v2k

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Manganese binding site 9 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3003

b:75.9
occ:1.00
 N7 J:DG185 2.4 69.6 1.0
O6 J:DG186 2.7 59.6 1.0
C8 J:DG185 3.3 58.1 1.0
C5 J:DG185 3.3 61.5 1.0
O6 J:DG185 3.6 66.4 1.0
C6 J:DG186 3.6 59.3 1.0
C6 J:DG185 3.8 60.5 1.0
N4 I:DC107 3.8 62.8 1.0
OP2 J:DG185 4.0 65.8 1.0
C5 J:DG186 4.3 56.5 1.0
N7 J:DG186 4.3 51.4 1.0
N9 J:DG185 4.4 62.6 1.0
C4 J:DG185 4.5 52.8 1.0
C2' J:DT184 4.7 48.8 1.0
N1 J:DG186 4.7 50.0 1.0
C4 I:DC107 5.0 58.6 1.0

Manganese binding site 10 out of 10 in 6v2k

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Manganese binding site 10 out of 10 in the The Nucleosome Structure After H2A-H2B Exchange


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Nucleosome Structure After H2A-H2B Exchange within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3004

b:90.8
occ:1.00
 N7 J:DG217 2.4 57.8 1.0
C8 J:DG217 3.1 55.5 1.0
C5 J:DG217 3.5 54.3 1.0
N6 J:DA218 3.9 50.8 1.0
O6 J:DG217 3.9 55.7 1.0
C6 J:DG217 4.1 54.8 1.0
C2' J:DT216 4.1 42.7 1.0
OP2 J:DG217 4.2 51.0 1.0
N9 J:DG217 4.3 55.0 1.0
C4 J:DG217 4.5 51.7 1.0
N7 J:DA218 4.7 51.1 1.0
C6 J:DA218 4.8 55.6 1.0
C6 J:DT216 4.8 52.4 1.0

Reference:

R.Hirano, A.Yasuhiro, H.Kurumizaka. A Histone Variant H2A.B Complexed with H2B Is Spontaneously Exchanged By Canonical H2A-H2B in the Nucleosome To Be Published.
Page generated: Sun Oct 6 07:18:12 2024

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