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Manganese in PDB 5b31: The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.

Protein crystallography data

The structure of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1., PDB code: 5b31 was solved by N.Horikoshi, H.Taguchi, Y.Arimura, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.62 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.110, 109.685, 181.487, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 27.1

Other elements in 5b31:

The structure of The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1. also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1. (pdb code 5b31). 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 Heterotypic H2AZ/H2A Nucleosome with H3.1., PDB code: 5b31:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5b31

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Manganese binding site 1 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:92.4
occ:1.00
 OD1 A:ASP81 2.4 59.6 1.0
O A:HOH430 3.1 66.4 1.0
NH1 A:ARG83 3.3 82.1 1.0
CG A:ASP81 3.4 62.1 1.0
OD2 A:ASP81 3.9 64.1 1.0
CZ A:ARG83 4.1 83.5 1.0
NH2 A:ARG83 4.5 79.7 1.0
CG A:ARG83 4.6 64.3 1.0
C A:ASP81 4.6 54.7 1.0
CB A:ASP81 4.6 53.7 1.0
O A:ASP81 4.6 59.4 1.0
CA A:ASP81 4.7 52.9 1.0
O A:LEU82 4.8 42.5 1.0
NE A:ARG83 4.9 80.3 1.0
C4' I:DC50 4.9 77.4 1.0

Manganese binding site 2 out of 8 in 5b31

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Manganese binding site 2 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:29.0
occ:1.00
 OD1 E:ASP77 2.1 36.1 1.0
O F:HOH232 2.1 24.7 1.0
O E:HOH436 2.3 34.2 1.0
CG E:ASP77 2.9 34.6 1.0
OD2 E:ASP77 3.1 31.9 1.0
O E:HOH414 4.1 36.0 1.0
O E:HOH448 4.1 32.5 1.0
O E:HOH427 4.3 27.1 1.0
CB E:ASP77 4.3 30.2 1.0
O F:LEU22 4.4 35.9 1.0
OE1 E:GLN76 4.5 33.5 1.0
N E:ASP77 4.6 29.9 1.0
O E:GLU73 4.6 39.2 1.0
CA E:ASP77 4.6 30.6 1.0
CG E:GLN76 4.9 35.3 1.0
CG E:GLU73 4.9 29.4 1.0

Manganese binding site 3 out of 8 in 5b31

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Manganese binding site 3 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn301

b:87.8
occ:1.00
 N7 I:DA133 2.7 77.6 1.0
N6 I:DA133 3.3 73.6 1.0
C5 I:DA133 3.6 79.5 1.0
C8 I:DA133 3.8 85.4 1.0
C6 I:DA133 3.9 80.7 1.0
O6 I:DG134 4.4 76.2 1.0
C5 I:DC132 4.5 77.9 1.0
C6 I:DC132 4.6 72.2 1.0
OP2 I:DC132 4.6 67.5 1.0
C4 I:DA133 4.9 78.7 1.0
N9 I:DA133 4.9 87.0 1.0

Manganese binding site 4 out of 8 in 5b31

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Manganese binding site 4 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn302

b:0.2
occ:1.00
 O6 I:DG68 3.1 74.7 1.0
O6 J:DG224 3.8 73.6 1.0
N7 I:DG68 4.0 68.1 1.0
C6 I:DG68 4.0 70.9 1.0
N4 J:DC225 4.2 80.0 1.0
C5 I:DG68 4.4 69.5 1.0
N7 I:DA67 4.7 65.2 1.0
C6 J:DG224 4.8 76.7 1.0
N7 J:DG224 4.9 78.9 1.0

Manganese binding site 5 out of 8 in 5b31

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Manganese binding site 5 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn401

b:81.8
occ:1.00
 N7 J:DG280 2.6 83.5 1.0
O6 J:DG280 3.5 93.1 1.0
C5 J:DG280 3.5 89.8 1.0
C8 J:DG280 3.6 91.2 1.0
C6 J:DG280 3.9 93.4 1.0
N7 J:DA279 4.1 77.6 1.0
C8 J:DA279 4.1 79.3 1.0
O6 J:DG281 4.4 96.1 1.0
C4 J:DG280 4.8 92.0 1.0
N9 J:DG280 4.8 95.2 1.0

Manganese binding site 6 out of 8 in 5b31

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Manganese binding site 6 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn402

b:0.8
occ:1.00
 N7 J:DG267 2.5 95.4 1.0
C8 J:DG267 3.0 92.0 1.0
O6 J:DG268 3.4 96.0 1.0
OP2 J:DG267 3.5 86.2 1.0
C5 J:DG267 3.6 92.5 1.0
O J:HOH501 3.7 72.8 1.0
N9 J:DG267 4.3 91.0 1.0
O6 J:DG267 4.3 91.2 1.0
C6 J:DG267 4.3 91.0 1.0
C6 J:DG268 4.4 95.1 1.0
C4 J:DG267 4.6 90.0 1.0
C2' J:DT266 4.6 87.4 1.0
P J:DG267 4.8 82.6 1.0

Manganese binding site 7 out of 8 in 5b31

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Manganese binding site 7 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn403

b:0.3
occ:1.00
 N7 J:DG185 2.4 85.9 1.0
C8 J:DG185 3.1 83.8 1.0
O6 J:DG186 3.1 87.2 1.0
C5 J:DG185 3.5 88.5 1.0
C6 J:DG186 3.9 90.7 1.0
O6 J:DG185 4.0 91.0 1.0
C6 J:DG185 4.1 88.8 1.0
N9 J:DG185 4.3 87.1 1.0
OP2 J:DG185 4.3 83.4 1.0
N7 J:DG186 4.4 86.3 1.0
C5 J:DG186 4.4 90.8 1.0
C4 J:DG185 4.5 86.9 1.0
C2' J:DT184 4.5 87.4 1.0
O3' J:DT184 4.7 89.8 1.0
N1 J:DG186 4.9 92.8 1.0

Manganese binding site 8 out of 8 in 5b31

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Manganese binding site 8 out of 8 in the The Crystal Structure of the Heterotypic H2AZ/H2A Nucleosome with H3.1.


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 Heterotypic H2AZ/H2A Nucleosome with H3.1. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn404

b:70.6
occ:1.00
 N7 J:DG217 2.3 48.4 1.0
C8 J:DG217 3.3 54.6 1.0
C5 J:DG217 3.3 54.8 1.0
O6 J:DG217 3.4 53.2 1.0
C6 J:DG217 3.7 54.9 1.0
C2' J:DT216 4.1 50.2 1.0
OP2 J:DG217 4.2 40.0 1.0
N6 J:DA218 4.3 54.1 1.0
N9 J:DG217 4.5 52.6 1.0
C4 J:DG217 4.5 53.7 1.0
C6 J:DT216 4.6 48.3 1.0
C3' J:DT216 5.0 42.5 1.0

Reference:

N.Horikoshi, Y.Arimura, H.Taguchi, H.Kurumizaka. Crystal Structures of Heterotypic Nucleosomes Containing Histones H2A.Z and H2A. Open Biology V. 6 2016.
ISSN: ESSN 2046-2441
PubMed: 27358293
DOI: 10.1098/RSOB.160127
Page generated: Sat Oct 5 23:34:16 2024

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