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Manganese in PDB 3a6n: The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T

Protein crystallography data

The structure of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T, PDB code: 3a6n was solved by H.Tachiwana, W.Kagawa, A.Osakabe, K.Koichiro, T.Shiga, H.Kimura, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.476, 109.521, 181.052, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.4

Other elements in 3a6n:

The structure of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T (pdb code 3a6n). 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 Nucleosome Containing A Testis-Specific Histone Variant, Human H3T, PDB code: 3a6n:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3a6n

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Manganese binding site 1 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn201

b:35.7
occ:1.00
 O D:HOH301 2.0 24.8 1.0
O D:VAL48 2.3 29.0 1.0
C D:VAL48 3.3 30.6 1.0
CA D:VAL48 3.7 31.0 1.0
OE1 C:GLU64 4.1 45.3 1.0
O C:HOH2105 4.3 35.0 1.0
OE2 C:GLU64 4.3 41.4 1.0
O D:GLN47 4.3 31.8 1.0
CD2 D:HIS49 4.4 32.8 1.0
N D:HIS49 4.4 32.4 1.0
CB D:VAL48 4.5 31.4 1.0
CD C:GLU64 4.7 40.1 1.0
NE2 D:HIS49 4.8 31.3 1.0
CA D:HIS49 4.9 34.0 1.0
N D:VAL48 4.9 30.7 1.0

Manganese binding site 2 out of 8 in 3a6n

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Manganese binding site 2 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn201

b:0.3
occ:1.00
 O6 I:DG68 2.8 76.1 1.0
N4 J:DC225 3.6 90.7 1.0
C6 I:DG68 3.8 73.3 1.0
O6 J:DG224 4.0 87.8 1.0
N7 J:DG224 4.1 87.5 1.0
C5 I:DG68 4.6 72.4 1.0
N7 I:DG68 4.6 71.7 1.0
C6 J:DG224 4.7 87.6 1.0
C5 J:DG224 4.7 87.9 1.0
C4 J:DC225 4.8 91.4 1.0
N1 I:DG68 4.9 73.2 1.0

Manganese binding site 3 out of 8 in 3a6n

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Manganese binding site 3 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn202

b:0.5
occ:1.00
 N7 I:DG121 2.5 83.5 1.0
O6 I:DG121 3.2 84.1 1.0
C5 I:DG121 3.4 83.8 1.0
C6 I:DG121 3.6 84.3 1.0
C8 I:DG121 3.6 82.7 1.0
C6 I:DT120 3.7 90.3 1.0
C7 I:DT120 4.0 89.9 1.0
C5 I:DT120 4.0 91.0 1.0
C2' I:DT120 4.2 87.0 1.0
O6 I:DG122 4.3 99.4 1.0
N4 J:DC171 4.4 0.8 1.0
N1 I:DT120 4.5 89.4 1.0
C4 I:DG121 4.6 82.9 1.0
N9 I:DG121 4.8 81.6 1.0
C1' I:DT120 4.9 88.3 1.0
C4 I:DT120 5.0 91.1 1.0
N1 I:DG121 5.0 83.8 1.0

Manganese binding site 4 out of 8 in 3a6n

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Manganese binding site 4 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn203

b:85.1
occ:1.00
 N7 I:DA133 2.8 87.4 1.0
N6 I:DA133 3.6 85.2 1.0
C5 I:DA133 3.8 87.5 1.0
C8 I:DA133 3.8 89.9 1.0
C6 I:DA133 4.1 86.2 1.0
C5 I:DC132 4.2 78.8 1.0
O6 I:DG134 4.3 90.6 1.0
C6 I:DC132 4.3 78.7 1.0
OP2 I:DC132 4.8 75.4 1.0

Manganese binding site 5 out of 8 in 3a6n

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Manganese binding site 5 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1001

b:0.1
occ:1.00
 O6 J:DG186 2.7 88.4 1.0
N7 J:DG185 2.9 88.2 1.0
C6 J:DG186 3.5 88.2 1.0
C8 J:DG185 3.6 87.7 1.0
OP2 J:DG185 3.8 92.0 1.0
C5 J:DG185 4.0 87.6 1.0
C5 J:DG186 4.1 87.1 1.0
N7 J:DG186 4.1 85.9 1.0
N4 I:DC107 4.2 0.5 1.0
C2' J:DT184 4.3 95.4 1.0
O6 J:DG185 4.5 86.9 1.0
N1 J:DG186 4.6 88.0 1.0
C6 J:DG185 4.6 87.1 1.0
N9 J:DG185 4.8 86.9 1.0
C3' J:DT184 4.9 95.6 1.0

Manganese binding site 6 out of 8 in 3a6n

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Manganese binding site 6 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1002

b:85.4
occ:1.00
 N7 J:DG267 2.6 88.7 1.0
C8 J:DG267 3.3 88.1 1.0
C5 J:DG267 3.7 87.5 1.0
O6 J:DG268 4.0 72.8 1.0
OP2 J:DG267 4.1 84.1 1.0
O6 J:DG267 4.1 88.8 1.0
C6 J:DG267 4.3 87.9 1.0
N9 J:DG267 4.6 86.7 1.0
C2' J:DT266 4.6 87.7 1.0
C4 J:DG267 4.8 87.3 1.0
N4 I:DC25 4.9 0.7 1.0
C6 J:DG268 4.9 72.2 1.0

Manganese binding site 7 out of 8 in 3a6n

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Manganese binding site 7 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1003

b:85.1
occ:1.00
 N7 J:DG217 2.3 60.6 1.0
C8 J:DG217 3.3 60.6 1.0
C5 J:DG217 3.3 60.0 1.0
O6 J:DG217 3.5 61.1 1.0
C6 J:DG217 3.7 60.5 1.0
C2' J:DT216 4.1 54.0 1.0
N6 J:DA218 4.2 61.2 1.0
C6 J:DT216 4.3 56.7 1.0
N9 J:DG217 4.5 59.8 1.0
C4 J:DG217 4.5 60.2 1.0
OP2 J:DG217 4.7 49.9 1.0
N1 J:DT216 4.8 56.1 1.0
C5 J:DT216 4.8 57.5 1.0
C1' J:DT216 4.9 54.8 1.0
C7 J:DT216 5.0 58.7 1.0

Manganese binding site 8 out of 8 in 3a6n

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Manganese binding site 8 out of 8 in the The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Nucleosome Containing A Testis-Specific Histone Variant, Human H3T within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1004

b:72.5
occ:1.00
 N7 J:DG280 2.6 90.5 1.0
O6 J:DG280 3.5 88.9 1.0
C5 J:DG280 3.5 90.8 1.0
C8 J:DG280 3.6 92.1 1.0
C6 J:DG280 3.9 90.3 1.0
C8 J:DA279 4.1 74.2 1.0
N7 J:DA279 4.1 73.7 1.0
O6 J:DG281 4.2 0.6 1.0
N7 J:DG281 4.6 0.8 1.0
C4 J:DG280 4.8 91.5 1.0
N9 J:DG280 4.8 92.7 1.0

Reference:

H.Tachiwana, W.Kagawa, A.Osakabe, K.Kawaguchi, T.Shiga, Y.Hayashi-Takanaka, H.Kimura, H.Kurumizaka. Structural Basis of Instability of the Nucleosome Containing A Testis-Specific Histone Variant, Human H3T Proc.Natl.Acad.Sci.Usa V. 107 10454 2010.
ISSN: ISSN 0027-8424
PubMed: 20498094
DOI: 10.1073/PNAS.1003064107
Page generated: Sat Oct 5 15:43:38 2024

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