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Manganese in PDB 3afa: The Human Nucleosome Structure

Protein crystallography data

The structure of The Human Nucleosome Structure, PDB code: 3afa 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 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.839, 109.509, 180.919, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27

Other elements in 3afa:

The structure of The Human Nucleosome Structure also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Human Nucleosome Structure (pdb code 3afa). 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 Human Nucleosome Structure, PDB code: 3afa:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3afa

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Manganese binding site 1 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

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

b:32.6
occ:1.00
 O D:HOH301 2.1 26.5 1.0
O D:VAL48 2.3 24.6 1.0
C D:VAL48 3.3 27.1 1.0
CA D:VAL48 3.9 28.1 1.0
OE1 C:GLU64 4.0 34.6 1.0
OE2 C:GLU64 4.2 36.0 1.0
O C:HOH301 4.3 25.2 1.0
CD2 D:HIS49 4.5 29.9 1.0
N D:HIS49 4.5 30.4 1.0
O D:GLN47 4.5 28.8 1.0
CD C:GLU64 4.5 31.3 1.0
CB D:VAL48 4.6 29.3 1.0
NE2 D:HIS49 4.8 30.6 1.0
CA D:HIS49 4.9 31.7 1.0
CD D:PRO50 5.0 33.3 1.0

Manganese binding site 2 out of 8 in 3afa

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Manganese binding site 2 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

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

b:0.1
occ:1.00
 O6 I:DG68 2.8 61.7 1.0
C6 I:DG68 3.8 61.4 1.0
N4 J:DC225 4.1 75.9 1.0
N7 I:DG68 4.2 61.0 1.0
O6 J:DG224 4.2 69.3 1.0
C5 I:DG68 4.4 60.6 1.0
N7 J:DG224 4.9 72.2 1.0
N7 I:DA67 4.9 53.7 1.0

Manganese binding site 3 out of 8 in 3afa

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Manganese binding site 3 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

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

b:0.7
occ:1.00
 N7 I:DG121 2.7 81.4 1.0
O6 I:DG121 3.0 82.8 1.0
C5 I:DG121 3.3 81.4 1.0
C6 I:DG121 3.4 82.5 1.0
O6 I:DG122 3.5 94.7 1.0
N4 J:DC171 3.5 0.1 1.0
C8 I:DG121 3.7 80.4 1.0
C4 I:DG121 4.5 80.7 1.0
C6 I:DT120 4.6 87.3 1.0
C6 I:DG122 4.6 92.7 1.0
N1 I:DG121 4.7 81.8 1.0
N9 I:DG121 4.7 79.9 1.0
C4 J:DC171 4.8 0.4 1.0
C5 I:DT120 4.8 87.7 1.0
C2' I:DT120 4.9 84.7 1.0
C7 I:DT120 4.9 86.7 1.0

Manganese binding site 4 out of 8 in 3afa

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Manganese binding site 4 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

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

b:79.3
occ:1.00
 N7 I:DA133 3.0 88.6 1.0
N6 I:DA133 3.8 87.5 1.0
C5 I:DA133 4.0 89.2 1.0
C8 I:DA133 4.0 90.5 1.0
O6 I:DG134 4.2 0.3 1.0
C6 I:DA133 4.3 88.4 1.0
C5 I:DC132 4.5 85.7 1.0
C6 I:DC132 4.5 85.2 1.0
OP2 I:DC132 4.9 84.7 1.0

Manganese binding site 5 out of 8 in 3afa

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Manganese binding site 5 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Human Nucleosome Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn301

b:97.0
occ:1.00
 N7 J:DG185 2.9 76.4 1.0
O6 J:DG186 2.9 76.5 1.0
C8 J:DG185 3.4 75.6 1.0
OP2 J:DG185 3.5 78.7 1.0
C6 J:DG186 3.8 77.4 1.0
C5 J:DG185 4.0 75.9 1.0
C2' J:DT184 4.2 84.1 1.0
N7 J:DG186 4.3 77.2 1.0
C5 J:DG186 4.4 77.5 1.0
N4 I:DC107 4.5 0.8 1.0
O6 J:DG185 4.6 75.1 1.0
O3' J:DT184 4.7 80.8 1.0
N9 J:DG185 4.7 75.2 1.0
P J:DG185 4.7 79.4 1.0
C6 J:DG185 4.7 75.1 1.0
C3' J:DT184 4.7 83.3 1.0
N1 J:DG186 4.9 76.3 1.0

Manganese binding site 6 out of 8 in 3afa

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Manganese binding site 6 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Human Nucleosome Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn302

b:86.4
occ:1.00
 N7 J:DG267 2.8 77.2 1.0
C8 J:DG267 3.6 75.5 1.0
C5 J:DG267 3.8 75.4 1.0
O6 J:DG267 4.0 74.8 1.0
OP2 J:DG267 4.0 81.4 1.0
O6 J:DG268 4.1 66.2 1.0
C6 J:DG267 4.3 74.4 1.0
C2' J:DT266 4.5 88.8 1.0
N4 I:DC25 4.7 0.6 1.0
N9 J:DG267 4.8 75.2 1.0
C4 J:DG267 4.9 75.8 1.0

Manganese binding site 7 out of 8 in 3afa

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Manganese binding site 7 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Human Nucleosome Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn303

b:68.8
occ:1.00
 N7 J:DG217 2.3 44.4 1.0
C8 J:DG217 3.3 44.3 1.0
C5 J:DG217 3.4 45.5 1.0
O6 J:DG217 3.6 46.9 1.0
C6 J:DG217 3.8 46.5 1.0
C2' J:DT216 4.0 45.1 1.0
N6 J:DA218 4.3 51.0 1.0
OP2 J:DG217 4.4 38.4 1.0
N9 J:DG217 4.5 45.3 1.0
C6 J:DT216 4.5 45.2 1.0
C4 J:DG217 4.5 45.6 1.0
N1 J:DT216 4.9 46.6 1.0
C1' J:DT216 4.9 44.4 1.0

Manganese binding site 8 out of 8 in 3afa

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Manganese binding site 8 out of 8 in the The Human Nucleosome Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Human Nucleosome Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn304

b:64.7
occ:1.00
 N7 J:DG280 2.6 78.9 1.0
C8 J:DG280 3.6 80.4 1.0
C5 J:DG280 3.6 79.5 1.0
O6 J:DG280 3.6 77.4 1.0
C6 J:DG280 3.9 78.8 1.0
N7 J:DA279 4.0 70.6 1.0
C8 J:DA279 4.1 71.5 1.0
O6 J:DG281 4.3 0.7 1.0
N7 J:DG281 4.7 0.0 1.0
N9 J:DG280 4.8 82.5 1.0
C4 J:DG280 4.8 80.7 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 15:45:48 2024

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