Atomistry » Manganese » PDB 2ypq-3au8 » 3a6n
Atomistry »
  Manganese »
    PDB 2ypq-3au8 »
      3a6n »

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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Go back to Manganese Binding Sites List in 3a6n
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy