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Manganese in PDB 5x7x: The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution

Protein crystallography data

The structure of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution, PDB code: 5x7x was solved by Y.Arimura, H.Taguchi, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.887, 107.509, 167.415, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.6

Other elements in 5x7x:

The structure of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Manganese atom in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution (pdb code 5x7x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution, PDB code: 5x7x:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 13 in 5x7x

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Manganese binding site 1 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn202

b:22.2
occ:1.00
 O E:HOH320 1.9 22.2 1.0
OD1 E:ASP77 2.3 21.7 1.0
CG E:ASP77 3.3 22.2 1.0
OD2 E:ASP77 3.7 22.6 1.0
O E:GLU73 4.5 18.8 1.0
CG E:GLN76 4.5 26.1 1.0
CB E:ASP77 4.5 19.8 1.0
N E:ASP77 4.6 18.1 1.0
CA E:ASP77 4.6 18.9 1.0
CB E:GLN76 4.9 17.9 1.0
C E:GLN76 4.9 19.6 1.0
O F:LEU22 5.0 21.7 1.0

Manganese binding site 2 out of 13 in 5x7x

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Manganese binding site 2 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn201

b:46.6
occ:1.00
 O J:HOH3165 2.1 38.4 1.0
O J:HOH3147 2.1 31.1 1.0
O I:HOH341 2.1 36.8 1.0
O I:HOH377 2.3 43.4 1.0
N3 I:DA113 4.3 21.7 1.0
O4' I:DC114 4.5 32.6 1.0
N3 J:DA181 4.6 23.6 1.0
O I:HOH358 4.6 36.0 1.0
O4' J:DT182 4.7 30.1 1.0
C2 I:DA113 4.9 22.4 1.0
C4' J:DT182 5.0 29.0 1.0

Manganese binding site 3 out of 13 in 5x7x

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Manganese binding site 3 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn202

b:83.1
occ:1.00
 N7 I:DG134 2.4 45.2 1.0
C8 I:DG134 3.3 45.6 1.0
C5 I:DG134 3.4 41.3 1.0
O6 I:DG134 3.6 41.9 1.0
C6 I:DG134 3.8 42.4 1.0
O6 I:DG135 4.1 47.3 1.0
N7 I:DA133 4.2 40.3 1.0
C8 I:DA133 4.3 45.7 1.0
N9 I:DG134 4.5 44.9 1.0
C4 I:DG134 4.6 43.2 1.0
N7 I:DG135 4.8 45.3 1.0
C6 I:DG135 5.0 45.6 1.0

Manganese binding site 4 out of 13 in 5x7x

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Manganese binding site 4 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn203

b:56.2
occ:1.00
 O6 I:DG68 2.1 38.7 1.0
C6 I:DG68 3.2 33.4 1.0
N4 J:DC225 3.9 32.3 1.0
C5 I:DG68 3.9 28.8 1.0
N7 I:DG68 4.0 33.3 1.0
O6 J:DG224 4.2 34.2 1.0
N1 I:DG68 4.3 30.3 1.0
N7 J:DG224 4.4 38.4 1.0
N7 I:DA67 4.7 33.0 1.0
C6 J:DG224 4.9 33.3 1.0

Manganese binding site 5 out of 13 in 5x7x

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Manganese binding site 5 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn204

b:37.1
occ:1.00
 O I:HOH352 1.8 35.4 1.0
O I:HOH306 1.9 30.9 1.0
N7 I:DG121 2.3 25.3 1.0
O I:HOH380 2.7 39.9 1.0
C8 I:DG121 3.2 25.1 1.0
O I:HOH381 3.3 32.1 1.0
C5 I:DG121 3.3 23.5 1.0
O6 I:DG121 3.6 24.1 1.0
C6 I:DG121 3.8 22.3 1.0
C2' I:DT120 4.0 27.3 1.0
O J:HOH3137 4.1 30.0 1.0
N9 I:DG121 4.4 23.3 1.0
C4 I:DG121 4.5 24.0 1.0
C6 I:DT120 4.7 20.9 1.0
O6 I:DG122 4.8 23.9 1.0
C1' I:DT120 5.0 23.8 1.0

Manganese binding site 6 out of 13 in 5x7x

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Manganese binding site 6 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn205

b:34.7
occ:1.00
 OP2 I:DA27 1.9 32.7 1.0
O I:HOH355 2.2 22.4 1.0
O I:HOH361 2.3 31.7 1.0
P I:DA27 3.4 27.9 1.0
OP1 I:DA27 4.2 29.2 1.0
O3' I:DC26 4.2 25.9 1.0
C8 I:DA27 4.3 27.3 1.0
O5' I:DA27 4.3 26.6 1.0
N7 I:DA27 4.3 26.4 1.0
C3' I:DC26 4.6 27.3 1.0

Manganese binding site 7 out of 13 in 5x7x

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Manganese binding site 7 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn206

b:51.8
occ:1.00
 N7 I:DG131 2.4 31.9 1.0
C5 I:DG131 3.4 29.9 1.0
O6 I:DG131 3.4 29.7 1.0
C8 I:DG131 3.4 34.1 1.0
C6 I:DG131 3.7 31.8 1.0
C2' I:DT130 3.9 33.9 1.0
N4 I:DC132 4.0 35.2 1.0
C6 I:DT130 4.4 30.3 1.0
C4 I:DG131 4.6 33.0 1.0
N9 I:DG131 4.6 32.6 1.0
O6 J:DG161 4.8 37.4 1.0
N1 I:DT130 4.8 30.7 1.0
C1' I:DT130 4.9 34.0 1.0
C5 I:DT130 4.9 31.9 1.0

Manganese binding site 8 out of 13 in 5x7x

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Manganese binding site 8 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


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 Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3001

b:36.6
occ:1.00
 O J:HOH3112 1.8 32.0 1.0
O J:HOH3123 2.1 27.5 1.0
O J:HOH3173 2.2 28.7 1.0
O J:HOH3119 2.4 26.6 1.0
N7 J:DG267 2.5 28.6 1.0
O J:HOH3167 2.7 28.5 1.0
C8 J:DG267 3.3 27.2 1.0
C5 J:DG267 3.6 26.0 1.0
O6 J:DG267 3.9 26.2 1.0
OP2 J:DG267 4.1 30.8 1.0
C6 J:DG267 4.1 26.1 1.0
O6 J:DG268 4.3 25.9 1.0
O J:HOH3132 4.4 21.3 1.0
N9 J:DG267 4.5 24.9 1.0
C2' J:DT266 4.5 31.0 1.0
C4 J:DG267 4.7 24.1 1.0

Manganese binding site 9 out of 13 in 5x7x

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Manganese binding site 9 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3002

b:46.9
occ:1.00
 O J:HOH3101 2.3 29.4 1.0
O I:HOH325 2.4 28.5 1.0
O J:HOH3164 4.1 28.3 1.0
O4' J:DG179 4.2 32.8 1.0
O2 J:DT178 4.3 24.1 1.0
O4' I:DT117 4.3 25.8 1.0
O2 I:DC116 4.3 23.6 1.0
C4' J:DG179 4.4 36.6 1.0
C4' I:DT117 4.5 25.9 1.0
C5' J:DG179 4.6 33.0 1.0
C5' I:DT117 4.9 24.9 1.0
N2 J:DG177 5.0 19.9 1.0

Manganese binding site 10 out of 13 in 5x7x

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Manganese binding site 10 out of 13 in the The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Crystal Structure of the Nucleosome Containing H3.3 at 2.18 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn3003

b:59.6
occ:1.00
 N7 J:DG280 2.1 55.9 1.0
C8 J:DG280 3.1 61.1 1.0
C5 J:DG280 3.1 58.4 1.0
O6 J:DG280 3.4 55.3 1.0
C6 J:DG280 3.6 55.4 1.0
C8 J:DA279 3.9 47.9 1.0
N7 J:DA279 4.1 46.7 1.0
O6 J:DG281 4.1 68.3 1.0
N9 J:DG280 4.3 60.6 1.0
C4 J:DG280 4.3 56.5 1.0
OP2 J:DA279 4.7 39.1 1.0
N9 J:DA279 4.9 50.6 1.0
C2' J:DA279 4.9 52.1 1.0
N7 J:DG281 5.0 66.3 1.0

Reference:

H.Taguchi, Y.Xie, N.Horikoshi, K.Maehara, A.Harada, J.Nogami, K.Sato, Y.Arimura, A.Osakabe, T.Kujirai, T.Iwasaki, Y.Semba, T.Tachibana, H.Kimura, Y.Ohkawa, H.Kurumizaka. Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8 Biochemistry V. 56 2184 2017.
ISSN: ISSN 1520-4995
PubMed: 28374988
DOI: 10.1021/ACS.BIOCHEM.6B01098
Page generated: Sun Oct 6 03:24:12 2024

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