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:
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
Go back to
Manganese Binding Sites List in 5b31
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
|