Atomistry » Manganese » PDB 3auz-3c5m » 3azj
Atomistry »
  Manganese »
    PDB 3auz-3c5m »
      3azj »

Manganese in PDB 3azj: Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation

Protein crystallography data

The structure of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation, PDB code: 3azj was solved by W.Iwasaki, H.Tachiwana, K.Kawaguchi, T.Shibata, W.Kagawa, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 2.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 105.955, 109.428, 180.904, 90.00, 90.00, 90.00
R / Rfree (%) 22 / 26.8

Other elements in 3azj:

The structure of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation (pdb code 3azj). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation, PDB code: 3azj:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 1 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn202

b:31.4
occ:1.00
O D:VAL48 2.3 28.6 1.0
C D:VAL48 3.2 29.7 1.0
CA D:VAL48 3.6 32.4 1.0
OE1 C:GLU64 4.0 51.0 1.0
O D:GLN47 4.3 34.2 1.0
CB D:VAL48 4.4 34.0 1.0
N D:HIS49 4.4 29.6 1.0
OE2 C:GLU64 4.5 46.5 1.0
CD C:GLU64 4.7 44.0 1.0
CD2 D:HIS49 4.8 25.3 1.0
CD D:PRO50 4.8 30.8 1.0
N D:VAL48 4.8 31.8 1.0
CA D:HIS49 4.9 32.4 1.0

Manganese binding site 2 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 2 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1001

b:0.6
occ:1.00
O6 I:DG68 2.7 67.6 1.0
C6 I:DG68 3.7 64.1 1.0
N7 I:DG68 3.9 62.9 1.0
N4 J:DC225 4.0 84.9 1.0
C5 I:DG68 4.1 62.2 1.0
N7 I:DA67 4.5 53.0 1.0
O6 J:DG224 4.5 80.5 1.0
C8 I:DA67 4.9 53.3 1.0
N1 I:DG68 4.9 63.8 1.0

Manganese binding site 3 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 3 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1002

b:94.9
occ:1.00
N7 I:DG121 2.5 78.2 1.0
O6 I:DG121 2.8 79.7 1.0
C5 I:DG121 3.1 77.6 1.0
C6 I:DG121 3.2 79.6 1.0
O6 I:DG122 3.5 88.8 1.0
C8 I:DG121 3.6 77.2 1.0
N4 J:DC171 3.9 0.1 1.0
C4 I:DG121 4.3 76.1 1.0
N1 I:DG121 4.5 79.5 1.0
N9 I:DG121 4.6 74.7 1.0
C6 I:DT120 4.6 85.3 1.0
C6 I:DG122 4.7 86.2 1.0
C2' I:DT120 4.8 78.5 1.0
C5 I:DT120 4.9 87.0 1.0

Manganese binding site 4 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 4 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1003

b:68.5
occ:1.00
N7 I:DA133 2.9 74.2 1.0
C8 I:DA133 3.9 77.6 1.0
N6 I:DA133 3.9 69.5 1.0
C5 I:DA133 3.9 74.5 1.0
C6 I:DA133 4.4 72.4 1.0
O6 I:DG134 4.4 91.2 1.0
C6 I:DC132 4.6 74.2 1.0
C5 I:DC132 4.7 75.8 1.0
OP2 I:DC132 4.8 64.6 1.0

Manganese binding site 5 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 5 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1004

b:74.4
occ:1.00
O2 I:DT86 4.0 63.8 1.0
O4' I:DG87 4.1 57.4 1.0
O4' J:DT208 4.3 44.4 1.0
O4' I:DC88 4.4 60.6 1.0
O2 J:DT208 4.4 51.0 1.0
C4' I:DC88 4.4 57.8 1.0
C4' I:DG87 4.5 56.9 1.0
C5' I:DC88 4.6 56.9 1.0
C2 J:DA207 4.6 47.7 1.0
C5' I:DG87 4.9 53.9 1.0
C1' J:DT208 5.0 42.2 1.0
N3 J:DA207 5.0 45.6 1.0

Manganese binding site 6 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 6 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1005

b:97.0
occ:1.00
N7 I:DG100 2.3 69.0 1.0
O6 I:DG100 3.1 69.4 1.0
C5 I:DG100 3.2 66.1 1.0
C8 I:DG100 3.4 67.8 1.0
C6 I:DG100 3.4 66.5 1.0
N7 I:DA99 4.0 71.1 1.0
C8 I:DA99 4.0 72.8 1.0
OP2 I:DA99 4.4 77.9 1.0
C4 I:DG100 4.4 64.2 1.0
N9 I:DG100 4.5 63.9 1.0
N1 I:DG100 4.8 67.5 1.0
O6 J:DG192 4.9 86.3 1.0
C5 I:DA99 5.0 73.5 1.0
N9 I:DA99 5.0 71.9 1.0

Manganese binding site 7 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 7 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn1006

b:97.7
occ:1.00
O6 I:DG78 2.7 75.8 1.0
C6 I:DG78 3.6 73.5 1.0
N7 I:DG78 4.0 72.6 1.0
N4 J:DC215 4.0 62.6 1.0
C5 I:DG78 4.1 72.8 1.0
O6 J:DG214 4.2 47.4 1.0
N7 J:DG214 4.4 48.2 1.0
N1 I:DG78 4.7 72.8 1.0
N7 I:DA77 4.7 57.8 1.0
C6 J:DG214 4.9 46.9 1.0

Manganese binding site 8 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 8 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1001

b:94.3
occ:1.00
O6 J:DG186 2.7 79.2 1.0
N7 J:DG185 2.7 81.9 1.0
C8 J:DG185 3.3 80.0 1.0
C6 J:DG186 3.5 79.5 1.0
C5 J:DG185 3.8 80.9 1.0
C5 J:DG186 4.1 78.8 1.0
C2' J:DT184 4.2 74.4 1.0
OP2 J:DG185 4.2 67.7 1.0
N7 J:DG186 4.2 77.8 1.0
O3' J:DT184 4.2 71.1 1.0
O6 J:DG185 4.3 81.3 1.0
N4 I:DC107 4.4 88.8 1.0
C6 J:DG185 4.4 80.7 1.0
N1 J:DG186 4.5 78.6 1.0
N9 J:DG185 4.6 79.0 1.0
C3' J:DT184 4.7 74.0 1.0
C4 J:DG185 4.8 79.9 1.0
P J:DG185 4.9 69.1 1.0

Manganese binding site 9 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 9 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1002

b:96.0
occ:1.00
N7 J:DG267 2.8 80.5 1.0
O6 J:DG268 3.5 62.2 1.0
C8 J:DG267 3.6 77.5 1.0
C5 J:DG267 3.8 75.5 1.0
OP2 J:DG267 4.0 76.2 1.0
O6 J:DG267 4.0 70.2 1.0
C6 J:DG267 4.2 73.2 1.0
C6 J:DG268 4.5 63.3 1.0
N4 I:DC25 4.6 0.7 1.0
N9 J:DG267 4.8 75.0 1.0
C2' J:DT266 4.8 78.7 1.0
N7 J:DG268 4.8 61.3 1.0
C4 J:DG267 4.9 74.8 1.0

Manganese binding site 10 out of 12 in 3azj

Go back to Manganese Binding Sites List in 3azj
Manganese binding site 10 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Human Nucleosome Core Particle Containing H4K44Q Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1003

b:77.1
occ:1.00
N7 J:DG217 2.2 46.1 1.0
C8 J:DG217 3.1 45.7 1.0
C5 J:DG217 3.3 50.0 1.0
O6 J:DG217 3.7 53.6 1.0
C6 J:DG217 3.9 51.9 1.0
C2' J:DT216 4.1 50.8 1.0
N6 J:DA218 4.1 63.6 1.0
N9 J:DG217 4.3 46.4 1.0
OP2 J:DG217 4.4 41.6 1.0
C4 J:DG217 4.4 48.1 1.0
C6 J:DT216 4.7 57.0 1.0
N1 J:DT216 4.9 56.9 1.0
C1' J:DT216 4.9 51.8 1.0
C6 J:DA218 5.0 66.3 1.0

Reference:

W.Iwasaki, H.Tachiwana, K.Kawaguchi, T.Shibata, W.Kagawa, H.Kurumizaka. Comprehensive Structural Analysis of Mutant Nucleosomes Containing Lysine to Glutamine (Kq) Substitutions in the H3 and H4 Histone-Fold Domains Biochemistry V. 50 7822 2011.
ISSN: ISSN 0006-2960
PubMed: 21812398
DOI: 10.1021/BI201021H
Page generated: Sat Aug 16 11:26:32 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy