Manganese in PDB 3azf: Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q Mutation

The structure of Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q Mutation, PDB code: 3azf 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)	48.80 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.552, 109.780, 182.217, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.3

The structure of Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q Mutation also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

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 H3K79Q Mutation (pdb code 3azf). 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 H3K79Q Mutation, PDB code: 3azf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q Mutation


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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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:36.9 occ:1.00 O D:HOH301 2.1 19.7 1.0 O D:HOH303 2.2 39.1 1.0 O D:VAL48 2.3 29.5 1.0 C D:VAL48 3.3 28.9 1.0 CA D:VAL48 3.6 32.8 1.0 OE1 C:GLU64 4.0 50.7 1.0 OE2 C:GLU64 4.0 43.3 1.0 O C:HOH2001 4.1 21.1 1.0 CB D:VAL48 4.3 32.7 1.0 CD2 D:HIS49 4.4 17.3 1.0 O D:GLN47 4.4 36.5 1.0 CD C:GLU64 4.4 39.8 1.0 N D:HIS49 4.4 33.7 1.0 NE2 D:HIS49 4.7 33.2 1.0 N D:VAL48 4.9 33.6 1.0 CA D:HIS49 4.9 36.3 1.0

Manganese binding site 2 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q Mutation


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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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1001 b:0.9 occ:1.00 O6 I:DG68 2.6 75.5 1.0 C6 I:DG68 3.6 72.7 1.0 N4 J:DC225 3.9 86.9 1.0 O6 J:DG224 4.0 73.7 1.0 N7 I:DG68 4.0 72.1 1.0 C5 I:DG68 4.2 71.1 1.0 N7 J:DG224 4.5 83.6 1.0 N7 I:DA67 4.6 59.7 1.0 C6 J:DG224 4.7 78.5 1.0 N1 I:DG68 4.7 71.5 1.0 C5 J:DG224 4.9 81.6 1.0

Manganese binding site 3 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1002 b:0.5 occ:1.00 N7 I:DG121 2.5 89.7 1.0 O6 I:DG121 3.0 94.9 1.0 C5 I:DG121 3.3 90.3 1.0 C6 I:DG121 3.4 94.3 1.0 C8 I:DG121 3.6 88.1 1.0 C6 I:DT120 3.9 97.7 1.0 O6 I:DG122 4.0 0.7 1.0 C5 I:DT120 4.1 1.0 1.0 C7 I:DT120 4.1 95.4 1.0 C2' I:DT120 4.4 89.4 1.0 N1 I:DT120 4.5 96.1 1.0 C4 I:DG121 4.5 88.7 1.0 N4 J:DC171 4.5 0.2 1.0 N9 I:DG121 4.7 85.9 1.0 N1 I:DG121 4.8 92.5 1.0 C4 I:DT120 5.0 0.7 1.0 C1' I:DT120 5.0 92.3 1.0 C6 I:DG122 5.0 0.2 1.0

Manganese binding site 4 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:86.0 occ:1.00 N7 I:DA133 2.7 66.4 1.0 N6 I:DA133 3.6 68.0 1.0 C5 I:DA133 3.7 74.9 1.0 C8 I:DA133 3.7 80.4 1.0 C5 I:DC132 4.0 88.5 1.0 C6 I:DA133 4.1 72.7 1.0 C6 I:DC132 4.2 85.2 1.0 O6 I:DG134 4.3 96.1 1.0 OP2 I:DC132 4.6 66.2 1.0 C4 I:DA133 4.9 75.0 1.0 N9 I:DA133 4.9 82.6 1.0 C4 I:DC132 5.0 94.5 1.0

Manganese binding site 5 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1004 b:85.3 occ:1.00 O2 I:DT86 3.8 71.4 1.0 O4' I:DG87 3.9 68.8 1.0 O4' I:DC88 4.1 72.2 1.0 C4' I:DC88 4.2 73.0 1.0 C5' I:DC88 4.3 76.4 1.0 O4' J:DT208 4.3 54.9 1.0 C4' I:DG87 4.4 68.0 1.0 C2 J:DA207 4.6 55.9 1.0 O2 J:DT208 4.7 57.1 1.0 N3 J:DA207 4.9 54.4 1.0 C5' I:DG87 4.9 68.6 1.0 N3 I:DG87 5.0 88.9 1.0

Manganese binding site 6 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1005 b:0.8 occ:1.00 N7 I:DG100 2.4 81.2 1.0 C8 I:DG100 3.4 72.5 1.0 C5 I:DG100 3.5 80.4 1.0 O6 I:DG100 3.6 84.8 1.0 C8 I:DA99 3.9 80.4 1.0 C6 I:DG100 3.9 83.5 1.0 N7 I:DA99 4.0 82.7 1.0 N9 I:DG100 4.6 72.9 1.0 C4 I:DG100 4.7 75.6 1.0 N9 I:DA99 4.9 83.9 1.0 C5 I:DA99 5.0 86.3 1.0 OP2 I:DA99 5.0 0.6 1.0

Manganese binding site 7 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:0.0 occ:1.00 O6 I:DG78 2.5 97.3 1.0 C6 I:DG78 3.5 91.5 1.0 N7 I:DG78 3.9 88.7 1.0 N4 J:DC215 4.0 69.8 1.0 C5 I:DG78 4.1 88.6 1.0 O6 J:DG214 4.2 56.3 1.0 N7 I:DA77 4.5 72.8 1.0 N7 J:DG214 4.5 57.6 1.0 N1 I:DG78 4.7 89.6 1.0 C6 J:DG214 4.9 55.4 1.0

Manganese binding site 8 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1001 b:0.8 occ:1.00 N7 J:DG185 2.7 92.7 1.0 O6 J:DG186 2.8 84.2 1.0 C8 J:DG185 3.3 91.1 1.0 C6 J:DG186 3.7 89.7 1.0 C5 J:DG185 3.7 92.6 1.0 OP2 J:DG185 4.0 92.6 1.0 N7 J:DG186 4.1 81.5 1.0 C5 J:DG186 4.2 87.8 1.0 O6 J:DG185 4.2 93.8 1.0 C6 J:DG185 4.4 90.3 1.0 C2' J:DT184 4.4 96.0 1.0 O3' J:DT184 4.5 98.2 1.0 N4 I:DC107 4.5 0.0 1.0 N9 J:DG185 4.5 91.0 1.0 C4 J:DG185 4.7 90.6 1.0 N1 J:DG186 4.8 89.0 1.0 P J:DG185 4.9 96.6 1.0 C3' J:DT184 4.9 97.3 1.0

Manganese binding site 9 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q Mutation


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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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1002 b:87.8 occ:1.00 N7 J:DG267 2.7 95.7 1.0 C8 J:DG267 3.3 91.2 1.0 C5 J:DG267 3.9 89.3 1.0 OP2 J:DG267 3.9 87.1 1.0 O6 J:DG268 4.0 82.3 1.0 C2' J:DT266 4.0 88.1 1.0 C3' J:DT266 4.4 90.5 1.0 O6 J:DG267 4.4 86.4 1.0 O3' J:DT266 4.5 89.5 1.0 C6 J:DG267 4.5 88.7 1.0 N9 J:DG267 4.6 89.9 1.0 N4 I:DC25 4.8 0.1 1.0 P J:DG267 4.9 88.0 1.0 C4 J:DG267 4.9 89.8 1.0 C6 J:DG268 5.0 78.0 1.0

Manganese binding site 10 out of 12 in the Crystal Structure of Human Nucleosome Core Particle Containing H3K79Q 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 H3K79Q Mutation within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1003 b:72.2 occ:1.00 N7 J:DG217 2.2 54.3 1.0 C5 J:DG217 3.2 53.9 1.0 C8 J:DG217 3.2 51.8 1.0 O6 J:DG217 3.3 50.6 1.0 C6 J:DG217 3.6 53.9 1.0 C2' J:DT216 3.9 59.2 1.0 N6 J:DA218 4.1 60.1 1.0 OP2 J:DG217 4.3 44.1 1.0 C4 J:DG217 4.4 54.2 1.0 N9 J:DG217 4.4 52.0 1.0 C6 J:DT216 4.5 54.5 1.0 N1 J:DT216 4.7 60.8 1.0 C1' J:DT216 4.7 57.4 1.0 C6 J:DA218 4.9 61.8 1.0 N1 J:DG217 5.0 54.8 1.0

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