Manganese in PDB 1f66: 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z

The structure of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z, PDB code: 1f66 was solved by R.K.Suto, M.J.Clarkson, D.J.Tremethick, K.Luger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.660, 183.207, 109.922, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Manganese atom in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z (pdb code 1f66). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 15 binding sites of Manganese where determined in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z, PDB code: 1f66:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1002 b:0.4 occ:1.00 O6 I:DG40 2.5 0.1 1.0 N7 I:DG39 2.6 0.8 1.0 O I:HOH1022 2.9 67.8 1.0 C8 I:DG39 3.4 0.3 1.0 C6 I:DG40 3.5 0.5 1.0 C5 I:DG39 3.7 0.7 1.0 O6 I:DG39 4.1 0.5 1.0 C5 I:DG40 4.2 0.6 1.0 OP2 I:DG39 4.2 0.9 1.0 C6 I:DG39 4.2 0.5 1.0 N7 I:DG40 4.2 0.4 1.0 N4 J:DC253 4.4 0.2 1.0 N1 I:DG40 4.5 0.9 1.0 C2' I:DT38 4.6 97.3 1.0 N9 I:DG39 4.6 0.3 1.0 O3' I:DT38 4.7 98.7 1.0 C4 I:DG39 4.7 0.0 1.0

Manganese binding site 2 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:0.1 occ:1.00 N7 I:DG70 2.3 60.1 1.0 C8 I:DG70 3.3 66.9 1.0 C5 I:DG70 3.3 64.4 1.0 O6 I:DG70 3.4 62.2 1.0 O6 I:DG71 3.6 75.5 1.0 C6 I:DG70 3.7 61.8 1.0 C6 I:DC69 4.3 56.6 1.0 C2' I:DC69 4.3 65.0 1.0 C6 I:DG71 4.4 77.8 1.0 N9 I:DG70 4.5 66.2 1.0 C4 I:DG70 4.5 64.9 1.0 C5 I:DC69 4.6 59.2 1.0 N4 J:DC222 4.6 67.5 1.0 N7 I:DG71 4.8 70.3 1.0 N1 I:DC69 4.8 63.8 1.0 C5 I:DG71 4.9 77.0 1.0

Manganese binding site 3 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1004 b:0.1 occ:1.00 N7 I:DG100 2.4 86.3 1.0 C8 I:DG100 3.2 84.3 1.0 C5 I:DG100 3.5 85.4 1.0 C8 I:DA99 3.6 96.1 1.0 N7 I:DA99 3.6 0.9 1.0 O6 I:DG100 3.7 97.6 1.0 C6 I:DG100 4.0 89.8 1.0 N9 I:DG100 4.5 85.8 1.0 N9 I:DA99 4.5 92.1 1.0 C5 I:DA99 4.6 98.2 1.0 C4 I:DG100 4.6 82.5 1.0 C2' I:DA99 4.8 92.9 1.0

Manganese binding site 4 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1005 b:0.4 occ:1.00 O I:HOH1060 2.0 62.7 1.0 N7 I:DG121 2.2 95.6 1.0 C5 I:DG121 3.0 96.4 1.0 O6 I:DG121 3.0 96.6 1.0 C8 I:DG121 3.3 90.5 1.0 C6 I:DG121 3.3 97.9 1.0 O6 I:DG122 3.9 0.1 1.0 C4 I:DG121 4.2 94.0 1.0 C2' I:DT120 4.3 0.9 1.0 O I:HOH1019 4.3 68.1 1.0 N9 I:DG121 4.4 93.0 1.0 N1 I:DG121 4.7 93.4 1.0 C6 I:DG122 4.8 0.3 1.0 N7 I:DG122 4.8 92.3 1.0 OP2 I:DG121 4.9 97.3 1.0 N6 J:DA170 5.0 0.9 1.0

Manganese binding site 5 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:92.9 occ:1.00 N7 I:DG134 2.4 0.4 1.0 O6 I:DG134 3.2 95.6 1.0 C5 I:DG134 3.3 0.3 1.0 O I:HOH1025 3.5 74.2 1.0 C8 I:DG134 3.5 0.2 1.0 C6 I:DG134 3.6 0.1 1.0 C8 I:DA133 4.0 89.3 1.0 N7 I:DA133 4.1 84.8 1.0 O6 I:DG135 4.3 81.8 1.0 C4 I:DG134 4.5 1.0 1.0 N9 I:DG134 4.6 0.7 1.0 OP2 I:DA133 5.0 69.3 1.0 N1 I:DG134 5.0 98.5 1.0

Manganese binding site 6 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1007 b:0.6 occ:1.00 O6 I:DG138 2.5 69.5 1.0 N7 I:DG138 2.7 74.8 1.0 O I:HOH1027 3.0 72.5 1.0 N7 I:DG137 3.1 96.0 1.0 C6 I:DG138 3.1 71.6 1.0 C5 I:DG138 3.2 75.6 1.0 C8 I:DG137 3.2 0.1 1.0 C8 I:DG138 3.9 83.5 1.0 C5 I:DG137 4.0 90.1 1.0 N9 I:DG137 4.1 1.0 1.0 N1 I:DG138 4.5 61.5 1.0 C4 I:DG138 4.5 79.1 1.0 C4 I:DG137 4.6 94.8 1.0 C2' I:DG137 4.8 0.3 1.0 N6 I:DA139 4.8 65.4 1.0 C6 I:DG137 4.9 87.1 1.0 N9 I:DG138 4.9 88.9 1.0

Manganese binding site 7 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1009 b:91.2 occ:1.00 O2 I:DT86 4.1 71.2 1.0 C2 J:DA207 4.2 65.5 1.0 N3 J:DA207 4.3 64.0 1.0 O4' I:DG87 4.3 68.6 1.0 O4' J:DT208 4.4 59.2 1.0 O2 J:DT208 4.5 68.5 1.0 N3 I:DG87 4.7 85.1 1.0 C5' I:DC88 4.7 74.7 1.0 O4' I:DC88 4.7 72.7 1.0 C4' I:DC88 4.7 76.2 1.0 C4' I:DG87 4.8 66.2 1.0 C1' J:DT208 5.0 57.4 1.0 C4' J:DT208 5.0 54.9 1.0

Manganese binding site 8 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1008 b:0.8 occ:1.00 O6 J:DG186 2.3 0.4 1.0 N7 J:DG185 2.5 0.8 1.0 C6 J:DG186 3.2 0.8 1.0 C8 J:DG185 3.2 0.9 1.0 C5 J:DG185 3.5 0.5 1.0 OP2 J:DG185 3.7 98.7 1.0 C5 J:DG186 3.9 0.4 1.0 N7 J:DG186 4.0 98.8 1.0 O6 J:DG185 4.0 0.7 1.0 C6 J:DG185 4.1 0.6 1.0 N1 J:DG186 4.2 98.6 1.0 N9 J:DG185 4.3 0.8 1.0 C4 J:DG185 4.4 0.1 1.0 C2' J:DT184 4.6 0.3 1.0 N4 I:DC107 4.7 0.0 1.0

Manganese binding site 9 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1010 b:0.4 occ:1.00 N7 J:DG217 2.5 62.0 1.0 C5 J:DG217 3.5 65.3 1.0 C8 J:DG217 3.5 64.4 1.0 O6 J:DG217 3.5 61.7 1.0 C6 J:DG217 3.8 66.4 1.0 N6 J:DA218 3.9 66.2 1.0 C8 J:DG216 4.0 64.6 1.0 C2' J:DG216 4.1 59.3 1.0 N7 J:DG216 4.4 67.7 1.0 N9 J:DG216 4.4 65.1 1.0 C4 J:DG217 4.7 65.9 1.0 N9 J:DG217 4.7 61.4 1.0 C6 J:DA218 4.9 69.8 1.0 C1' J:DG216 4.9 61.9 1.0 C5 J:DG216 5.0 65.5 1.0

Manganese binding site 10 out of 15 in the 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of 2.6 A Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1011 b:94.3 occ:1.00 N7 J:DG246 2.7 95.6 1.0 O6 J:DG246 3.4 0.6 1.0 C5 J:DG246 3.6 100.0 1.0 C8 J:DG246 3.8 95.8 1.0 C6 J:DG246 3.9 0.8 1.0 C8 J:DA245 4.4 0.1 1.0 O6 I:DG46 4.5 0.1 1.0 N7 J:DA245 4.7 0.1 1.0 C4 J:DG246 4.9 100.0 1.0 C2' J:DA245 4.9 98.4 1.0 N9 J:DG246 4.9 95.4 1.0

R.K.Suto, M.J.Clarkson, D.J.Tremethick, K.Luger. Crystal Structure of A Nucleosome Core Particle Containing the Variant Histone H2A.Z. Nat.Struct.Biol. V. 7 1121 2000.
ISSN: ISSN 1072-8368
PubMed: 11101893
DOI: 10.1038/81971