Manganese in PDB 2pyo: Drosophila Nucleosome Core

The structure of Drosophila Nucleosome Core, PDB code: 2pyo was solved by C.R.Clapier, C.Petosa, C.W.Mueller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	500.00 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.030, 182.040, 109.420, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 26.2

The structure of Drosophila Nucleosome Core also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Drosophila Nucleosome Core (pdb code 2pyo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Drosophila Nucleosome Core, PDB code: 2pyo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:86.7 occ:1.00 O4' I:DG14 3.9 70.4 1.0 O2 I:DT13 4.0 74.5 1.0 O4' I:DC15 4.0 77.5 1.0 C4' I:DG14 4.2 70.3 1.0 C5' I:DC15 4.3 73.5 1.0 C4' I:DC15 4.3 75.5 1.0 C2 J:DA-13 4.5 64.8 1.0 N3 I:DG14 4.5 80.2 1.0 N3 J:DA-13 4.6 63.2 1.0 C1' I:DG14 4.7 73.4 1.0 O4' J:DT-12 4.7 60.1 1.0

Manganese binding site 2 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1007 b:0.7 occ:1.00 N7 I:DG48 2.6 99.6 1.0 C8 I:DG48 3.5 98.4 1.0 C5 I:DG48 3.7 0.3 1.0 O6 I:DG48 3.9 0.1 1.0 C2' I:DT47 4.0 99.8 1.0 C6 I:DG48 4.2 0.7 1.0 OP2 I:DG48 4.6 95.6 1.0 N9 I:DG48 4.8 97.8 1.0 O6 I:DG49 4.8 93.0 1.0 C4 I:DG48 4.9 100.0 1.0

Manganese binding site 3 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1008 b:90.1 occ:1.00 N7 I:DG61 2.5 93.1 1.0 C5 I:DG61 3.4 93.6 1.0 C8 I:DG61 3.4 94.3 1.0 O6 I:DG61 3.5 92.5 1.0 C6 I:DG61 3.8 93.4 1.0 C8 I:DA60 4.4 91.9 1.0 O6 I:DG62 4.4 0.6 1.0 N7 I:DA60 4.4 91.6 1.0 C4 I:DG61 4.6 94.1 1.0 N9 I:DG61 4.6 95.4 1.0 N7 I:DG62 4.9 1.0 1.0

Manganese binding site 4 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1010 b:0.0 occ:1.00 N7 I:DG27 2.3 82.2 1.0 C5 I:DG27 3.2 81.2 1.0 O6 I:DG27 3.2 82.3 1.0 C8 I:DG27 3.4 81.4 1.0 C6 I:DG27 3.6 81.6 1.0 N7 I:DA26 4.3 0.2 1.0 C8 I:DA26 4.4 0.6 1.0 C4 I:DG27 4.5 81.0 1.0 O6 J:DG-28 4.5 0.8 1.0 N9 I:DG27 4.5 81.0 1.0 N4 I:DC28 4.7 89.5 1.0 C7 J:DT-29 4.9 1.0 1.0 N1 I:DG27 4.9 81.6 1.0

Manganese binding site 5 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1011 b:98.2 occ:1.00 O6 I:DG5 3.0 85.3 1.0 O6 J:DG-6 3.5 62.1 1.0 N7 J:DG-6 3.7 59.0 1.0 C6 I:DG5 3.8 83.0 1.0 N7 I:DG5 4.1 83.7 1.0 N4 J:DC-5 4.2 59.6 1.0 C5 I:DG5 4.2 83.0 1.0 C6 J:DG-6 4.2 60.2 1.0 C5 J:DG-6 4.3 59.8 1.0 N1 I:DG5 4.8 82.8 1.0 C8 J:DG-6 4.8 57.9 1.0 C2' J:DA-7 4.8 65.6 1.0

Manganese binding site 6 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1012 b:94.8 occ:1.00 N7 I:DG-3 2.6 66.4 1.0 O6 I:DG-2 3.4 73.8 1.0 C5 I:DG-3 3.5 67.2 1.0 C8 I:DG-3 3.5 67.0 1.0 O6 I:DG-3 3.6 69.1 1.0 C6 I:DG-3 3.9 67.9 1.0 C6 I:DG-2 4.3 74.2 1.0 N7 I:DG-2 4.5 72.2 1.0 C2' I:DT-4 4.6 60.2 1.0 C4 I:DG-3 4.7 66.7 1.0 N9 I:DG-3 4.7 65.4 1.0 C5 I:DG-2 4.8 74.0 1.0 C6 I:DT-4 4.8 63.8 1.0 OP2 I:DG-3 5.0 53.2 1.0

Manganese binding site 7 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1013 b:94.1 occ:1.00 O6 I:DG-34 2.3 69.6 1.0 N7 I:DG-35 2.5 82.8 1.0 O I:HOH1023 3.1 58.5 1.0 C6 I:DG-34 3.2 69.7 1.0 C8 I:DG-35 3.4 81.7 1.0 C5 I:DG-35 3.5 81.4 1.0 O6 I:DG-35 3.7 83.3 1.0 C5 I:DG-34 3.8 70.2 1.0 N7 I:DG-34 3.9 68.8 1.0 C6 I:DG-35 3.9 81.5 1.0 N4 J:DC34 4.1 0.3 1.0 N1 I:DG-34 4.3 68.5 1.0 OP2 I:DG-35 4.5 72.6 1.0 N9 I:DG-35 4.6 80.0 1.0 C4 I:DG-35 4.6 81.1 1.0 C2' I:DT-36 4.6 81.8 1.0

Manganese binding site 8 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1001 b:87.9 occ:1.00 N7 J:DG61 2.6 93.0 1.0 O6 J:DG61 3.4 94.3 1.0 C5 J:DG61 3.5 92.9 1.0 C8 J:DG61 3.6 94.3 1.0 C6 J:DG61 3.8 93.5 1.0 N7 J:DA60 3.8 85.2 1.0 C8 J:DA60 3.9 85.0 1.0 O6 J:DG62 4.2 0.4 1.0 C4 J:DG61 4.7 93.6 1.0 N9 J:DG61 4.7 95.0 1.0 C5 J:DA60 4.9 84.0 1.0 N9 J:DA60 4.9 84.5 1.0

Manganese binding site 9 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1003 b:76.5 occ:1.00 N7 J:DG27 2.4 72.3 1.0 C8 J:DG27 3.3 70.4 1.0 C5 J:DG27 3.5 71.8 1.0 O6 J:DG27 3.7 76.0 1.0 C6 J:DG27 4.0 73.8 1.0 O6 I:DG-28 4.5 99.8 1.0 C8 J:DA26 4.5 74.9 1.0 N7 J:DA26 4.5 76.5 1.0 N9 J:DG27 4.5 69.6 1.0 C4 J:DG27 4.6 69.6 1.0

Manganese binding site 10 out of 14 in the Drosophila Nucleosome Core


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Drosophila Nucleosome Core within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1004 b:89.2 occ:1.00 N7 J:DG-3 2.6 59.1 1.0 C8 J:DG-3 3.5 57.5 1.0 C5 J:DG-3 3.6 59.0 1.0 O6 J:DG-3 3.7 59.7 1.0 O6 J:DG-2 3.9 81.7 1.0 C6 J:DG-3 4.0 59.1 1.0 C2' J:DT-4 4.4 52.8 1.0 N9 J:DG-3 4.7 58.4 1.0 C6 J:DT-4 4.7 54.2 1.0 C4 J:DG-3 4.8 58.9 1.0 C6 J:DG-2 4.9 82.1 1.0 OP2 J:DG-3 5.0 46.1 1.0

C.R.Clapier, S.Chakravarthy, C.Petosa, C.Fernandez-Tornero, K.Luger, C.W.Muller. Structure of the Drosophila Nucleosome Core Particle Highlights Evolutionary Constraints on the H2A-H2B Histone Dimer. Proteins V. 71 1 2007.
ISSN: ISSN 0887-3585
PubMed: 17957772
DOI: 10.1002/PROT.21720