Manganese in PDB 2nzd: Nucleosome Core Particle Containing 145 Bp of Dna

The structure of Nucleosome Core Particle Containing 145 Bp of Dna, PDB code: 2nzd was solved by M.S.Ong, T.J.Richmond, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.617, 109.856, 181.217, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.3

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Nucleosome Core Particle Containing 145 Bp of Dna (pdb code 2nzd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Nucleosome Core Particle Containing 145 Bp of Dna, PDB code: 2nzd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1002 b:0.5 occ:1.00 O2 J:DT-11 4.5 57.6 1.0 O4' I:DG13 4.6 89.9 1.0 C5' J:DG-10 4.9 54.4 1.0 C4' I:DG13 4.9 89.0 1.0

Manganese binding site 2 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:97.6 occ:1.00 N7 I:DG-34 2.2 69.1 1.0 O6 I:DG-33 2.7 69.6 1.0 C8 I:DG-34 3.1 69.0 1.0 C5 I:DG-34 3.2 68.9 1.0 C6 I:DG-33 3.4 69.5 1.0 O6 I:DG-34 3.6 68.7 1.0 C6 I:DG-34 3.7 68.4 1.0 N7 I:DG-33 3.8 69.3 1.0 C5 I:DG-33 3.9 69.7 1.0 N4 J:DC33 4.1 93.1 1.0 C2' I:DT-35 4.2 75.2 1.0 N9 I:DG-34 4.2 68.9 1.0 C4 I:DG-34 4.3 69.2 1.0 OP2 I:DG-34 4.4 68.6 1.0 N1 I:DG-33 4.5 69.4 1.0 O3' I:DT-35 4.7 72.4 1.0 O4 J:DT32 4.8 0.2 1.0 C3' I:DT-35 4.9 75.2 1.0 C8 I:DG-33 5.0 69.7 1.0

Manganese binding site 3 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1008 b:0.2 occ:1.00 N7 I:DG47 2.1 78.1 1.0 O6 I:DG47 2.8 77.6 1.0 C5 I:DG47 2.9 77.6 1.0 C6 I:DG47 3.2 77.5 1.0 C8 I:DG47 3.3 77.7 1.0 C2' I:DT46 3.9 84.1 1.0 C4 I:DG47 4.2 77.8 1.0 N9 I:DG47 4.4 77.3 1.0 N1 I:DG47 4.6 77.3 1.0 OP2 I:DG47 4.7 80.1 1.0 C6 I:DT46 4.8 85.6 1.0 N1 I:DT46 4.8 85.0 1.0 O6 I:DG48 4.9 79.5 1.0 C1' I:DT46 4.9 84.8 1.0

Manganese binding site 4 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1009 b:81.7 occ:1.00 O I:HOH1013 2.2 45.4 1.0 N7 I:DG60 2.3 74.6 1.0 C5 I:DG60 3.2 74.9 1.0 O6 I:DG60 3.2 74.7 1.0 C8 I:DG60 3.3 75.2 1.0 C6 I:DG60 3.6 74.9 1.0 C8 I:DA59 4.1 71.1 1.0 N7 I:DA59 4.2 70.9 1.0 O6 I:DG61 4.2 84.6 1.0 C4 I:DG60 4.4 74.7 1.0 N9 I:DG60 4.5 75.0 1.0 N7 I:DG61 4.9 84.6 1.0 N9 I:DA59 4.9 71.1 1.0 N1 I:DG60 5.0 74.8 1.0 OP2 I:DA59 5.0 63.9 1.0

Manganese binding site 5 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1011 b:1.0 occ:1.00 N7 I:DG26 2.1 75.7 1.0 C5 I:DG26 3.0 75.9 1.0 O6 I:DG26 3.1 75.8 1.0 C8 I:DG26 3.2 75.6 1.0 C6 I:DG26 3.4 76.0 1.0 C8 I:DA25 3.5 88.3 1.0 N7 I:DA25 3.6 88.1 1.0 N9 I:DA25 4.2 88.3 1.0 C4 I:DG26 4.2 75.9 1.0 N9 I:DG26 4.3 75.7 1.0 C5 I:DA25 4.3 88.1 1.0 O6 J:DG-27 4.6 0.5 1.0 C4 I:DA25 4.7 88.3 1.0 C2' I:DA25 4.7 87.0 1.0 N1 I:DG26 4.8 76.1 1.0 C1' I:DA25 4.9 88.0 1.0

Manganese binding site 6 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1004 b:75.1 occ:1.00 N7 J:DG60 2.5 86.0 1.0 O6 J:DG60 3.1 85.8 1.0 C5 J:DG60 3.3 86.0 1.0 C6 J:DG60 3.5 86.0 1.0 C8 J:DG60 3.5 86.1 1.0 O6 J:DG61 3.7 0.1 1.0 C8 J:DA59 4.2 71.2 1.0 N7 J:DA59 4.2 71.3 1.0 C4 J:DG60 4.5 86.0 1.0 N9 J:DG60 4.7 86.2 1.0 C6 J:DG61 4.7 0.1 1.0 N1 J:DG60 4.9 85.9 1.0

Manganese binding site 7 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1005 b:76.5 occ:1.00 N7 J:DG26 2.3 69.2 1.0 C8 J:DG26 3.3 68.8 1.0 C5 J:DG26 3.3 69.0 1.0 O6 J:DG26 3.4 68.2 1.0 C6 J:DG26 3.7 68.5 1.0 O6 I:DG-27 4.4 92.7 1.0 N9 J:DG26 4.5 68.7 1.0 C4 J:DG26 4.5 68.6 1.0 C8 J:DA25 4.6 75.0 1.0 N7 J:DA25 4.8 74.9 1.0 N4 J:DC27 4.9 69.4 1.0

Manganese binding site 8 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1006 b:0.2 occ:1.00 N7 J:DG4 2.6 72.0 1.0 O6 J:DG4 3.5 72.4 1.0 C5 J:DG4 3.5 72.1 1.0 C8 J:DG4 3.6 72.2 1.0 C6 J:DG4 3.9 72.3 1.0 O6 I:DG-5 4.2 59.8 1.0 C8 J:DA3 4.4 80.0 1.0 C2' J:DA3 4.6 81.5 1.0 C4 J:DG4 4.7 72.9 1.0 N7 J:DA3 4.7 79.8 1.0 N9 J:DG4 4.7 72.5 1.0 N4 J:DC5 4.8 78.5 1.0 N9 J:DA3 4.9 80.2 1.0

Manganese binding site 9 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1007 b:84.9 occ:1.00 O J:HOH1019 2.1 45.0 1.0 O J:HOH1015 2.3 49.9 1.0 N7 J:DG47 2.4 79.8 1.0 C5 J:DG47 3.3 79.6 1.0 C8 J:DG47 3.3 79.4 1.0 O6 J:DG47 3.4 79.5 1.0 C6 J:DG47 3.7 79.7 1.0 C2' J:DT46 4.2 85.4 1.0 O6 J:DG48 4.4 80.9 1.0 C4 J:DG47 4.5 79.3 1.0 OP2 J:DG47 4.5 78.6 1.0 N9 J:DG47 4.5 79.2 1.0 N7 J:DG48 4.8 80.6 1.0

Manganese binding site 10 out of 11 in the Nucleosome Core Particle Containing 145 Bp of Dna


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1010 b:0.5 occ:1.00 O6 J:DG-33 2.3 79.9 1.0 N7 J:DG-34 2.5 79.9 1.0 O J:HOH1012 2.7 47.9 1.0 C8 J:DG-34 3.0 80.0 1.0 C6 J:DG-33 3.1 79.9 1.0 N7 J:DG-33 3.3 80.0 1.0 C5 J:DG-33 3.5 80.1 1.0 C5 J:DG-34 3.5 80.0 1.0 N9 J:DG-34 4.1 80.0 1.0 C6 J:DG-34 4.2 80.1 1.0 O6 J:DG-34 4.2 80.1 1.0 N1 J:DG-33 4.3 80.1 1.0 C4 J:DG-34 4.3 80.1 1.0 N4 I:DC33 4.5 0.3 1.0 C8 J:DG-33 4.5 80.0 1.0 OP2 J:DG-34 4.6 82.1 1.0 O4 I:DT32 4.7 0.5 1.0 C4 J:DG-33 4.7 80.1 1.0 C2' J:DT-35 4.7 88.4 1.0 O3' J:DT-35 4.8 85.1 1.0

M.S.Ong, T.J.Richmond, C.A.Davey. Dna Stretching and Extreme Kinking in the Nucleosome Core J.Mol.Biol. V. 368 1067 2007.
ISSN: ISSN 0022-2836
PubMed: 17379244
DOI: 10.1016/J.JMB.2007.02.062