Manganese in PDB 3ut9: Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)

The structure of Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L), PDB code: 3ut9 was solved by E.Y.D.Chua, D.Vasudevan, G.E.Davey, B.Wu, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.55 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.494, 109.533, 174.822, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 28.9

The structure of Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) also contains other interesting chemical elements:

Potassium	(K)	2 atoms
Chlorine	(Cl)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 29;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) (pdb code 3ut9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 29 binding sites of Manganese where determined in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L), PDB code: 3ut9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1001 b:45.6 occ:1.00 O E:HOH150 1.8 32.4 1.0 O E:HOH146 1.8 33.6 1.0 O F:HOH115 2.1 21.8 1.0 OD1 E:ASP77 2.2 50.6 1.0 O E:HOH145 2.6 54.4 1.0 CG E:ASP77 2.9 50.7 1.0 OD2 E:ASP77 3.0 48.9 1.0 O E:HOH154 3.6 61.3 1.0 CB E:ASP77 4.2 52.4 1.0 O E:GLU73 4.4 50.9 1.0 CA E:ASP77 4.6 53.2 1.0 O F:HOH110 4.6 44.6 1.0 N E:ASP77 4.6 53.8 1.0 CG E:GLN76 4.6 54.7 1.0 OE1 E:GLN76 4.7 55.3 1.0 O F:LEU22 4.7 57.9 1.0 CB E:GLN76 5.0 54.2 1.0 CG E:GLU73 5.0 47.5 1.0

Manganese binding site 2 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:90.1 occ:1.00 N7 I:DG-61 2.3 0.6 1.0 C8 I:DG-61 3.1 0.8 1.0 C5 I:DG-61 3.5 0.8 1.0 OP2 I:DG-61 3.8 98.5 1.0 O6 I:DG-61 3.9 0.5 1.0 C6 I:DG-61 4.1 0.6 1.0 N9 I:DG-61 4.3 0.0 1.0 C4 I:DG-61 4.5 0.0 1.0 O6 I:DG-60 4.5 0.9 1.0 C5 I:DC-62 4.7 0.8 1.0 C6 I:DC-62 4.8 0.5 1.0

Manganese binding site 3 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1005 b:0.0 occ:1.00 N7 I:DG-3 2.4 96.9 1.0 O6 I:DG-3 3.4 97.4 1.0 C5 I:DG-3 3.4 97.3 1.0 O6 I:DG-2 3.4 0.9 1.0 C8 I:DG-3 3.5 96.8 1.0 C6 I:DG-3 3.7 97.5 1.0 C6 I:DG-2 4.3 1.0 1.0 N4 J:DC2 4.5 0.9 1.0 C4 I:DG-3 4.6 97.2 1.0 N7 I:DG-2 4.6 0.9 1.0 N9 I:DG-3 4.6 96.6 1.0 C6 I:DC-4 4.7 91.4 1.0 C2' I:DC-4 4.7 90.9 1.0 C5 I:DG-2 4.8 0.0 1.0 C5 I:DC-4 4.8 91.7 1.0

Manganese binding site 4 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:0.4 occ:1.00 N7 I:DG38 2.6 0.7 1.0 C8 I:DG38 3.4 0.5 1.0 C5 I:DG38 3.8 0.7 1.0 C2' I:DC37 3.9 0.7 1.0 C6 I:DC37 4.0 0.8 1.0 O6 I:DG38 4.0 99.9 1.0 C6 I:DG38 4.3 0.5 1.0 C5 I:DC37 4.4 0.0 1.0 N1 I:DC37 4.4 0.3 1.0 N9 I:DG38 4.7 0.1 1.0 C1' I:DC37 4.7 0.6 1.0 C4 I:DG38 4.9 0.5 1.0

Manganese binding site 5 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1007 b:0.6 occ:1.00 O I:HOH134 2.3 69.0 1.0 N7 I:DG50 2.5 0.3 1.0 C8 I:DG50 3.2 0.1 1.0 C5 I:DG50 3.5 0.1 1.0 O6 I:DG51 3.7 0.3 1.0 O6 I:DG50 3.9 0.4 1.0 C6 I:DG50 4.0 1.0 1.0 N9 I:DG50 4.4 0.6 1.0 N7 I:DG51 4.4 0.5 1.0 C4 I:DG50 4.5 0.1 1.0 C6 I:DG51 4.6 0.2 1.0 N4 J:DC-51 4.7 0.2 1.0 OP2 I:DG50 4.8 1.0 1.0 O6 J:DG-52 4.8 0.9 1.0 C5 I:DG51 4.9 0.3 1.0

Manganese binding site 6 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1011 b:0.3 occ:1.00 N7 I:DG-34 2.8 0.2 1.0 C8 I:DG-34 3.6 0.1 1.0 C5 I:DG-34 3.8 0.1 1.0 O6 I:DG-34 4.0 0.7 1.0 C8 I:DA-35 4.1 0.1 1.0 N7 I:DA-35 4.2 0.3 1.0 C6 I:DG-34 4.3 0.2 1.0 OP2 I:DA-35 4.7 0.0 1.0 N9 I:DG-34 4.9 0.8 1.0 C4 I:DG-34 5.0 0.1 1.0

Manganese binding site 7 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1013 b:0.9 occ:1.00 O6 I:DG29 3.2 87.1 1.0 N7 I:DG29 3.9 87.5 1.0 O6 J:DG-30 4.1 0.9 1.0 C6 I:DG29 4.1 87.6 1.0 N7 I:DA28 4.2 78.5 1.0 N4 I:DC30 4.3 97.0 1.0 C5 I:DG29 4.3 87.5 1.0 N6 I:DA28 4.9 78.4 1.0 N4 J:DC-29 4.9 0.1 1.0 C8 I:DA28 4.9 78.1 1.0

Manganese binding site 8 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1014 b:0.7 occ:1.00 N7 I:DG-49 3.5 0.7 1.0 O6 I:DG-49 4.2 0.1 1.0 C8 I:DG-49 4.4 0.6 1.0 C5 I:DG-49 4.5 0.7 1.0 O6 J:DG48 4.7 89.2 1.0 C6 I:DG-49 4.7 0.4 1.0 C5 I:DC-50 5.0 0.9 1.0

Manganese binding site 9 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1016 b:0.2 occ:1.00 N7 I:DG-53 2.6 77.1 1.0 C8 I:DG-53 3.4 76.5 1.0 C5 I:DG-53 3.8 76.8 1.0 O6 I:DG-53 4.1 77.6 1.0 C6 I:DG-53 4.4 77.1 1.0 C8 I:DA-54 4.4 69.4 1.0 N7 I:DA-54 4.4 70.2 1.0 O6 I:DG-52 4.5 97.7 1.0 N9 I:DG-53 4.7 76.4 1.0 C4 I:DG-53 4.9 76.6 1.0

Manganese binding site 10 out of 29 in the Crystal Structure of Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L)


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 Nucleosome Core Particle Assembled with A Palindromic Widom '601' Derivative (Ncp-601L) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1018 b:0.9 occ:1.00 N7 I:DG27 2.7 79.0 1.0 C8 I:DG27 3.6 77.7 1.0 C5 I:DG27 3.7 79.1 1.0 O6 I:DG27 3.8 77.8 1.0 C6 I:DG27 4.1 78.8 1.0 C8 I:DA26 4.2 84.7 1.0 N7 I:DA26 4.4 85.0 1.0 OP2 I:DA26 4.5 84.6 1.0 O4 J:DT-28 4.8 1.0 1.0 N9 I:DG27 4.8 77.3 1.0 C4 I:DG27 4.9 78.3 1.0

E.Y.D.Chua, D.Vasudevan, G.E.Davey, B.Wu, C.A.Davey. The Mechanics Behind Dna Sequence-Dependent Properties of the Nucleosome Nucleic Acids Res. V. 40 6338 2012.
ISSN: ISSN 0305-1048
PubMed: 22453276
DOI: 10.1093/NAR/GKS261