Manganese in PDB 3utb: Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)

The structure of Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B), PDB code: 3utb 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)	57.46 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.460, 109.280, 175.920, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.5

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B) (pdb code 3utb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 21 binding sites of Manganese where determined in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B), PDB code: 3utb:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:37.8 occ:1.00 O A:HOH154 2.1 34.7 1.0 O A:HOH150 2.1 30.7 1.0 OD1 A:ASP77 2.2 45.4 1.0 O A:HOH451 2.5 42.4 1.0 CG A:ASP77 3.2 42.3 1.0 OD2 A:ASP77 3.5 41.7 1.0 O A:HOH300 4.3 33.8 1.0 OE1 A:GLN76 4.3 36.7 1.0 O A:GLU73 4.4 35.1 1.0 O B:LEU22 4.4 43.4 1.0 CB A:ASP77 4.5 39.8 1.0 O A:HOH281 4.6 49.2 1.0 N A:ASP77 4.6 41.2 1.0 CA A:ASP77 4.7 41.0 1.0 CG A:GLU73 4.9 35.5 1.0 CG A:GLN76 5.0 40.3 1.0

Manganese binding site 2 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1007 b:0.5 occ:1.00 O D:VAL45 2.7 59.5 1.0 C D:VAL45 3.6 59.5 1.0 CA D:VAL45 4.1 59.5 1.0 OE1 C:GLU64 4.2 58.2 1.0 O D:GLN44 4.5 60.5 1.0 N D:HIS46 4.7 59.6 1.0 CD D:PRO47 4.8 60.1 1.0 CB D:VAL45 4.9 59.6 1.0 O3 D:SO41101 4.9 0.1 1.0 OE2 C:GLU64 5.0 60.4 1.0

Manganese binding site 3 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1002 b:94.1 occ:1.00 OD2 E:ASP81 2.3 57.2 1.0 CG E:ASP81 3.5 56.9 1.0 OD1 E:ASP81 4.2 61.2 1.0 OP1 I:DG27 4.4 70.3 1.0 CB E:ASP81 4.6 54.9 1.0 CA E:ASP81 4.6 54.5 1.0

Manganese binding site 4 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:78.0 occ:1.00 N7 I:DG-53 2.3 83.0 1.0 C8 I:DG-53 3.2 82.7 1.0 C5 I:DG-53 3.4 83.1 1.0 O6 I:DG-53 3.7 82.7 1.0 C6 I:DG-53 3.9 83.1 1.0 C6 I:DC-54 4.4 71.0 1.0 N9 I:DG-53 4.5 82.7 1.0 C4 I:DG-53 4.6 82.9 1.0 OP2 I:DC-54 4.6 72.4 1.0 C5 I:DC-54 4.6 71.2 1.0 O6 I:DG-52 4.8 96.8 1.0 C2' I:DC-54 4.8 72.8 1.0

Manganese binding site 5 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1004 b:0.6 occ:1.00 O6 I:DG69 3.3 98.4 1.0 N7 I:DG68 3.5 0.7 1.0 N7 I:DG69 3.8 98.2 1.0 C6 I:DG69 4.2 98.3 1.0 C8 I:DG68 4.3 0.6 1.0 C5 I:DG68 4.3 0.7 1.0 C5 I:DG69 4.4 98.4 1.0 O6 I:DG68 4.4 0.4 1.0 N4 J:DC-69 4.4 0.7 1.0 C6 I:DG68 4.7 0.5 1.0 O4 J:DT-70 4.9 0.3 1.0 C8 I:DG69 5.0 98.3 1.0

Manganese binding site 6 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1005 b:83.3 occ:1.00 O I:HOH563 2.1 56.7 1.0 O J:HOH564 2.4 70.8 1.0 N7 I:DG27 2.4 69.4 1.0 C8 I:DG27 3.2 68.9 1.0 C5 I:DG27 3.6 69.2 1.0 O6 I:DG27 4.0 69.6 1.0 C6 I:DG27 4.2 69.5 1.0 C6 I:DC26 4.3 76.6 1.0 C5 I:DC26 4.4 76.9 1.0 N9 I:DG27 4.5 69.1 1.0 C4 I:DG27 4.7 69.5 1.0 O6 J:DG-28 4.7 0.1 1.0 OP2 I:DC26 4.8 81.9 1.0 C2' I:DC26 5.0 75.1 1.0

Manganese binding site 7 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:83.2 occ:1.00 N7 I:DG-14 2.3 53.9 1.0 C8 I:DG-14 3.1 53.3 1.0 C5 I:DG-14 3.5 53.8 1.0 O I:HOH115 3.6 75.1 1.0 O6 I:DG-14 4.1 53.4 1.0 C6 I:DG-14 4.2 54.3 1.0 N9 I:DG-14 4.3 52.9 1.0 C4 I:DG-14 4.6 53.6 1.0 C8 I:DG-15 4.7 65.9 1.0 C2' I:DG-15 4.8 67.8 1.0 N6 I:DA-13 4.9 48.9 1.0

Manganese binding site 8 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1013 b:0.9 occ:1.00 N7 I:DG-45 2.5 91.6 1.0 C8 I:DG-45 3.3 91.4 1.0 C8 I:DA-46 3.3 0.4 1.0 C5 I:DG-45 3.6 91.4 1.0 N7 I:DA-46 3.7 0.5 1.0 O6 I:DG-45 3.9 91.2 1.0 O I:HOH561 4.0 59.9 1.0 C6 I:DG-45 4.1 91.3 1.0 N9 I:DA-46 4.2 0.4 1.0 C2' I:DA-46 4.3 0.1 1.0 N9 I:DG-45 4.5 91.2 1.0 C5 I:DA-46 4.7 0.5 1.0 C4 I:DG-45 4.7 91.5 1.0 C1' I:DA-46 4.8 0.1 1.0 C4 I:DA-46 4.9 0.6 1.0 N6 I:DA-44 5.0 81.0 1.0

Manganese binding site 9 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1014 b:0.7 occ:1.00 O J:HOH441 2.7 67.3 1.0 C5' I:DA-32 4.6 0.2 1.0 O2 I:DC-33 4.8 98.6 1.0 C4' J:DC35 4.8 0.7 1.0 O4' I:DA-32 4.8 0.5 1.0 C4' I:DA-32 4.8 0.6 1.0 C5' J:DA36 4.9 0.1 1.0 O4' J:DC35 5.0 0.5 1.0

Manganese binding site 10 out of 21 in the Crystal Structure of Nucleosome Core Particle Assembled with the 146B Alpha-Satellite Sequence (NCP146B)


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 the 146B Alpha-Satellite Sequence (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1017 b:0.6 occ:1.00 N7 I:DG5 2.9 82.9 1.0 C8 I:DG5 3.7 82.8 1.0 C5 I:DG5 4.1 83.0 1.0 C8 I:DA4 4.2 84.1 1.0 N7 I:DA4 4.3 84.3 1.0 O6 I:DG5 4.3 82.8 1.0 C6 I:DG5 4.6 82.7 1.0 N6 J:DA-6 4.7 63.8 1.0 N9 I:DG5 5.0 83.2 1.0 N9 I:DA4 5.0 83.9 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