Manganese in PDB 3uta: Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)

The structure of Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2), PDB code: 3uta 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)	94.13 / 2.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.510, 109.910, 182.330, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 26.6

The structure of Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) (pdb code 3uta). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 17 binding sites of Manganese where determined in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2), PDB code: 3uta:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1001 b:30.9 occ:1.00 O E:HOH136 1.7 27.8 1.0 O E:HOH138 1.8 22.4 1.0 O F:HOH103 2.0 26.8 1.0 OD1 E:ASP77 2.0 35.0 1.0 O E:HOH137 2.2 38.2 1.0 CG E:ASP77 2.9 38.2 1.0 OD2 E:ASP77 3.1 36.9 1.0 O E:HOH140 4.2 38.8 1.0 OE1 E:GLN76 4.2 38.4 1.0 O E:HOH139 4.3 49.6 1.0 CB E:ASP77 4.3 38.2 1.0 O F:LEU22 4.4 41.5 1.0 O E:GLU73 4.5 34.8 1.0 N E:ASP77 4.6 37.5 1.0 CA E:ASP77 4.7 38.8 1.0 CG E:GLU73 4.8 35.0 1.0 O E:HOH141 4.9 45.2 1.0 CB E:GLN76 5.0 37.4 1.0

Manganese binding site 2 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn1016 b:0.9 occ:1.00 NE2 F:HIS18 2.3 87.7 1.0 CE1 F:HIS18 3.0 86.9 1.0 CD2 F:HIS18 3.2 86.9 1.0 ND1 F:HIS18 4.0 86.4 1.0 CG F:HIS18 4.1 85.0 1.0

Manganese binding site 3 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:0.4 occ:1.00 O6 I:DG-33 2.7 89.4 1.0 N7 I:DG-34 2.8 88.0 1.0 C8 I:DG-34 3.4 87.5 1.0 C6 I:DG-33 3.5 89.1 1.0 N7 I:DG-33 3.7 88.0 1.0 C5 I:DG-34 3.8 87.8 1.0 C5 I:DG-33 3.8 88.8 1.0 O6 I:DG-34 4.4 88.2 1.0 C6 I:DG-34 4.5 88.0 1.0 N9 I:DG-34 4.5 86.8 1.0 O4 J:DT32 4.6 0.6 1.0 OP2 I:DG-34 4.7 88.2 1.0 N1 I:DG-33 4.7 88.9 1.0 N4 J:DC33 4.7 0.4 1.0 C4 I:DG-34 4.8 87.4 1.0 C8 I:DG-33 4.8 88.2 1.0

Manganese binding site 4 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:0.9 occ:1.00 N7 J:DG4 3.2 85.0 1.0 O6 I:DG-5 3.4 68.9 1.0 O6 J:DG4 3.5 84.2 1.0 C5 J:DG4 4.0 84.9 1.0 C6 J:DG4 4.1 84.6 1.0 C8 J:DG4 4.3 85.3 1.0 C6 I:DG-5 4.4 68.5 1.0 N4 J:DC5 4.5 86.0 1.0 C8 J:DA3 4.7 89.9 1.0 C2' J:DA3 5.0 91.6 1.0

Manganese binding site 5 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1007 b:0.2 occ:1.00 N7 I:DG-2 2.3 61.1 1.0 C8 I:DG-2 3.0 61.5 1.0 C5 I:DG-2 3.5 61.1 1.0 O6 I:DG-2 4.0 60.2 1.0 C6 I:DG-2 4.1 61.2 1.0 N9 I:DG-2 4.2 61.8 1.0 N6 I:DA-1 4.3 63.3 1.0 C4 I:DG-2 4.5 62.0 1.0 C2' I:DT-3 4.8 52.8 1.0 N7 I:DA-1 4.9 65.7 1.0 C6 I:DT-3 4.9 55.8 1.0

Manganese binding site 6 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1008 b:81.8 occ:1.00 N7 I:DG47 2.2 86.9 1.0 C8 I:DG47 3.1 86.3 1.0 C5 I:DG47 3.4 86.4 1.0 OP2 I:DG47 3.6 91.9 1.0 O6 I:DG47 3.7 87.7 1.0 C6 I:DG47 3.9 86.9 1.0 O6 I:DG48 4.3 74.1 1.0 N9 I:DG47 4.4 85.5 1.0 C4 I:DG47 4.5 85.9 1.0 C3' I:DT46 4.6 96.4 1.0 C2' I:DT46 4.6 97.0 1.0 P I:DG47 4.9 92.1 1.0

Manganese binding site 7 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1010 b:72.3 occ:1.00 N7 I:DG60 2.4 81.3 1.0 C8 I:DG60 3.4 81.6 1.0 C5 I:DG60 3.5 81.2 1.0 O6 I:DG60 3.6 80.6 1.0 C6 I:DG60 3.9 80.8 1.0 N7 I:DA59 4.1 73.8 1.0 C8 I:DA59 4.1 74.3 1.0 O6 I:DG61 4.6 88.7 1.0 N9 I:DG60 4.6 82.0 1.0 C4 I:DG60 4.7 81.5 1.0

Manganese binding site 8 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1011 b:0.3 occ:1.00 N7 I:DG64 2.5 93.5 1.0 O6 I:DG64 2.9 92.8 1.0 C8 I:DG63 3.2 98.7 1.0 C5 I:DG64 3.3 93.3 1.0 N7 I:DG63 3.3 98.1 1.0 C6 I:DG64 3.4 92.9 1.0 C8 I:DG64 3.7 94.2 1.0 N9 I:DG63 4.1 99.2 1.0 C5 I:DG63 4.1 97.9 1.0 C2' I:DG63 4.5 0.8 1.0 OP2 I:DG63 4.5 0.7 1.0 C4 I:DG63 4.5 98.5 1.0 C4 I:DG64 4.5 93.7 1.0 N9 I:DG64 4.7 94.7 1.0 N1 I:DG64 4.8 91.8 1.0 C1' I:DG63 4.8 0.1 1.0

Manganese binding site 9 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1014 b:0.5 occ:1.00 N7 I:DG7 2.5 49.1 1.0 C8 I:DG7 3.3 48.4 1.0 C5 I:DG7 3.6 50.2 1.0 C2' I:DT6 3.9 58.6 1.0 O6 I:DG7 3.9 53.8 1.0 C6 I:DT6 3.9 62.1 1.0 C6 I:DG7 4.2 51.2 1.0 C7 I:DT6 4.3 63.1 1.0 C5 I:DT6 4.4 62.8 1.0 OP2 I:DT6 4.4 70.3 1.0 N9 I:DG7 4.6 47.9 1.0 N1 I:DT6 4.6 61.2 1.0 C4 I:DG7 4.7 48.0 1.0 C1' I:DT6 4.8 59.1 1.0

Manganese binding site 10 out of 17 in the Crystal Structure of Nucleosome Core Particle Assembled with An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2)


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 An Alpha- Satellite Sequence Containing Two Ttaaa Elements (Ncp-TA2) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1017 b:96.5 occ:1.00 C5' I:DT66 4.0 88.5 1.0 O4' I:DT66 4.2 84.6 1.0 C4' I:DT66 4.3 85.9 1.0 O4' J:DC-63 4.3 76.0 1.0 O2 J:DC-64 4.4 78.2 1.0 N3 I:DA65 4.4 86.1 1.0 C5' J:DC-63 4.6 77.3 1.0 C4' J:DC-63 4.6 76.6 1.0 O5' I:DT66 4.7 91.1 1.0 C1' J:DC-64 4.7 76.8 1.0 C2 I:DA65 4.8 85.5 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