Manganese in PDB 3rej: 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)

The structure of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B), PDB code: 3rej was solved by B.Wu, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.85 / 2.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.067, 109.374, 176.465, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 26.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Manganese atom in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) (pdb code 3rej). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B), PDB code: 3rej:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:35.3 occ:1.00 OD1 A:ASP77 1.9 42.1 1.0 O A:HOH154 2.2 34.0 1.0 O A:HOH151 2.2 15.7 1.0 O A:HOH451 2.5 42.3 1.0 CG A:ASP77 3.0 42.3 1.0 OD2 A:ASP77 3.4 44.0 1.0 OE1 A:GLN76 4.2 37.7 1.0 CB A:ASP77 4.3 40.0 1.0 O A:GLU73 4.3 32.2 1.0 N A:ASP77 4.4 40.5 1.0 O B:LEU22 4.5 36.0 1.0 CA A:ASP77 4.5 40.8 1.0 O A:HOH300 4.5 34.1 1.0 O A:HOH281 4.7 47.7 1.0 CB A:GLN76 4.8 40.0 1.0 C A:GLN76 5.0 40.1 1.0

Manganese binding site 2 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1007 b:93.3 occ:1.00 O D:VAL45 2.6 63.5 1.0 C D:VAL45 3.3 63.7 1.0 CA D:VAL45 3.7 63.5 1.0 OE1 C:GLU64 4.3 53.0 1.0 N D:HIS46 4.4 64.2 1.0 CB D:VAL45 4.4 63.6 1.0 O D:GLN44 4.5 64.2 1.0 CD D:PRO47 4.7 65.1 1.0 O3 D:SO41101 4.7 53.1 1.0 CA D:HIS46 4.9 65.1 1.0 N D:VAL45 4.9 63.6 1.0

Manganese binding site 3 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1003 b:83.7 occ:1.00 N7 I:DG-53 2.1 89.4 1.0 C8 I:DG-53 3.0 89.3 1.0 C5 I:DG-53 3.2 89.3 1.0 O6 I:DG-53 3.5 89.1 1.0 C6 I:DG-53 3.7 89.1 1.0 N9 I:DG-53 4.3 89.1 1.0 C6 I:DC-54 4.3 78.0 1.0 C4 I:DG-53 4.3 89.2 1.0 C5 I:DC-54 4.4 78.1 1.0 OP2 I:DC-54 4.4 76.8 1.0 O6 I:DG-52 4.8 0.6 1.0 C2' I:DC-54 5.0 78.2 1.0

Manganese binding site 4 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1004 b:0.9 occ:1.00 N7 I:DG68 2.6 0.7 1.0 O6 I:DG69 3.3 95.7 1.0 C8 I:DG68 3.3 0.5 1.0 N7 I:DG69 3.5 95.8 1.0 C5 I:DG68 3.7 0.6 1.0 C6 I:DG69 4.0 95.7 1.0 C5 I:DG69 4.1 95.8 1.0 O6 I:DG68 4.1 0.3 1.0 C6 I:DG68 4.2 0.4 1.0 N9 I:DG68 4.5 0.4 1.0 C8 I:DG69 4.6 95.7 1.0 C4 I:DG68 4.7 0.5 1.0 N4 J:DC-69 4.8 1.0 1.0

Manganese binding site 5 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1005 b:96.2 occ:1.00 N7 I:DG27 2.3 74.9 1.0 C8 I:DG27 3.2 74.5 1.0 C5 I:DG27 3.3 74.8 1.0 O6 I:DG27 3.5 74.5 1.0 C6 I:DG27 3.8 75.0 1.0 C6 I:DC26 4.3 79.9 1.0 C5 I:DC26 4.3 79.8 1.0 N9 I:DG27 4.4 74.5 1.0 O6 J:DG-28 4.5 0.2 1.0 C4 I:DG27 4.5 74.6 1.0 OP2 I:DC26 4.8 86.9 1.0

Manganese binding site 6 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn1006 b:85.5 occ:1.00 N7 I:DG-14 2.2 56.7 1.0 C8 I:DG-14 3.0 56.5 1.0 C5 I:DG-14 3.3 57.3 1.0 O I:HOH115 3.8 56.1 1.0 O6 I:DG-14 3.8 57.3 1.0 C6 I:DG-14 3.9 57.4 1.0 N9 I:DG-14 4.3 56.3 1.0 C8 I:DG-15 4.4 69.6 1.0 C4 I:DG-14 4.4 57.0 1.0 C2' I:DG-15 4.5 70.5 1.0 N9 I:DG-15 4.8 70.1 1.0 N7 I:DG-15 4.8 69.2 1.0 OP2 I:DG-14 4.9 69.5 1.0 N6 I:DA-13 4.9 53.6 1.0

Manganese binding site 7 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1002 b:0.6 occ:1.00 OP2 J:DT66 3.7 90.3 1.0 C3' J:DT65 4.7 91.8 1.0 C2' J:DT65 4.7 91.5 1.0 OP1 J:DT65 5.0 98.2 1.0

Manganese binding site 8 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1008 b:0.5 occ:1.00 O I:HOH77 2.3 77.5 1.0 O J:HOH78 2.6 76.8 1.0 O4' J:DA-2 3.5 72.4 1.0 C4' J:DA-2 3.8 72.6 1.0 N2 J:DG-3 4.1 68.6 1.0 N3 I:DA4 4.2 85.0 1.0 C5' J:DA-2 4.2 70.8 1.0 N3 J:DG-3 4.3 68.9 1.0 C2 I:DA4 4.4 85.0 1.0 C1' J:DA-2 4.6 72.8 1.0 C2 J:DG-3 4.7 69.0 1.0 O4' I:DG5 4.8 87.5 1.0 C4' I:DG5 5.0 87.5 1.0

Manganese binding site 9 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1009 b:0.3 occ:1.00 N7 J:DG60 3.0 0.1 1.0 O6 J:DG60 3.3 0.2 1.0 C5 J:DG60 3.8 0.3 1.0 C6 J:DG60 3.9 0.2 1.0 N7 J:DG59 4.0 0.1 1.0 C8 J:DG59 4.0 0.0 1.0 C8 J:DG60 4.1 0.0 1.0 C5 J:DG59 4.7 0.1 1.0 N6 J:DA61 4.8 0.8 1.0 N9 J:DG59 4.8 0.9 1.0

Manganese binding site 10 out of 13 in the 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of 2.55 Angstrom Crystal Structure of the Nucleosome Core Particle Assembled with A 146 Bp Alpha-Satellite Dna (NCP146B) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn1010 b:0.3 occ:1.00 O6 J:DG-54 2.8 0.1 1.0 C5 J:DC-55 3.2 93.2 1.0 N7 J:DG-54 3.2 0.1 1.0 C6 J:DG-54 3.5 0.0 1.0 C6 J:DC-55 3.6 93.0 1.0 C5 J:DG-54 3.7 0.1 1.0 C4 J:DC-55 3.9 92.9 1.0 N4 J:DC-55 4.2 93.2 1.0 O6 J:DG-53 4.4 0.8 1.0 C8 J:DG-54 4.4 0.0 1.0 O J:HOH454 4.5 45.5 1.0 N1 J:DC-55 4.6 92.8 1.0 N4 I:DC53 4.8 0.1 1.0 N3 J:DC-55 4.8 92.9 1.0 N1 J:DG-54 4.9 0.3 1.0

B.Wu, G.E.Davey, A.A.Nazarov, P.J.Dyson, C.A.Davey. Specific Dna Structural Attributes Modulate Platinum Anticancer Drug Site Selection and Cross-Link Generation. Nucleic Acids Res. V. 39 8200 2011.
ISSN: ISSN 0305-1048
PubMed: 21724603
DOI: 10.1093/NAR/GKR491