Manganese in PDB 6ipu: Human Nucleosome Core Particle Containing 145 Bp of Dna

The structure of Human Nucleosome Core Particle Containing 145 Bp of Dna, PDB code: 6ipu was solved by L.Defalco, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.16 / 1.99
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.560, 109.710, 183.480, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 26.3

The structure of Human Nucleosome Core Particle Containing 145 Bp of Dna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

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

Manganese binding site 1 out of 5 in the Human 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 Human Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:55.0 occ:1.00 O D:HOH301 2.1 35.0 1.0 O D:HOH308 2.1 36.8 1.0 O D:VAL45 2.1 37.8 1.0 C D:VAL45 3.1 33.6 1.0 CA D:VAL45 3.6 36.6 1.0 OE2 C:GLU64 4.0 48.2 1.0 O D:HOH302 4.1 37.7 1.0 O D:GLN44 4.2 37.1 1.0 N D:HIS46 4.2 35.0 1.0 CB D:VAL45 4.4 37.6 1.0 CD D:PRO47 4.7 42.1 1.0 CA D:HIS46 4.7 36.7 1.0 ND1 D:HIS46 4.7 38.6 1.0 N D:VAL45 4.7 37.8 1.0 OE1 C:GLU64 4.9 57.3 1.0 CD C:GLU64 4.9 45.5 1.0 C D:GLN44 4.9 42.6 1.0

Manganese binding site 2 out of 5 in the Human 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 Human Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:84.2 occ:1.00 N7 I:DG60 3.2 0.9 1.0 O6 I:DG60 3.9 94.0 1.0 C8 I:DG60 4.1 0.1 1.0 C5 I:DG60 4.1 95.3 1.0 N7 I:DA59 4.3 89.6 1.0 C6 I:DG60 4.4 89.2 1.0 C8 I:DA59 4.6 92.5 1.0 O6 I:DG61 4.9 89.7 1.0 N4 J:DC-61 4.9 82.3 1.0

Manganese binding site 3 out of 5 in the Human 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 Human Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:81.2 occ:1.00 N7 I:DG29 3.3 99.4 1.0 N7 I:DA28 3.7 86.5 1.0 O6 I:DG29 3.8 86.5 1.0 C8 I:DA28 4.0 86.2 1.0 C5 I:DG29 4.2 97.2 1.0 C6 I:DG29 4.3 95.4 1.0 C8 I:DG29 4.4 99.6 1.0 C5 I:DA28 4.5 89.4 1.0 O4 I:DT30 4.7 0.3 1.0 N9 I:DA28 4.8 86.5 1.0

Manganese binding site 4 out of 5 in the Human 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 Human Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn101 b:81.5 occ:1.00 O2 J:DT-11 3.9 74.7 1.0 O2 I:DT12 4.0 70.1 1.0 O4' I:DG13 4.6 83.7 1.0 O4' J:DG-10 4.7 86.2 1.0 C1' J:DT-11 4.8 77.0 1.0 C2 J:DT-11 4.9 75.8 1.0 C4' I:DG13 4.9 82.6 1.0

Manganese binding site 5 out of 5 in the Human 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 Human Nucleosome Core Particle Containing 145 Bp of Dna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn102 b:80.7 occ:1.00 C4' I:DT66 4.0 0.8 1.0 C5' I:DT66 4.2 0.9 1.0 O4' I:DT66 4.2 0.7 1.0 O2 J:DC-64 4.4 81.1 1.0 O4' J:DC-63 4.6 81.3 1.0 C5' J:DC-63 4.7 85.2 1.0 C4' J:DC-63 4.7 85.3 1.0 N3 I:DA65 4.8 76.5 1.0 O4' J:DC-64 4.9 87.8 1.0

D.Sharma, L.De Falco, S.Padavattan, C.Rao, S.Geifman-Shochat, C.F.Liu, C.A.Davey. PARP1 Exhibits Enhanced Association and Catalytic Efficiency with Gamma H2A.X-Nucleosome. Nat Commun V. 10 5751 2019.
ISSN: ESSN 2041-1723
PubMed: 31848352
DOI: 10.1038/S41467-019-13641-0