Manganese in PDB 6k1k: Human Nucleosome Core Particle with H2A.X S139E Variant

The structure of Human Nucleosome Core Particle with H2A.X S139E Variant, PDB code: 6k1k was solved by D.Sharma, L.De Falco, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.20 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.950, 109.460, 183.380, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.5

The structure of Human Nucleosome Core Particle with H2A.X S139E Variant 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 - 30; Page 4, Binding sites: 31 - 33;

Binding sites:

The binding sites of Manganese atom in the Human Nucleosome Core Particle with H2A.X S139E Variant (pdb code 6k1k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 33 binding sites of Manganese where determined in the Human Nucleosome Core Particle with H2A.X S139E Variant, PDB code: 6k1k:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


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 with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ H:Mn201 b:35.4 occ:1.00 O H:HOH306 1.9 31.8 1.0 O H:VAL45 2.2 38.2 1.0 C H:VAL45 3.2 31.6 1.0 CA H:VAL45 3.7 32.5 1.0 OE1 G:GLU64 4.0 40.2 1.0 O H:HOH303 4.3 50.3 1.0 N H:HIS46 4.3 33.0 1.0 CB H:VAL45 4.5 37.6 1.0 O H:GLN44 4.5 47.4 1.0 ND1 H:HIS46 4.7 39.8 1.0 CA H:HIS46 4.7 36.2 1.0 CD H:PRO47 4.9 38.5 1.0 N H:VAL45 4.9 36.3 1.0 CD G:GLU64 4.9 43.4 1.0 CE1 H:HIS46 5.0 35.6 1.0

Manganese binding site 2 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


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 with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn101 b:0.4 occ:1.00 N7 I:DG62 2.4 0.3 1.0 C8 I:DG62 3.1 0.1 1.0 C5 I:DG62 3.6 98.9 1.0 O6 I:DG63 3.8 96.1 1.0 O6 I:DG62 4.3 87.5 1.0 OP2 I:DG62 4.3 73.4 1.0 C6 I:DG62 4.3 92.8 1.0 N9 I:DG62 4.3 97.0 1.0 N7 I:DG63 4.5 0.0 1.0 C2' I:DC61 4.6 87.4 1.0 C4 I:DG62 4.6 0.1 1.0 C6 I:DG63 4.7 94.0 1.0 C6 I:DC61 4.9 82.8 1.0 C5 I:DG63 4.9 0.9 1.0

Manganese binding site 3 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


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 with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn102 b:89.9 occ:1.00 N7 I:DG50 2.5 91.6 1.0 C8 I:DG50 3.4 80.0 1.0 C5 I:DG50 3.5 81.3 1.0 O6 I:DG50 3.7 77.5 1.0 C6 I:DG50 4.0 81.0 1.0 O6 I:DG51 4.1 97.2 1.0 N9 I:DG50 4.6 77.8 1.0 C4 I:DG50 4.7 87.5 1.0 OP2 I:DG50 4.7 58.4 1.0 C5 I:DC49 4.8 72.8 1.0 N4 J:DC-51 5.0 87.1 1.0 C6 I:DC49 5.0 72.8 1.0

Manganese binding site 4 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


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 with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn103 b:0.7 occ:1.00 O6 I:DG29 3.5 72.6 1.0 N7 I:DA28 4.1 88.2 1.0 N7 I:DG29 4.1 84.0 1.0 C6 I:DG29 4.4 82.4 1.0 C8 I:DA28 4.6 80.1 1.0 O6 J:DG-30 4.6 0.7 1.0 C5 I:DG29 4.6 89.2 1.0 N4 I:DC30 4.7 92.3 1.0

Manganese binding site 5 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


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 with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn104 b:0.8 occ:1.00 N7 I:DG20 2.8 0.1 1.0 C8 I:DG20 3.6 0.1 1.0 C5 I:DG20 3.7 0.3 1.0 O6 I:DG20 3.9 0.5 1.0 C6 I:DG20 4.1 0.8 1.0 O6 I:DG21 4.2 0.3 1.0 N7 I:DG21 4.4 0.1 1.0 C5 I:DC19 4.7 82.8 1.0 N9 I:DG20 4.7 0.5 1.0 C4 I:DG20 4.8 0.5 1.0 C6 I:DC19 4.8 86.6 1.0 C6 I:DG21 5.0 0.2 1.0

Manganese binding site 6 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Nucleosome Core Particle with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn105 b:80.2 occ:1.00 N7 I:DG-3 2.4 61.1 1.0 C8 I:DG-3 3.3 65.1 1.0 C5 I:DG-3 3.5 70.3 1.0 O6 I:DG-3 3.8 74.3 1.0 O6 I:DG-2 3.9 71.9 1.0 C6 I:DG-3 4.0 67.6 1.0 N9 I:DG-3 4.5 67.5 1.0 C4 I:DG-3 4.6 71.1 1.0 C6 I:DG-2 4.7 79.2 1.0 C6 I:DC-4 4.8 64.9 1.0 N7 I:DG-2 4.9 70.9 1.0 C5 I:DC-4 4.9 65.8 1.0 C2' I:DC-4 4.9 60.2 1.0

Manganese binding site 7 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Nucleosome Core Particle with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn106 b:0.7 occ:1.00 N7 I:DG-34 2.6 83.9 1.0 C8 I:DG-34 3.6 91.6 1.0 C5 I:DG-34 3.6 89.1 1.0 O6 I:DG-34 3.6 86.0 1.0 C6 I:DG-34 4.0 89.3 1.0 C8 I:DA-35 4.5 0.8 1.0 N7 I:DA-35 4.6 97.4 1.0 N9 I:DG-34 4.8 84.0 1.0 C4 I:DG-34 4.8 83.5 1.0 O4 J:DT33 4.9 0.5 1.0 N6 I:DA-33 5.0 0.1 1.0

Manganese binding site 8 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Human Nucleosome Core Particle with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn107 b:0.5 occ:1.00 N7 I:DG-53 2.7 76.8 1.0 C8 I:DG-53 3.5 72.6 1.0 C5 I:DG-53 3.8 78.2 1.0 O6 I:DG-53 4.0 80.9 1.0 C6 I:DG-53 4.3 84.9 1.0 O6 I:DG-52 4.4 80.8 1.0 N7 I:DA-54 4.6 76.3 1.0 C8 I:DA-54 4.7 83.4 1.0 N9 I:DG-53 4.7 67.1 1.0 C4 I:DG-53 4.9 75.9 1.0

Manganese binding site 9 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Human Nucleosome Core Particle with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn108 b:93.4 occ:1.00 N7 I:DG-61 2.2 95.9 1.0 C8 I:DG-61 3.1 90.6 1.0 C5 I:DG-61 3.3 91.3 1.0 O6 I:DG-61 3.6 80.3 1.0 C6 I:DG-61 3.8 89.1 1.0 N9 I:DG-61 4.3 95.7 1.0 C4 I:DG-61 4.4 89.8 1.0 OP2 I:DG-61 4.8 0.1 1.0 N7 I:DG-60 4.9 0.2 1.0 C6 I:DC-62 4.9 66.6 1.0 C5 I:DC-62 4.9 64.2 1.0 O6 I:DG-60 5.0 0.3 1.0

Manganese binding site 10 out of 33 in the Human Nucleosome Core Particle with H2A.X S139E Variant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Human Nucleosome Core Particle with H2A.X S139E Variant within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn109 b:0.9 occ:1.00 O4' I:DA36 3.8 0.9 1.0 C4' I:DA36 3.9 1.0 1.0 C5' I:DA36 4.2 0.5 1.0 O4' J:DA-33 4.3 95.6 1.0 O4' I:DT35 4.7 0.6 1.0 C4' J:DA-33 4.8 0.9 1.0 N3 J:DA-33 4.8 1.0 1.0 C4' I:DT35 4.9 0.8 1.0 O2 I:DT35 5.0 0.3 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