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Potassium in PDB 6k1i: Human Nucleosome Core Particle with GAMMAH2A.X Variant

Protein crystallography data

The structure of Human Nucleosome Core Particle with GAMMAH2A.X Variant, PDB code: 6k1i 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) 93.70 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 102.850, 109.420, 181.470, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 27.7

Other elements in 6k1i:

The structure of Human Nucleosome Core Particle with GAMMAH2A.X Variant also contains other interesting chemical elements:

Manganese (Mn) 23 atoms
Chlorine (Cl) 2 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Human Nucleosome Core Particle with GAMMAH2A.X Variant (pdb code 6k1i). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Human Nucleosome Core Particle with GAMMAH2A.X Variant, PDB code: 6k1i:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 6k1i

Go back to Potassium Binding Sites List in 6k1i
Potassium binding site 1 out of 2 in the Human Nucleosome Core Particle with GAMMAH2A.X Variant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human Nucleosome Core Particle with GAMMAH2A.X Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K110

b:0.7
occ:1.00
O2 I:DT-26 2.9 0.0 1.0
O4' J:DA28 3.7 0.4 1.0
O4' I:DA-25 3.8 0.0 1.0
C2 I:DT-26 4.1 0.3 1.0
C4' I:DA-25 4.1 0.3 1.0
C4' J:DA28 4.1 95.2 1.0
C2 J:DA26 4.3 0.2 1.0
N2 J:DG27 4.4 0.8 1.0
C5' J:DA28 4.6 89.9 1.0
N3 J:DG27 4.6 0.1 1.0
C5' I:DA-25 4.6 0.9 1.0
N3 I:DT-26 4.8 0.3 1.0
N3 J:DA26 4.8 0.2 1.0
C1' I:DA-25 4.8 0.4 1.0
C1' J:DA28 4.9 0.2 1.0
N3 I:DA-25 4.9 0.3 1.0
O4' I:DG-24 4.9 94.1 1.0

Potassium binding site 2 out of 2 in 6k1i

Go back to Potassium Binding Sites List in 6k1i
Potassium binding site 2 out of 2 in the Human Nucleosome Core Particle with GAMMAH2A.X Variant


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Human Nucleosome Core Particle with GAMMAH2A.X Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:K114

b:0.3
occ:1.00
O2 J:DT-26 3.4 96.8 1.0
O4' J:DA-25 3.6 74.4 1.0
C4' J:DA-25 3.9 72.5 1.0
O4' I:DA28 4.1 80.9 1.0
C4' I:DA28 4.3 81.2 1.0
C2 I:DA26 4.4 0.4 1.0
N3 J:DA-25 4.4 92.1 1.0
C2 J:DT-26 4.5 90.7 1.0
C5' I:DA28 4.5 83.0 1.0
O4' J:DG-24 4.5 72.4 1.0
C5' J:DA-25 4.6 75.5 1.0
C1' J:DA-25 4.6 81.5 1.0
C5' J:DG-24 4.7 74.8 1.0
N3 I:DA26 4.8 98.8 1.0
N2 I:DG27 4.9 0.7 1.0
C4' J:DG-24 5.0 73.3 1.0

Reference:

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
Page generated: Mon Dec 14 00:44:15 2020

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