Nickel in PDB 3mgq: Binding of Nickel Ions to the Nucleosome Core Particle

The structure of Binding of Nickel Ions to the Nucleosome Core Particle, PDB code: 3mgq was solved by K.Mohideen, R.Muhammad, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.00 / 2.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.129, 109.643, 183.109, 90.00, 90.00, 90.00
R / Rfree (%)	23.2 / 27.6

The structure of Binding of Nickel Ions to the Nucleosome Core Particle also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 47;

Binding sites:

The binding sites of Nickel atom in the Binding of Nickel Ions to the Nucleosome Core Particle (pdb code 3mgq). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 47 binding sites of Nickel where determined in the Binding of Nickel Ions to the Nucleosome Core Particle, PDB code: 3mgq:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni136 b:0.1 occ:0.35 OD2 A:ASP77 2.5 76.2 1.0 CG A:ASP77 3.4 73.0 1.0 OD1 A:ASP77 3.5 74.4 1.0 O A:GLU73 4.2 61.0 1.0 CG A:GLU73 4.7 64.7 1.0 CB A:ASP77 4.8 70.2 1.0

Nickel binding site 2 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni120 b:0.8 occ:0.33 OD1 C:ASP90 2.4 52.4 1.0 CG C:ASP90 3.3 48.6 1.0 OD2 C:ASP90 3.5 51.2 1.0 OE1 C:GLU92 4.3 49.9 1.0 OE2 C:GLU61 4.7 62.9 1.0 CB C:ASP90 4.7 46.1 1.0 CB C:GLU92 4.9 46.6 1.0 CD C:GLU92 5.0 49.0 1.0

Nickel binding site 3 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni123 b:0.2 occ:0.75 NE2 D:HIS106 2.5 63.4 1.0 OE2 D:GLU102 2.6 66.0 1.0 CE1 D:HIS106 2.7 63.6 1.0 CD D:GLU102 3.7 64.4 1.0 CD2 D:HIS106 3.7 61.5 1.0 ND1 D:HIS106 3.9 61.5 1.0 OE1 D:GLU102 4.1 65.5 1.0 CG D:HIS106 4.4 59.5 1.0 CG D:GLU102 4.9 59.8 1.0

Nickel binding site 4 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni124 b:83.4 occ:0.41 NE2 D:HIS79 2.1 76.6 1.0 CD2 D:HIS79 3.0 75.6 1.0 CE1 D:HIS79 3.1 75.8 1.0 ND1 D:HIS79 4.1 76.0 1.0 CG D:HIS79 4.2 73.4 1.0 OE2 H:GLU68 4.2 58.2 1.0 NZ G:LYS36 4.9 77.0 1.0

Nickel binding site 5 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni136 b:88.6 occ:1.00 OD1 E:ASP77 2.0 46.3 1.0 CG E:ASP77 3.1 47.6 1.0 OD2 E:ASP77 3.4 48.3 1.0 O F:LEU22 4.1 55.2 1.0 OE1 E:GLN76 4.3 50.6 1.0 CB E:ASP77 4.5 46.3 1.0 O E:GLU73 4.6 43.6 1.0 N E:ASP77 4.6 46.7 1.0 CG E:GLU73 4.7 40.7 1.0 CA E:ASP77 4.8 47.3 1.0

Nickel binding site 6 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni103 b:0.7 occ:0.09 OD2 F:ASP24 3.0 59.4 1.0 CG F:ASP24 4.0 56.2 1.0 CB F:ASP24 4.2 52.9 1.0 O F:ASP24 4.8 52.2 1.0 CB F:GLN27 4.8 50.5 1.0

Nickel binding site 7 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni120 b:82.5 occ:0.18 OD1 G:ASP90 2.2 60.9 1.0 OD2 G:ASP90 2.7 59.4 1.0 CG G:ASP90 2.8 57.2 1.0 CB G:ASP90 4.2 55.6 1.0 CB G:GLU92 4.4 57.3 1.0 OE2 G:GLU61 4.6 65.9 1.0 N G:GLU92 4.7 57.5 1.0 OE1 G:GLU92 4.8 67.0 1.0 CG G:GLU92 4.8 60.0 1.0 CA G:ASP90 4.9 55.5 1.0 CD1 G:LEU65 5.0 58.4 1.0

Nickel binding site 8 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni123 b:72.6 occ:0.34 NE2 H:HIS79 2.5 65.5 1.0 CD2 H:HIS79 3.1 64.2 1.0 CE1 H:HIS79 3.6 64.6 1.0 CG H:HIS79 4.3 63.0 1.0 ND1 H:HIS79 4.5 64.8 1.0 OH F:TYR88 4.8 50.0 1.0

Nickel binding site 9 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni124 b:0.5 occ:0.51 NE2 H:HIS106 2.0 74.7 1.0 CE1 H:HIS106 2.4 73.3 1.0 OE2 H:GLU102 3.0 71.8 1.0 CD2 H:HIS106 3.2 71.6 1.0 NZ H:LYS105 3.5 71.0 1.0 ND1 H:HIS106 3.6 73.0 1.0 CG H:HIS106 4.1 69.4 1.0 CD H:GLU102 4.2 70.4 1.0 CE H:LYS105 4.7 70.8 1.0 CG H:GLU102 4.8 65.0 1.0

Nickel binding site 10 out of 47 in the Binding of Nickel Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Binding of Nickel Ions to the Nucleosome Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni125 b:0.1 occ:0.38 ND1 H:HIS46 2.8 78.5 1.0 CE1 H:HIS46 3.3 78.3 1.0 CG H:HIS46 3.6 78.1 1.0 OD1 H:ASP48 3.8 77.3 1.0 O H:VAL45 4.0 77.3 1.0 CB H:HIS46 4.1 77.5 1.0 CA H:HIS46 4.2 77.1 1.0 NE2 H:HIS46 4.2 78.0 1.0 CD2 H:HIS46 4.3 78.3 1.0 OD2 H:ASP48 4.4 78.9 1.0 CG H:ASP48 4.5 77.4 1.0 C H:VAL45 5.0 76.9 1.0

K.Mohideen, R.Muhammad, C.A.Davey. Perturbations in Nucleosome Structure From Heavy Metal Association. Nucleic Acids Res. V. 38 6301 2010.
ISSN: ISSN 0305-1048
PubMed: 20494975
DOI: 10.1093/NAR/GKQ420