Manganese in PDB 1kx3: X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution

The structure of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution, PDB code: 1kx3 was solved by C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.400, 181.540, 109.600, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 27.5

Pages:

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

Binding sites:

The binding sites of Manganese atom in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution (pdb code 1kx3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution, PDB code: 1kx3:
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 X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn944 b:84.0 occ:1.00 O6 I:DG-33 2.4 57.9 1.0 N7 I:DG-34 2.4 64.5 1.0 O I:HOH1031 2.4 49.2 1.0 C8 I:DG-34 3.2 62.2 1.0 C6 I:DG-33 3.2 58.8 1.0 C5 I:DG-34 3.5 64.4 1.0 C5 I:DG-33 3.8 58.4 1.0 N7 I:DG-33 3.8 56.2 1.0 O6 I:DG-34 3.9 67.7 1.0 C6 I:DG-34 4.0 65.7 1.0 N1 I:DG-33 4.3 57.5 1.0 N9 I:DG-34 4.4 63.6 1.0 N4 J:DC33 4.4 0.1 1.0 C4 I:DG-34 4.5 63.8 1.0 C2' I:DT-35 4.5 73.9 1.0 OP2 I:DG-34 4.7 63.5 1.0 O3' I:DT-35 4.8 67.7 1.0

Manganese binding site 2 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn950 b:51.2 occ:1.00 O J:HOH1024 2.1 33.6 1.0 O J:HOH983 2.3 34.3 1.0 O J:HOH1060 2.3 49.1 1.0 O4' I:DC15 4.1 50.1 1.0 O4' J:DT-12 4.2 35.7 1.0 O2 I:DT13 4.3 46.6 1.0 O J:HOH967 4.3 48.0 1.0 C4' I:DC15 4.4 51.5 1.0 C2 J:DA-13 4.4 45.0 1.0 O4' I:DG14 4.4 46.1 1.0 O2 J:DT-12 4.4 43.4 1.0 N3 J:DA-13 4.5 43.6 1.0 O I:HOH1063 4.6 44.5 1.0 C5' I:DC15 4.7 47.1 1.0 C4' J:DT-12 4.7 34.9 1.0 C1' J:DT-12 4.7 33.5 1.0 C4' I:DG14 4.9 46.5 1.0

Manganese binding site 3 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn951 b:78.5 occ:1.00 N7 I:DG48 2.5 61.8 1.0 C8 I:DG48 3.4 59.3 1.0 C5 I:DG48 3.5 62.6 1.0 O6 I:DG48 3.6 66.1 1.0 C6 I:DG48 3.9 64.1 1.0 OP2 I:DG48 3.9 72.0 1.0 C2' I:DT47 4.1 76.9 1.0 O I:HOH1003 4.5 70.9 1.0 N9 I:DG48 4.6 61.5 1.0 C4 I:DG48 4.6 62.6 1.0 O6 I:DG49 4.8 66.1 1.0 C6 I:DT47 5.0 80.0 1.0

Manganese binding site 4 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn952 b:63.2 occ:1.00 O I:HOH1060 2.3 62.0 1.0 O I:HOH990 2.4 64.3 1.0 N7 I:DG61 2.4 65.2 1.0 O I:HOH962 2.5 75.7 1.0 O6 I:DG61 3.3 56.0 1.0 C5 I:DG61 3.3 63.4 1.0 C8 I:DG61 3.4 68.0 1.0 C6 I:DG61 3.6 60.1 1.0 C8 I:DA60 3.9 64.9 1.0 N7 I:DA60 3.9 62.8 1.0 O6 I:DG62 4.4 72.6 1.0 C4 I:DG61 4.5 66.5 1.0 N9 I:DG61 4.6 69.6 1.0 N9 I:DA60 4.8 64.6 1.0 O I:HOH971 4.8 74.2 1.0 C5 I:DA60 4.9 62.0 1.0 OP2 I:DA60 4.9 54.9 1.0 N1 I:DG61 5.0 61.2 1.0

Manganese binding site 5 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn955 b:83.2 occ:1.00 O I:HOH1061 2.3 64.3 1.0 N7 I:DG27 2.3 55.7 1.0 O I:HOH1079 2.4 58.3 1.0 C8 I:DG27 3.2 53.6 1.0 C5 I:DG27 3.3 57.0 1.0 O6 I:DG27 3.5 60.1 1.0 C6 I:DG27 3.7 56.4 1.0 N9 I:DG27 4.4 53.4 1.0 C4 I:DG27 4.4 54.8 1.0 N7 I:DA26 4.5 67.4 1.0 O6 J:DG-28 4.6 83.5 1.0 C8 I:DA26 4.6 68.4 1.0 N4 I:DC28 4.7 63.3 1.0

Manganese binding site 6 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn956 b:93.1 occ:1.00 O I:HOH958 2.4 67.3 1.0 N7 I:DG65 2.5 69.8 1.0 C5 I:DG65 3.4 70.2 1.0 O6 I:DG65 3.4 68.9 1.0 C8 I:DG65 3.5 72.8 1.0 C6 I:DG65 3.8 69.6 1.0 C8 I:DG64 4.4 80.3 1.0 N6 I:DA66 4.4 52.4 1.0 N7 I:DG64 4.4 77.5 1.0 C4 I:DG65 4.6 71.8 1.0 N9 I:DG65 4.6 74.6 1.0

Manganese binding site 7 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn945 b:66.6 occ:1.00 O J:HOH1032 2.4 51.0 1.0 N7 J:DG60 2.5 66.0 1.0 O6 J:DG60 3.4 63.7 1.0 C5 J:DG60 3.4 67.6 1.0 C8 J:DG60 3.5 69.0 1.0 C6 J:DG60 3.7 67.9 1.0 O6 J:DG61 4.2 90.3 1.0 C8 J:DA59 4.2 57.4 1.0 N7 J:DA59 4.2 56.8 1.0 C4 J:DG60 4.6 69.3 1.0 N9 J:DG60 4.7 71.4 1.0 OP2 J:DA59 4.9 48.0 1.0

Manganese binding site 8 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn947 b:66.9 occ:1.00 O J:HOH1021 2.3 56.1 1.0 N7 J:DG26 2.5 61.1 1.0 C8 J:DG26 3.3 61.2 1.0 C5 J:DG26 3.6 63.4 1.0 O6 J:DG26 4.0 67.9 1.0 C6 J:DG26 4.2 63.1 1.0 N9 J:DG26 4.5 62.1 1.0 N7 J:DA25 4.6 77.3 1.0 O6 I:DG-27 4.6 90.5 1.0 C8 J:DA25 4.7 77.0 1.0 C4 J:DG26 4.7 61.3 1.0

Manganese binding site 9 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn948 b:61.6 occ:1.00 N7 J:DG-3 2.2 41.0 1.0 C8 J:DG-3 3.1 39.3 1.0 C5 J:DG-3 3.4 45.1 1.0 O6 J:DG-3 3.8 44.5 1.0 C2' J:DT-4 3.9 41.2 1.0 C6 J:DG-3 4.0 44.2 1.0 N9 J:DG-3 4.3 41.1 1.0 C6 J:DT-4 4.4 42.0 1.0 OP2 J:DG-3 4.4 32.2 1.0 N6 J:DA-2 4.4 49.1 1.0 C4 J:DG-3 4.5 44.6 1.0 O J:HOH961 4.8 49.2 1.0 N1 J:DT-4 4.8 40.3 1.0 C5 J:DT-4 4.9 42.5 1.0 C1' J:DT-4 4.9 42.2 1.0

Manganese binding site 10 out of 13 in the X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn949 b:84.5 occ:1.00 O J:HOH1023 2.3 56.5 1.0 N7 J:DG47 2.4 63.6 1.0 O6 J:DG47 3.0 61.1 1.0 C5 J:DG47 3.1 62.5 1.0 C6 J:DG47 3.4 62.6 1.0 C8 J:DG47 3.4 62.7 1.0 O6 J:DG48 3.9 75.1 1.0 OP2 J:DG47 4.1 76.1 1.0 C4 J:DG47 4.4 62.6 1.0 C2' J:DT46 4.5 80.3 1.0 N9 J:DG47 4.5 62.4 1.0 N7 J:DG48 4.7 70.9 1.0 C6 J:DG48 4.7 73.2 1.0 N1 J:DG47 4.8 62.3 1.0

C.A.Davey, D.F.Sargent, K.Luger, A.W.Maeder, T.J.Richmond. Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9 A Resolution J.Mol.Biol. V. 319 1097 2002.
ISSN: ISSN 0022-2836
PubMed: 12079350
DOI: 10.1016/S0022-2836(02)00386-8