Manganese in PDB 1id3: Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions

The structure of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions, PDB code: 1id3 was solved by C.L.White, R.K.Suto, K.Luger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.922, 110.398, 192.617, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 29.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions (pdb code 1id3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 17 binding sites of Manganese where determined in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions, PDB code: 1id3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn147 b:56.7 occ:1.00 N7 I:DG134 2.7 0.2 1.0 O6 I:DG134 3.0 0.2 1.0 C5 I:DG134 3.4 0.2 1.0 N7 I:DA133 3.5 97.1 1.0 C6 I:DG134 3.6 0.2 1.0 C8 I:DA133 3.7 97.1 1.0 O6 I:DG135 3.8 0.7 1.0 C8 I:DG134 3.8 0.2 1.0 C5 I:DA133 4.4 97.1 1.0 C4 I:DG134 4.7 0.2 1.0 N9 I:DA133 4.8 97.1 1.0 C6 I:DG135 4.9 0.7 1.0 N9 I:DG134 4.9 0.2 1.0 N1 I:DG134 4.9 0.2 1.0

Manganese binding site 2 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn148 b:56.7 occ:1.00 N7 I:DG70 2.7 72.7 1.0 O6 I:DG70 3.4 72.7 1.0 C5 I:DG70 3.6 72.7 1.0 C8 I:DG70 3.7 72.7 1.0 C6 I:DG70 3.9 72.7 1.0 C6 I:DC69 4.1 88.0 1.0 C2' I:DC69 4.2 87.2 1.0 O6 I:DG71 4.3 84.4 1.0 C5 I:DC69 4.5 88.0 1.0 N1 I:DC69 4.8 88.0 1.0 C4 I:DG70 4.8 72.7 1.0 N9 I:DG70 4.9 72.7 1.0

Manganese binding site 3 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn149 b:56.7 occ:1.00 N7 I:DG121 2.3 1.0 1.0 O6 I:DG121 2.8 1.0 1.0 C5 I:DG121 3.0 1.0 1.0 C6 I:DG121 3.2 1.0 1.0 C8 I:DG121 3.5 1.0 1.0 O6 I:DG122 4.3 0.3 1.0 C4 I:DG121 4.3 1.0 1.0 N9 I:DG121 4.5 1.0 1.0 C2' I:DT120 4.5 0.6 1.0 OP2 I:DG121 4.6 1.0 1.0 N1 I:DG121 4.6 1.0 1.0

Manganese binding site 4 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn150 b:56.7 occ:1.00 O6 I:DG78 3.1 87.0 1.0 O6 J:DG214 3.5 0.5 1.0 N7 J:DG214 3.9 0.5 1.0 C6 I:DG78 4.0 87.0 1.0 N4 J:DC215 4.2 0.5 1.0 C6 J:DG214 4.3 0.5 1.0 C5 J:DG214 4.5 0.5 1.0 C5 I:DG78 4.7 87.0 1.0 N7 I:DG78 4.8 87.0 1.0 C2' J:DA213 4.8 0.6 1.0 N1 I:DG78 4.9 87.0 1.0

Manganese binding site 5 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn103 b:56.7 occ:1.00 N7 J:DG267 2.4 0.1 1.0 O6 J:DG267 3.1 0.1 1.0 C5 J:DG267 3.3 0.1 1.0 C6 J:DG267 3.5 0.1 1.0 C8 J:DG267 3.5 0.1 1.0 C2' J:DT266 4.0 0.6 1.0 C6 J:DT266 4.3 0.4 1.0 OP2 J:DG267 4.4 0.1 1.0 C4 J:DG267 4.5 0.1 1.0 N9 J:DG267 4.6 0.1 1.0 O6 J:DG268 4.7 0.2 1.0 C5 J:DT266 4.9 0.4 1.0 N1 J:DG267 4.9 0.1 1.0 N1 J:DT266 4.9 0.4 1.0 C7 J:DT266 4.9 0.4 1.0 C1' J:DT266 5.0 0.6 1.0

Manganese binding site 6 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn108 b:56.7 occ:1.00 O6 J:DG280 2.5 0.5 1.0 N7 J:DG280 3.0 0.5 1.0 C6 J:DG280 3.2 0.5 1.0 C5 J:DG280 3.4 0.5 1.0 N7 J:DA279 3.5 98.9 1.0 C8 J:DA279 3.7 98.9 1.0 C8 J:DG280 4.2 0.5 1.0 O6 J:DG281 4.4 1.0 1.0 N1 J:DG280 4.6 0.5 1.0 OP2 J:DA279 4.6 98.9 1.0 C5 J:DA279 4.7 98.9 1.0 C4 J:DG280 4.8 0.5 1.0 N9 J:DA279 4.9 98.9 1.0

Manganese binding site 7 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn111 b:56.7 occ:1.00 N7 J:DG216 2.2 99.5 1.0 C8 J:DG216 2.8 99.5 1.0 C5 J:DG216 3.3 99.5 1.0 O6 J:DG217 3.3 85.8 1.0 O J:HOH7 3.6 56.7 1.0 N9 J:DG216 4.0 99.5 1.0 C6 J:DG216 4.0 99.5 1.0 O6 J:DG216 4.0 99.5 1.0 C4 J:DG216 4.2 99.5 1.0 C6 J:DG217 4.2 85.8 1.0 N7 J:DG217 4.6 85.8 1.0 OP2 J:DG216 4.6 99.5 1.0 C2' J:DC215 4.7 99.6 1.0 C5 J:DG217 4.7 85.8 1.0 N4 I:DC76 4.8 93.5 1.0

Manganese binding site 8 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn113 b:56.7 occ:1.00 OP1 J:DC168 3.2 0.1 1.0 P J:DC168 4.3 0.3 1.0 O3' J:DT167 4.7 0.8 1.0 OP2 J:DC168 4.8 0.1 1.0

Manganese binding site 9 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn114 b:56.7 occ:1.00 N7 J:DG246 2.8 0.2 1.0 O6 J:DG246 3.0 0.2 1.0 C7 I:DT45 3.5 0.7 1.0 C5 J:DG246 3.5 0.2 1.0 C6 J:DG246 3.6 0.2 1.0 C8 J:DG246 3.9 0.2 1.0 N7 J:DA245 4.0 0.3 1.0 O6 I:DG46 4.2 0.5 1.0 C8 J:DA245 4.2 0.3 1.0 C5 I:DT45 4.2 0.7 1.0 N4 J:DC247 4.6 85.0 1.0 C4 J:DG246 4.8 0.2 1.0 O4 I:DT45 4.8 0.7 1.0 C4 I:DT45 4.8 0.7 1.0 N1 J:DG246 4.9 0.2 1.0 C6 I:DT45 5.0 0.7 1.0 N9 J:DG246 5.0 0.2 1.0

Manganese binding site 10 out of 17 in the Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Differences in Inter-Nucleosome Interactions within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn115 b:56.7 occ:1.00 N3 J:DG185 2.5 0.2 1.0 N2 J:DG185 2.5 0.2 1.0 C2 J:DG185 2.8 0.2 1.0 O2 J:DT184 2.9 0.3 1.0 N1 J:DG186 3.2 0.4 1.0 C2 J:DG186 3.4 0.4 1.0 C6 J:DG186 3.6 0.4 1.0 C4 J:DG185 3.6 0.2 1.0 C2 J:DT184 3.6 0.3 1.0 N2 J:DG186 3.7 0.4 1.0 N3 J:DG186 3.9 0.4 1.0 N1 J:DG185 4.0 0.2 1.0 N3 I:DC108 4.0 0.4 1.0 O4' J:DG185 4.1 95.8 1.0 O6 J:DG186 4.1 0.4 1.0 C2 I:DA109 4.1 0.1 1.0 C5 J:DG186 4.1 0.4 1.0 C4 J:DG186 4.2 0.4 1.0 C1' J:DT184 4.3 0.5 1.0 N1 J:DT184 4.3 0.3 1.0 N9 J:DG185 4.4 0.2 1.0 C1' J:DG185 4.4 95.8 1.0 N3 J:DT184 4.4 0.3 1.0 N1 I:DA109 4.5 0.1 1.0 O2 I:DC108 4.6 0.4 1.0 C2 I:DC108 4.7 0.4 1.0 C5 J:DG185 4.7 0.2 1.0 N4 I:DC108 4.7 0.4 1.0 C4 I:DC108 4.8 0.4 1.0 C2' J:DT184 4.9 0.5 1.0 C6 J:DG185 4.9 0.2 1.0 N3 I:DC107 4.9 98.2 1.0

C.L.White, R.K.Suto, K.Luger. Structure of the Yeast Nucleosome Core Particle Reveals Fundamental Changes in Internucleosome Interactions. Embo J. V. 20 5207 2001.
ISSN: ISSN 0261-4189
PubMed: 11566884
DOI: 10.1093/EMBOJ/20.18.5207