Manganese in PDB 3lel: Structural Insight Into the Sequence-Dependence of Nucleosome Positioning

The structure of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning, PDB code: 3lel was solved by B.Wu, D.Vasudevan, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.00 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.747, 178.508, 110.412, 90.00, 102.78, 90.00
R / Rfree (%)	22.9 / 30

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Manganese atom in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning (pdb code 3lel). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 34 binding sites of Manganese where determined in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning, PDB code: 3lel:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ N:Mn3132 b:0.1 occ:1.00 OE1 N:GLU102 3.0 83.8 1.0 CD N:GLU102 3.8 83.0 1.0 OD2 E:ASP77 4.0 78.2 1.0 OE2 N:GLU102 4.3 83.8 1.0 CE N:LYS105 4.4 83.7 1.0 OE2 E:GLU73 4.5 66.1 1.0 CD N:LYS105 4.5 83.5 1.0 OD1 E:ASP77 4.5 76.4 1.0 NZ F:LYS59 4.6 63.3 1.0 CG E:ASP77 4.7 76.6 1.0 CG E:GLU73 4.9 65.3 1.0 CG N:GLU102 4.9 80.6 1.0

Manganese binding site 2 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ O:Mn3152 b:67.8 occ:1.00 OD1 O:ASP77 2.5 63.9 1.0 CG O:ASP77 3.5 62.4 1.0 OD2 O:ASP77 3.7 63.3 1.0 O P:LEU22 3.9 83.7 1.0 O O:GLU73 4.6 58.9 1.0 CB O:ASP77 4.9 62.1 1.0 CG O:GLU73 5.0 57.9 1.0

Manganese binding site 3 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ S:Mn3133 b:91.5 occ:1.00 C4' S:DT67 4.3 75.1 1.0 O4' S:DT67 4.3 73.3 1.0 C5' S:DT67 4.4 77.6 1.0 O4' T:DC-64 4.4 73.6 1.0 O2 T:DC-65 4.4 75.1 1.0 N3 S:DA66 4.5 74.8 1.0 C5' T:DC-64 4.7 76.1 1.0 C4' T:DC-64 4.7 75.2 1.0

Manganese binding site 4 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ T:Mn3134 b:95.0 occ:1.00 N7 T:DG61 2.5 0.5 1.0 C8 T:DG61 3.4 0.8 1.0 C5 T:DG61 3.5 0.5 1.0 O6 T:DG61 3.6 0.2 1.0 C6 T:DG61 3.9 0.9 1.0 C8 T:DA60 4.2 94.0 1.0 N7 T:DA60 4.3 93.5 1.0 OP2 T:DA60 4.5 0.4 1.0 N9 T:DG61 4.6 0.4 1.0 O6 T:DG62 4.7 1.0 1.0 C4 T:DG61 4.7 0.6 1.0 N9 T:DA60 4.8 94.5 1.0 C2' T:DA60 5.0 97.8 1.0 C5 T:DA60 5.0 93.2 1.0

Manganese binding site 5 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn3135 b:0.3 occ:1.00 N7 J:DG27 2.6 91.3 1.0 O6 J:DG27 3.3 91.4 1.0 C5 J:DG27 3.3 91.3 1.0 C8 J:DG27 3.5 91.3 1.0 C6 J:DG27 3.6 91.4 1.0 O6 I:DG-28 4.2 0.2 1.0 C4 J:DG27 4.4 91.1 1.0 N9 J:DG27 4.5 91.1 1.0 N1 J:DG27 4.9 91.1 1.0 O4 I:DT-29 4.9 0.5 1.0

Manganese binding site 6 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn3136 b:0.7 occ:1.00 N7 I:DG27 2.1 97.6 1.0 O6 I:DG27 2.8 97.5 1.0 C5 I:DG27 2.9 97.5 1.0 C6 I:DG27 3.2 97.5 1.0 C8 I:DG27 3.2 97.6 1.0 C8 I:DA26 4.0 0.0 1.0 C4 I:DG27 4.1 97.4 1.0 N7 I:DA26 4.2 0.3 1.0 N9 I:DG27 4.3 97.4 1.0 OP2 I:DA26 4.4 0.6 1.0 N1 I:DG27 4.5 97.3 1.0 N9 I:DA26 4.6 0.6 1.0 C2' I:DA26 4.6 0.9 1.0 C5 I:DA26 4.9 0.8 1.0

Manganese binding site 7 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn3137 b:85.2 occ:1.00 N7 J:DG61 2.2 89.7 1.0 C8 J:DG61 3.2 89.8 1.0 C5 J:DG61 3.3 89.8 1.0 O6 J:DG61 3.6 89.7 1.0 C6 J:DG61 3.8 89.7 1.0 N7 J:DA60 4.0 80.0 1.0 C8 J:DA60 4.0 80.0 1.0 OP2 J:DA60 4.1 78.6 1.0 N9 J:DG61 4.4 90.2 1.0 C4 J:DG61 4.5 89.9 1.0 N9 J:DA60 4.7 80.2 1.0 C5 J:DA60 4.7 79.7 1.0 O6 J:DG62 4.8 0.1 1.0 C2' J:DA60 4.9 81.5 1.0

Manganese binding site 8 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn3138 b:0.8 occ:1.00 N7 J:DG48 2.3 97.6 1.0 C5 J:DG48 3.2 97.6 1.0 O6 J:DG48 3.2 97.5 1.0 C8 J:DG48 3.3 97.5 1.0 C6 J:DG48 3.6 97.8 1.0 O6 J:DG49 3.9 99.6 1.0 C2' J:DT47 4.3 0.9 1.0 OP2 J:DG48 4.4 97.4 1.0 C4 J:DG48 4.4 97.5 1.0 N9 J:DG48 4.5 97.2 1.0 N7 J:DG49 4.7 0.2 1.0 C6 J:DG49 4.8 99.8 1.0 N1 J:DG48 4.9 97.6 1.0

Manganese binding site 9 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ T:Mn3139 b:0.7 occ:1.00 N7 T:DG64 2.5 0.1 1.0 C8 T:DG64 2.7 0.1 1.0 C5 T:DG64 3.9 0.9 1.0 OP2 T:DG64 4.0 0.8 1.0 N7 T:DG65 4.0 0.2 1.0 N9 T:DG64 4.1 0.1 1.0 O6 T:DG65 4.1 0.3 1.0 C6 T:DT63 4.3 0.1 1.0 C2' T:DT63 4.3 0.5 1.0 C5 T:DT63 4.5 0.0 1.0 N1 T:DT63 4.6 0.2 1.0 C4 T:DG64 4.6 0.1 1.0 C5 T:DG65 4.6 0.2 1.0 C6 T:DG65 4.7 1.0 1.0 C6 T:DG64 4.8 0.5 1.0 C2' T:DG64 4.9 0.7 1.0 C7 T:DT63 4.9 0.1 1.0 O5' T:DG64 4.9 0.5 1.0 O6 T:DG64 4.9 0.3 1.0 C1' T:DT63 5.0 0.6 1.0 C4 T:DT63 5.0 0.1 1.0 C8 T:DG65 5.0 0.2 1.0

Manganese binding site 10 out of 34 in the Structural Insight Into the Sequence-Dependence of Nucleosome Positioning


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structural Insight Into the Sequence-Dependence of Nucleosome Positioning within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn3140 b:0.6 occ:1.00 OE1 G:GLU91 2.9 82.4 1.0 CD G:GLU91 4.1 81.3 1.0 O N:VAL45 4.3 91.3 1.0 OE2 M:GLU64 4.5 87.1 1.0 OE1 M:GLU64 4.7 86.4 1.0 OE2 G:GLU91 4.9 82.6 1.0

B.Wu, K.Mohideen, D.Vasudevan, C.A.Davey. Structural Insight Into the Sequence Dependence of Nucleosome Positioning Structure V. 18 528 2010.
ISSN: ISSN 0969-2126
PubMed: 20399189
DOI: 10.1016/J.STR.2010.01.015