Manganese in PDB 3lja: Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome

The structure of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome, PDB code: 3lja was solved by B.Wu, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.19 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.348, 109.785, 182.424, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 25.9

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 - 45;

Binding sites:

The binding sites of Manganese atom in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome (pdb code 3lja). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 45 binding sites of Manganese where determined in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome, PDB code: 3lja:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn136 b:60.1 occ:1.00 OD1 E:ASP77 2.2 35.2 1.0 CG E:ASP77 3.1 33.0 1.0 OD2 E:ASP77 3.4 34.1 1.0 OE1 E:GLN76 4.1 31.9 1.0 O F:LEU22 4.2 42.0 1.0 CB E:ASP77 4.5 31.7 1.0 O E:GLU73 4.6 23.9 1.0 CA E:ASP77 4.8 32.1 1.0 N E:ASP77 4.8 31.0 1.0 CD E:GLN76 4.9 30.8 1.0

Manganese binding site 2 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn74 b:68.0 occ:0.80 N7 J:DG61 2.6 66.7 1.0 C8 J:DG61 3.5 67.3 1.0 C5 J:DG61 3.7 66.9 1.0 O6 J:DG61 3.8 67.3 1.0 C6 J:DG61 4.1 67.2 1.0 C8 J:DA60 4.2 58.7 1.0 N7 J:DA60 4.3 58.6 1.0 O6 J:DG62 4.6 82.9 1.0 N9 J:DG61 4.7 67.8 1.0 C4 J:DG61 4.8 67.3 1.0 OP2 J:DA60 4.9 51.1 1.0

Manganese binding site 3 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn74 b:72.5 occ:0.65 N7 I:DG61 2.7 64.3 1.0 O6 I:DG61 3.5 64.4 1.0 C5 I:DG61 3.6 64.6 1.0 C8 I:DG61 3.7 64.6 1.0 C6 I:DG61 3.9 64.7 1.0 N7 I:DA60 4.2 64.0 1.0 C8 I:DA60 4.3 64.5 1.0 O6 I:DG62 4.5 78.1 1.0 C4 I:DG61 4.8 64.7 1.0 N9 I:DG61 4.9 65.0 1.0

Manganese binding site 4 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn75 b:72.8 occ:0.50 O2 I:DT13 4.1 53.3 1.0 O2 J:DT-12 4.4 40.4 1.0 C5' I:DC15 4.4 54.2 1.0 O4' J:DT-12 4.4 38.2 1.0 O4' I:DG14 4.5 55.3 1.0 C2 J:DA-13 4.5 41.2 1.0 N3 J:DA-13 4.6 41.4 1.0 C4' I:DG14 4.7 54.7 1.0 C4' I:DC15 4.8 55.0 1.0 O4' I:DC15 4.8 55.4 1.0 C4' J:DT-12 4.9 38.4 1.0 C1' J:DT-12 4.9 39.4 1.0

Manganese binding site 5 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn75 b:82.5 occ:0.71 N7 J:DG27 2.3 57.5 1.0 C8 J:DG27 3.2 57.3 1.0 C5 J:DG27 3.3 57.3 1.0 O6 J:DG27 3.6 57.4 1.0 C6 J:DG27 3.8 57.3 1.0 O6 I:DG-28 4.1 81.4 1.0 N9 J:DG27 4.4 57.5 1.0 C4 J:DG27 4.5 57.1 1.0 C8 J:DA26 4.5 63.1 1.0 N7 J:DA26 4.6 63.2 1.0 C7 I:DT-29 4.9 83.2 1.0 N4 J:DC28 4.9 55.0 1.0

Manganese binding site 6 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn76 b:77.1 occ:0.75 N7 I:DG48 2.2 68.1 1.0 C8 I:DG48 3.2 68.1 1.0 C5 I:DG48 3.2 68.6 1.0 O6 I:DG48 3.4 68.2 1.0 C6 I:DG48 3.7 68.4 1.0 C2' I:DT47 4.0 74.2 1.0 O6 I:DG49 4.2 65.3 1.0 N9 I:DG48 4.4 68.3 1.0 C4 I:DG48 4.4 68.7 1.0 OP2 I:DG48 4.7 68.8 1.0

Manganese binding site 7 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn76 b:74.6 occ:0.61 N7 J:DG48 2.2 59.7 1.0 C5 J:DG48 3.1 59.5 1.0 C8 J:DG48 3.2 59.6 1.0 O6 J:DG48 3.2 59.7 1.0 C6 J:DG48 3.5 59.3 1.0 C2' J:DT47 4.3 65.3 1.0 O6 J:DG49 4.3 54.7 1.0 C4 J:DG48 4.3 59.2 1.0 N9 J:DG48 4.4 58.9 1.0 OP2 J:DG48 4.6 59.4 1.0 N1 J:DG48 4.9 59.0 1.0

Manganese binding site 8 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn77 b:64.9 occ:0.37 N7 J:DG-3 2.3 34.8 1.0 C8 J:DG-3 3.2 34.5 1.0 C5 J:DG-3 3.5 34.8 1.0 O6 J:DG-3 3.7 35.5 1.0 C6 J:DG-3 4.0 35.1 1.0 C2' J:DT-4 4.1 37.9 1.0 O6 J:DG-2 4.1 49.2 1.0 N9 J:DG-3 4.5 34.5 1.0 C4 J:DG-3 4.6 34.9 1.0 C6 J:DT-4 4.7 39.1 1.0 C6 J:DG-2 4.9 49.0 1.0 OP2 J:DG-3 5.0 32.7 1.0

Manganese binding site 9 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn77 b:77.5 occ:0.48 N7 I:DG-35 2.3 56.9 1.0 O6 I:DG-34 3.1 51.5 1.0 C8 I:DG-35 3.1 56.7 1.0 C5 I:DG-35 3.4 57.2 1.0 O6 I:DG-35 3.7 56.9 1.0 MN I:MN89 3.8 0.2 0.3 C6 I:DG-34 3.8 51.0 1.0 C2' I:DT-36 3.9 59.7 1.0 C6 I:DG-35 3.9 56.8 1.0 N7 I:DG-34 4.2 51.2 1.0 C5 I:DG-34 4.3 51.5 1.0 O3' I:DT-36 4.4 57.9 1.0 N9 I:DG-35 4.4 56.8 1.0 N4 J:DC34 4.5 81.1 1.0 C3' I:DT-36 4.5 59.8 1.0 C4 I:DG-35 4.5 57.2 1.0 OP2 I:DG-35 4.6 55.5 1.0 N1 I:DG-34 4.8 50.9 1.0

Manganese binding site 10 out of 45 in the Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn78 b:78.7 occ:0.35 N7 I:DG-3 2.3 34.1 1.0 C8 I:DG-3 3.2 35.0 1.0 C5 I:DG-3 3.3 34.5 1.0 O6 I:DG-3 3.5 35.2 1.0 O6 I:DG-2 3.6 48.8 1.0 C6 I:DG-3 3.8 34.3 1.0 MN I:MN87 3.9 80.2 0.2 C2' I:DT-4 4.2 39.4 1.0 N9 I:DG-3 4.4 35.1 1.0 C4 I:DG-3 4.4 34.7 1.0 C6 I:DG-2 4.4 48.8 1.0 C6 I:DT-4 4.7 37.7 1.0 OP2 I:DG-3 4.7 34.2 1.0 N7 I:DG-2 4.8 48.3 1.0 C5 I:DG-2 4.9 48.5 1.0

B.Wu, C.A.Davey. Using Soft X-Rays For A Detailed Picture of Divalent Metal Binding in the Nucleosome J.Mol.Biol. V. 398 633 2010.
ISSN: ISSN 0022-2836
PubMed: 20350553
DOI: 10.1016/J.JMB.2010.03.038