Manganese in PDB 5jrg: Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)

The structure of Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf), PDB code: 5jrg was solved by A.Osakabe, Y.Arimura, N.Horikoshi, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.491, 108.773, 169.571, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24.5

The structure of Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) (pdb code 5jrg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 15 binding sites of Manganese where determined in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf), PDB code: 5jrg:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn3001 b:26.8 occ:1.00 OD1 E:ASP77 2.2 27.5 1.0 O E:HOH3110 2.2 28.5 1.0 CG E:ASP77 3.1 26.6 1.0 OD2 E:ASP77 3.5 29.8 1.0 O E:GLU73 4.3 22.9 1.0 CB E:ASP77 4.4 20.6 1.0 O E:HOH3109 4.4 31.8 1.0 CA E:ASP77 4.5 21.4 1.0 N E:ASP77 4.5 24.2 1.0 CG E:GLN76 4.7 30.5 1.0 O F:LEU22 4.8 24.7 1.0 C E:GLN76 4.9 22.3 1.0 CG E:GLU73 4.9 19.6 1.0 NE2 E:GLN76 5.0 38.6 1.0

Manganese binding site 2 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:46.0 occ:1.00 OP1 I:DT135 2.3 56.0 1.0 P I:DT135 3.5 59.0 1.0 O5' I:DT135 3.6 55.0 1.0 OP2 I:DT135 4.4 55.4 1.0 O3' I:DG134 4.7 58.5 1.0 C5' I:DT135 4.8 57.9 1.0

Manganese binding site 3 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:55.6 occ:1.00 N3 I:DA112 4.2 35.0 1.0 C5' I:DC113 4.4 40.2 1.0 O4' I:DC113 4.5 42.1 1.0 N3 J:DA35 4.6 32.6 1.0 C4' I:DC113 4.7 43.2 1.0 C2 I:DA112 4.8 34.6 1.0

Manganese binding site 4 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:54.4 occ:1.00 N7 I:DG120 2.4 35.1 1.0 C8 I:DG120 3.2 37.4 1.0 C5 I:DG120 3.5 33.2 1.0 O6 I:DG120 3.9 34.7 1.0 O6 I:DG121 4.1 37.9 1.0 C6 I:DG120 4.1 36.4 1.0 C2' I:DT119 4.2 43.2 1.0 N9 I:DG120 4.4 36.3 1.0 OP2 I:DG120 4.6 41.2 1.0 C4 I:DG120 4.6 31.2 1.0 C6 I:DT119 4.8 39.4 1.0 C6 I:DG121 5.0 34.5 1.0

Manganese binding site 5 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn204 b:50.2 occ:1.00 O I:HOH310 2.4 37.1 1.0 O J:HOH315 2.4 33.6 1.0 O I:HOH342 2.4 44.5 1.0 N7 I:DG99 2.4 36.2 1.0 O I:HOH348 2.5 38.3 1.0 C8 I:DG99 3.3 30.6 1.0 C5 I:DG99 3.5 29.8 1.0 O6 I:DG99 3.8 33.6 1.0 C6 I:DG99 4.1 31.2 1.0 N9 I:DG99 4.5 30.7 1.0 C8 I:DA98 4.6 32.9 1.0 O I:HOH330 4.6 44.5 1.0 C4 I:DG99 4.6 29.5 1.0 O6 J:DG46 4.7 36.7 1.0 N7 I:DA98 4.8 32.7 1.0

Manganese binding site 6 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn205 b:65.7 occ:1.00 O6 I:DG97 2.5 37.5 1.0 N7 I:DG96 2.6 43.1 1.0 O I:HOH339 2.8 39.7 1.0 C8 I:DG96 3.4 38.9 1.0 C6 I:DG97 3.5 35.0 1.0 C5 I:DG96 3.7 38.2 1.0 N4 J:DC49 3.8 31.9 1.0 OP2 I:DG96 4.0 50.8 1.0 O6 I:DG96 4.0 31.6 1.0 N7 I:DG97 4.1 38.2 1.0 C5 I:DG97 4.1 37.3 1.0 C6 I:DG96 4.2 36.2 1.0 N1 I:DG97 4.5 34.1 1.0 N9 I:DG96 4.6 37.8 1.0 C4 I:DG96 4.8 36.2 1.0 C2' I:DT95 4.8 43.1 1.0

Manganese binding site 7 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn206 b:69.3 occ:1.00 O6 I:DG40 2.3 58.8 1.0 N7 I:DG39 2.6 54.2 1.0 O I:HOH306 3.0 54.8 1.0 C6 I:DG40 3.3 55.7 1.0 C8 I:DG39 3.4 53.0 1.0 C5 I:DG39 3.6 53.0 1.0 N4 J:DC106 3.6 56.6 1.0 O6 I:DG39 3.9 54.0 1.0 O I:HOH301 4.0 49.3 1.0 C5 I:DG40 4.0 55.0 1.0 C6 I:DG39 4.1 55.8 1.0 N7 I:DG40 4.1 49.3 1.0 N1 I:DG40 4.3 53.7 1.0 N9 I:DG39 4.5 51.2 1.0 O4 J:DT105 4.6 64.5 1.0 C4 I:DG39 4.6 49.1 1.0 C4 J:DC106 4.8 59.1 1.0 OP2 I:DG39 4.8 48.6 1.0 C2' I:DT38 4.9 56.2 1.0

Manganese binding site 8 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn207 b:91.8 occ:1.00 O I:HOH325 2.7 50.4 1.0 N7 I:DG133 3.4 58.3 1.0 N7 I:DA132 3.6 60.4 1.0 O6 I:DG133 3.8 56.5 1.0 C8 I:DA132 3.9 66.1 1.0 C5 I:DG133 4.2 56.8 1.0 O6 I:DG134 4.3 62.2 1.0 C6 I:DG133 4.4 54.4 1.0 C8 I:DG133 4.4 57.1 1.0 C5 I:DA132 4.6 59.4 1.0

Manganese binding site 9 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn208 b:67.8 occ:1.00 O6 I:DG68 2.9 52.7 1.0 O I:HOH347 3.0 45.0 1.0 C6 I:DG68 3.8 46.7 1.0 N4 J:DC78 3.9 55.4 1.0 N7 I:DG68 4.0 50.8 1.0 O6 J:DG77 4.1 53.3 1.0 C5 I:DG68 4.3 44.9 1.0 N7 J:DG77 4.4 59.4 1.0 C6 J:DG77 4.9 51.9 1.0

Manganese binding site 10 out of 15 in the Crystal Structure of the Nucleosome Containing the Dna with Tetrahydrofuran (Thf)


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 Nucleosome Containing the Dna with Tetrahydrofuran (Thf) within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn201 b:55.1 occ:1.00 O J:HOH326 2.2 42.3 1.0 N7 J:DG120 2.5 50.8 1.0 O J:HOH344 2.6 41.3 1.0 C8 J:DG120 3.3 46.3 1.0 OP2 J:DG120 3.4 56.2 1.0 C5 J:DG120 3.7 50.1 1.0 O6 J:DG120 4.1 58.1 1.0 O J:HOH322 4.3 41.0 1.0 C6 J:DG120 4.3 52.5 1.0 C2' J:DT119 4.5 49.4 1.0 N9 J:DG120 4.6 43.7 1.0 O6 J:DG121 4.7 49.0 1.0 C4 J:DG120 4.8 46.8 1.0 P J:DG120 4.8 46.8 1.0

A.Osakabe, Y.Arimura, S.Matsumoto, N.Horikoshi, K.Sugasawa, H.Kurumizaka. Polymorphism of Apyrimidinic Dna Structures in the Nucleosome Sci Rep V. 7 41783 2017.
ISSN: ESSN 2045-2322
PubMed: 28139742
DOI: 10.1038/SREP41783