Manganese in PDB 3x1v: Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming

The structure of Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming, PDB code: 3x1v was solved by P.Sivaraman, T.S.Kumarevel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.81 / 2.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.327, 108.471, 168.677, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 25.9

The structure of Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming (pdb code 3x1v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 19 binding sites of Manganese where determined in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming, PDB code: 3x1v:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:66.5 occ:1.00 O6 I:DG68 2.5 46.3 1.0 C6 I:DG68 3.7 43.6 1.0 N7 J:DG224 4.1 39.9 1.0 N4 J:DC225 4.3 34.6 1.0 N7 I:DG68 4.4 36.9 1.0 C5 I:DG68 4.4 40.7 1.0 O6 J:DG224 4.6 44.8 1.0 N1 I:DG68 4.7 45.3 1.0 C5 J:DG224 5.0 44.4 1.0

Manganese binding site 2 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:75.0 occ:1.00 O6 I:DG121 2.0 49.8 1.0 N7 I:DG121 2.1 43.2 1.0 C6 I:DG121 2.4 43.1 1.0 C5 I:DG121 2.4 43.2 1.0 MN I:MN207 3.3 44.4 1.0 C8 I:DG121 3.4 44.0 1.0 C5 I:DT120 3.5 48.2 1.0 C4 I:DT120 3.5 46.6 1.0 C6 I:DT120 3.6 43.8 1.0 N3 I:DT120 3.6 42.6 1.0 N1 I:DT120 3.6 43.6 1.0 C2 I:DT120 3.7 44.5 1.0 C4 I:DG121 3.7 50.0 1.0 N1 I:DG121 3.7 41.8 1.0 O6 I:DG122 3.7 41.3 1.0 N4 J:DC171 3.8 39.2 1.0 N4 J:DC172 4.1 37.8 1.0 O4 I:DT120 4.1 46.8 1.0 C6 I:DG122 4.2 42.3 1.0 N9 I:DG121 4.2 49.3 1.0 C2' I:DT120 4.2 44.2 1.0 C7 I:DT120 4.3 45.8 1.0 O2 I:DT120 4.3 46.0 1.0 N3 J:DC172 4.4 39.8 1.0 C1' I:DT120 4.5 43.1 1.0 N1 I:DG122 4.6 46.6 1.0 C4 J:DC171 4.6 44.6 1.0 C2 I:DG121 4.7 53.4 1.0 N3 I:DG121 4.8 56.9 1.0 C4 J:DC172 4.8 38.9 1.0 C5 I:DG122 4.9 39.9 1.0 N3 J:DC171 5.0 40.4 1.0

Manganese binding site 3 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:0.1 occ:1.00 O I:HOH310 2.6 91.2 1.0 N7 I:DG134 3.3 91.2 1.0 C8 I:DG134 4.0 95.1 1.0 C8 I:DA133 4.3 94.7 1.0 N7 I:DA133 4.5 93.9 1.0 C5 I:DG134 4.5 91.6 1.0 O6 I:DG134 4.7 89.1 1.0 MN I:MN206 4.8 1.0 1.0 C6 I:DG134 5.0 88.3 1.0

Manganese binding site 4 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn204 b:55.1 occ:1.00 O6 I:DG78 2.5 48.9 1.0 O J:HOH401 3.1 30.3 1.0 C6 I:DG78 3.6 43.8 1.0 O6 J:DG214 4.1 31.1 1.0 N4 J:DC215 4.2 41.7 1.0 N7 J:DG214 4.3 38.0 1.0 C5 I:DG78 4.4 43.4 1.0 N7 I:DG78 4.4 46.4 1.0 N1 I:DG78 4.7 37.5 1.0 C6 J:DG214 4.9 31.8 1.0 C5 J:DG214 5.0 33.0 1.0

Manganese binding site 5 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn205 b:81.6 occ:1.00 O4' I:DG87 3.7 41.0 1.0 C4' I:DG87 3.7 39.1 1.0 O2 I:DT86 4.1 43.5 1.0 C5' I:DG87 4.3 36.0 1.0 C5' I:DC88 4.5 45.6 1.0 O3' I:DG87 4.7 53.2 1.0 O4' I:DC88 4.7 47.6 1.0 C1' I:DG87 4.7 43.5 1.0 C4' I:DC88 4.8 47.0 1.0 C3' I:DG87 4.9 49.0 1.0 C2 J:DA207 4.9 30.1 1.0

Manganese binding site 6 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn206 b:1.0 occ:1.00 O6 I:DG134 2.9 89.1 1.0 C5 I:DC132 4.0 93.1 1.0 N4 J:DC159 4.1 76.8 1.0 C6 I:DG134 4.1 88.3 1.0 N6 I:DA133 4.2 76.9 1.0 C6 I:DC132 4.3 91.0 1.0 N7 I:DA133 4.3 93.9 1.0 MN I:MN203 4.8 0.1 1.0 C5 I:DG134 5.0 91.6 1.0

Manganese binding site 7 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn207 b:44.4 occ:1.00 N7 I:DG121 3.3 43.2 1.0 MN I:MN202 3.3 75.0 1.0 C8 I:DG121 3.8 44.0 1.0 O6 I:DG122 4.1 41.3 1.0 C2' I:DT120 4.5 44.2 1.0 C5 I:DG121 4.6 43.2 1.0 N4 J:DC171 4.7 39.2 1.0 OP2 I:DG121 4.8 32.4 1.0

Manganese binding site 8 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn208 b:63.8 occ:1.00 OP1 I:DC84 2.5 42.4 1.0 OP2 I:DC84 2.8 39.2 1.0 P I:DC84 3.0 54.5 1.0 OP1 I:DT6 3.2 43.7 1.0 O3' I:DA83 4.2 40.5 1.0 O5' I:DC84 4.3 30.3 1.0 P I:DT6 4.4 39.0 1.0 O5' I:DT6 4.4 34.2 1.0 C3' I:DA83 4.7 27.4 1.0 O E:HIS39 4.9 35.8 1.0

Manganese binding site 9 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn209 b:98.3 occ:1.00 OP2 I:DT146 1.8 87.5 1.0 P I:DT146 3.2 89.5 1.0 C3' I:DA145 3.4 72.0 1.0 C2' I:DA145 3.5 65.3 1.0 O3' I:DA145 3.8 95.8 1.0 OP1 I:DT146 4.1 91.1 1.0 O5' I:DT146 4.1 82.4 1.0 C5' I:DT146 4.4 85.8 1.0 O5' I:DA145 4.7 55.0 1.0 C4' I:DA145 4.9 58.8 1.0 C1' I:DA145 5.0 60.4 1.0

Manganese binding site 10 out of 19 in the Crystal Structure of Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming


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 Nucleosome Core Particle in the Presence of Histone Variant Involved in Reprogramming within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn210 b:83.5 occ:1.00 N7 I:DA17 2.9 47.9 1.0 C8 I:DA17 3.6 46.8 1.0 C5 I:DA17 4.1 49.1 1.0 O6 I:DG18 4.2 51.3 1.0 OP2 I:DA17 4.4 56.0 1.0 N6 I:DA17 4.4 60.8 1.0 N7 I:DG18 4.6 41.1 1.0 C6 I:DA17 4.7 50.6 1.0 N9 I:DA17 4.8 49.6 1.0 C6 I:DG18 5.0 43.4 1.0

S.Padavattan, T.Shinagawa, K.Hasegawa, T.Kumasaka, S.Ishii, T.Kumarevel. Structural and Functional Analyses of Nucleosome Complexes with Mouse Histone Variants TH2A and TH2B, Involved in Reprogramming Biochem.Biophys.Res.Commun. V. 464 929 2015.
ISSN: ISSN 0006-291X
PubMed: 26188507
DOI: 10.1016/J.BBRC.2015.07.070