Manganese in PDB 3x1s: Crystal Structure of the Nucleosome Core Particle

The structure of Crystal Structure of the Nucleosome Core Particle, PDB code: 3x1s 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)	34.83 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.381, 109.363, 175.572, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 27

The structure of Crystal Structure of the Nucleosome Core Particle also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Crystal Structure of the Nucleosome Core Particle (pdb code 3x1s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Crystal Structure of the Nucleosome Core Particle, PDB code: 3x1s:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Crystal Structure of the Nucleosome Core Particle


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 Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:69.0 occ:1.00 MN D:MN202 1.7 68.6 1.0 O D:VAL48 2.7 59.3 1.0 C D:VAL48 3.4 52.0 1.0 CA D:VAL48 3.6 52.7 1.0 O D:GLN47 3.7 63.9 1.0 OE1 C:GLU64 4.6 59.9 1.0 CB D:VAL48 4.6 55.8 1.0 C D:GLN47 4.6 52.7 1.0 N D:HIS49 4.6 55.3 1.0 N D:VAL48 4.6 48.4 1.0 CD D:PRO50 4.9 59.1 1.0

Manganese binding site 2 out of 6 in the Crystal Structure of the Nucleosome Core Particle


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 Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:68.6 occ:1.00 MN D:MN201 1.7 69.0 1.0 O D:VAL48 2.5 59.3 1.0 C D:VAL48 3.6 52.0 1.0 OE1 C:GLU64 3.7 59.9 1.0 OE2 C:GLU64 3.8 53.9 1.0 CA D:VAL48 4.1 52.7 1.0 CD C:GLU64 4.2 54.9 1.0 CE1 D:HIS49 4.4 56.7 1.0 ND1 D:HIS49 4.5 60.2 1.0 CB D:VAL48 4.7 55.8 1.0 N D:HIS49 4.8 55.3 1.0 NE2 D:HIS49 4.9 56.1 1.0 CG D:HIS49 5.0 46.7 1.0

Manganese binding site 3 out of 6 in the Crystal Structure of the Nucleosome Core Particle


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 Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ G:Mn201 b:99.3 occ:1.00 CA G:GLY44 3.4 70.0 1.0 N G:GLY46 3.4 59.6 1.0 N H:SER91 3.6 63.8 1.0 N G:ALA45 3.6 74.7 1.0 CA H:THR90 3.6 62.3 1.0 C G:GLY44 3.7 73.2 1.0 OP1 I:DA111 3.7 95.5 1.0 CB H:THR90 3.7 65.2 1.0 N G:ALA47 3.9 64.0 1.0 C H:THR90 4.0 59.0 1.0 CA G:GLY46 4.1 61.0 1.0 CG2 H:THR90 4.3 64.0 1.0 C G:GLY46 4.3 67.8 1.0 OG H:SER91 4.4 69.3 1.0 C G:ALA45 4.5 65.1 1.0 O G:GLY44 4.5 71.0 1.0 CA G:ALA45 4.5 66.8 1.0 CB H:SER91 4.6 62.6 1.0 N G:GLY44 4.6 70.8 1.0 CA H:SER91 4.6 65.3 1.0 CB G:ALA47 4.7 59.5 1.0 CA G:ALA47 4.8 58.7 1.0 O H:ILE89 4.8 63.8 1.0 N H:THR90 4.9 65.2 1.0 OG1 H:THR90 5.0 62.5 1.0

Manganese binding site 4 out of 6 in the Crystal Structure of the Nucleosome Core Particle


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 Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:0.3 occ:1.00 O4' I:DG138 3.5 0.7 1.0 C1' I:DG138 3.8 0.1 1.0 C4' I:DG138 3.8 0.9 1.0 O3' I:DG138 3.9 0.4 1.0 O4' I:DA139 3.9 0.1 1.0 C5' I:DA139 4.2 0.5 1.0 C4' I:DA139 4.3 0.3 1.0 N2 I:DG137 4.4 0.5 1.0 C3' I:DG138 4.4 0.7 1.0 N3 I:DG138 4.5 0.1 1.0 C2' I:DG138 4.7 0.0 1.0 N9 I:DG138 4.8 0.4 1.0

Manganese binding site 5 out of 6 in the Crystal Structure of the Nucleosome Core Particle


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 Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:0.3 occ:1.00 N7 I:DG18 3.5 0.4 1.0 O6 I:DG18 3.5 0.6 1.0 C6 I:DG18 4.2 0.9 1.0 C5 I:DG18 4.2 0.2 1.0 N6 I:DA19 4.5 0.1 1.0 N7 I:DA17 4.6 0.8 1.0 C8 I:DG18 4.6 0.1 1.0 C8 I:DA17 4.7 0.8 1.0 O4 J:DT274 4.8 0.6 1.0

Manganese binding site 6 out of 6 in the Crystal Structure of the Nucleosome Core Particle


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 Core Particle within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:0.2 occ:1.00 O4' I:DC114 4.0 0.5 1.0 O2 I:DC114 4.0 0.4 1.0 N3 I:DA113 4.1 0.7 1.0 C1' I:DC114 4.3 0.1 1.0 C1' I:DA113 4.6 0.8 1.0 O3' I:DA113 4.7 0.3 1.0 C2 I:DC114 4.7 0.5 1.0 C4' I:DC114 4.7 0.8 1.0 N1 I:DC114 4.8 0.2 1.0 C2 I:DA113 4.8 0.7 1.0 OP1 I:DC114 5.0 0.4 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