Manganese in PDB 5gt0: Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A

The structure of Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A, PDB code: 5gt0 was solved by T.Kumarevel, P.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.80 / 2.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.788, 108.966, 170.951, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 28

The structure of Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A (pdb code 5gt0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A, PDB code: 5gt0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn201 b:42.1 occ:1.00 CL E:CL202 2.2 37.5 1.0 OD1 E:ASP77 2.5 27.1 1.0 CG E:ASP77 3.2 23.3 1.0 OD2 E:ASP77 3.2 19.2 1.0 O F:LEU22 4.1 24.3 1.0 CG E:GLU73 4.1 19.9 1.0 O E:GLU73 4.2 27.0 1.0 CB E:ASP77 4.7 19.6 1.0 O E:HOH302 4.8 19.9 1.0 CD E:GLU73 4.9 24.6 1.0

Manganese binding site 2 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:48.0 occ:1.00 N C:GLY46 3.0 18.4 1.0 N D:SER91 3.2 23.6 1.0 CA C:GLY46 3.4 20.1 1.0 N C:ALA47 3.5 23.7 1.0 CA C:GLY44 3.5 19.3 1.0 C C:GLY44 3.6 24.7 1.0 CA D:THR90 3.6 26.0 1.0 N C:ALA45 3.7 22.5 1.0 CB D:THR90 3.7 25.6 1.0 C C:GLY46 3.8 23.8 1.0 C D:THR90 3.8 23.7 1.0 OP1 J:DT258 4.1 39.2 1.0 CB D:SER91 4.1 24.1 1.0 OG D:SER91 4.1 25.4 1.0 C C:ALA45 4.2 23.5 1.0 O C:GLY44 4.2 26.2 1.0 CA D:SER91 4.2 23.2 1.0 CA C:ALA47 4.5 20.0 1.0 CA C:ALA45 4.5 19.9 1.0 N C:GLY44 4.6 23.7 1.0 CB C:ALA47 4.6 20.9 1.0 CG2 D:THR90 4.6 25.4 1.0 OG1 D:THR90 4.8 25.9 1.0 O D:ILE89 4.9 27.1 1.0 N D:THR90 4.9 24.6 1.0 O C:GLY46 4.9 24.0 1.0

Manganese binding site 3 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:54.0 occ:1.00 N7 I:DG121 2.5 39.9 1.0 C8 I:DG121 3.4 45.2 1.0 C5 I:DG121 3.5 41.7 1.0 O6 I:DG121 3.6 48.3 1.0 C6 I:DG121 3.9 43.0 1.0 O6 I:DG122 4.2 40.2 1.0 N9 I:DG121 4.6 43.2 1.0 C4 I:DG121 4.7 40.7 1.0 C2' I:DT120 4.8 49.8 1.0 N4 J:DC171 4.9 50.1 1.0

Manganese binding site 4 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:77.8 occ:1.00 N7 I:DG134 2.5 94.5 1.0 N7 I:DA133 3.0 0.8 1.0 C8 I:DA133 3.0 0.8 1.0 C8 I:DG134 3.5 91.7 1.0 C5 I:DG134 3.6 94.2 1.0 O6 I:DG134 3.7 0.2 1.0 CL I:CL208 3.7 73.4 1.0 C6 I:DG134 4.0 97.2 1.0 N9 I:DA133 4.2 0.9 1.0 C5 I:DA133 4.2 0.5 1.0 OP2 I:DA133 4.4 0.6 1.0 N9 I:DG134 4.7 96.1 1.0 C2' I:DA133 4.7 95.6 1.0 C4 I:DG134 4.7 97.3 1.0 C4 I:DA133 4.8 0.0 1.0

Manganese binding site 5 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:87.3 occ:1.00 O H:HOH201 2.8 16.4 1.0 OP1 I:DA111 3.0 37.2 1.0 P I:DA111 4.0 55.8 1.0 O3' I:DA110 4.2 50.3 1.0 CB H:THR90 4.4 17.7 1.0 OP2 I:DA111 4.4 36.1 1.0 C3' I:DA110 4.5 41.7 1.0 CA G:GLY44 4.8 18.2 1.0 N G:GLY46 4.8 19.0 1.0 CG2 H:THR90 4.8 17.5 1.0 N G:ALA45 4.9 24.8 1.0

Manganese binding site 6 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn204 b:0.7 occ:1.00 O I:HOH313 2.1 76.0 1.0 O6 I:DG131 2.9 82.8 1.0 N7 I:DG131 3.4 95.3 1.0 C6 I:DG131 3.7 86.5 1.0 C5 I:DG131 3.9 90.9 1.0 O6 J:DG161 4.0 87.0 1.0 C8 I:DG131 4.7 96.5 1.0 N4 I:DC132 4.7 95.3 1.0 C6 I:DT130 4.8 80.1 1.0 C2' I:DT130 4.8 87.6 1.0 C7 I:DT130 4.9 79.0 1.0

Manganese binding site 7 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn205 b:66.2 occ:1.00 N7 I:DG100 2.2 44.8 1.0 C5 I:DG100 3.0 41.7 1.0 O6 I:DG100 3.1 43.1 1.0 C8 I:DG100 3.2 41.8 1.0 C6 I:DG100 3.4 44.4 1.0 O6 J:DG192 4.2 44.6 1.0 C4 I:DG100 4.2 40.7 1.0 N9 I:DG100 4.3 39.6 1.0 N1 I:DG100 4.7 45.2 1.0 C8 I:DA99 4.8 45.1 1.0 N4 I:DC101 4.8 43.4 1.0 N7 I:DA99 5.0 44.8 1.0 C7 J:DT191 5.0 47.0 1.0

Manganese binding site 8 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn206 b:87.2 occ:1.00 OP2 I:DT106 2.8 64.9 1.0 P I:DT106 3.6 65.6 1.0 C3' I:DT105 3.7 67.2 1.0 OP1 I:DT106 3.9 62.6 1.0 O3' I:DT105 4.1 66.8 1.0 C2' I:DT105 4.4 67.3 1.0 O5' I:DT105 4.6 67.5 1.0 C4' I:DT105 4.9 62.7 1.0

Manganese binding site 9 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:82.8 occ:1.00 O J:HOH422 1.9 77.0 1.0 O J:HOH421 1.9 67.1 1.0 O J:HOH415 2.4 71.3 1.0 N7 J:DG280 2.9 74.3 1.0 O6 J:DG280 3.1 83.1 1.0 C5 J:DG280 3.6 77.9 1.0 C6 J:DG280 3.7 77.9 1.0 C8 J:DA279 3.9 66.5 1.0 N7 J:DA279 3.9 64.5 1.0 C8 J:DG280 4.1 75.4 1.0 O6 J:DG281 4.2 87.7 1.0 N9 J:DA279 4.9 70.0 1.0 C4 J:DG280 5.0 82.0 1.0 C5 J:DA279 5.0 64.4 1.0

Manganese binding site 10 out of 14 in the Crystal Structure of Nucleosome Complex with Human Testis-Specific Histone Variants, TH2A


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 Complex with Human Testis-Specific Histone Variants, TH2A within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn302 b:49.6 occ:1.00 N3 J:DA181 4.0 43.3 1.0 N3 I:DA113 4.1 38.2 1.0 O4' I:DC114 4.5 47.8 1.0 C2 I:DA113 4.6 37.2 1.0 C2 J:DA181 4.6 41.7 1.0 O4' J:DT182 4.8 62.4 1.0 C1' J:DA181 4.8 66.2 1.0 O4' J:DA181 4.9 68.4 1.0

S.Padavattan, V.Thiruselvam, T.Shinagawa, K.Hasegawa, T.Kumasaka, S.Ishii, T.Kumarevel. Structural Analyses of the Nucleosome Complexes with Human Testis-Specific Histone Variants, HTH2A and HTH2B Biophys. Chem. V. 221 41 2017.
ISSN: ISSN 1873-4200
PubMed: 27992841
DOI: 10.1016/J.BPC.2016.11.013