Manganese in PDB 5gsu: Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B, PDB code: 5gsu 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)	35.33 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.095, 109.740, 182.445, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25.7

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B (pdb code 5gsu). 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 Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B, PDB code: 5gsu:
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 Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:69.3 occ:1.00 MN D:MN202 1.6 77.0 1.0 O D:VAL46 2.3 60.9 1.0 OE2 C:GLU66 3.0 69.0 1.0 C D:VAL46 3.4 54.5 1.0 CA D:VAL46 3.9 52.6 1.0 CD C:GLU66 4.3 68.8 1.0 CB D:VAL46 4.5 53.3 1.0 N D:HIS47 4.5 54.8 1.0 NE2 D:HIS47 4.6 49.4 1.0 CD2 D:HIS47 4.7 51.2 1.0 CE1 D:HIS47 4.9 57.6 1.0 CA D:HIS47 4.9 56.8 1.0 O D:GLN45 4.9 59.8 1.0 OE1 C:GLU66 4.9 79.5 1.0 CG D:HIS47 5.0 50.9 1.0

Manganese binding site 2 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:77.0 occ:1.00 MN D:MN201 1.6 69.3 1.0 O D:VAL46 2.2 60.9 1.0 C D:VAL46 3.0 54.5 1.0 CA D:VAL46 3.2 52.6 1.0 O D:GLN45 3.5 59.8 1.0 OE2 C:GLU66 4.2 69.0 1.0 CB D:VAL46 4.2 53.3 1.0 N D:VAL46 4.2 51.1 1.0 N D:HIS47 4.3 54.8 1.0 C D:GLN45 4.3 51.6 1.0 CD D:PRO48 4.7 61.5 1.0 CG1 D:VAL46 4.9 55.4 1.0 CA D:HIS47 4.9 56.8 1.0

Manganese binding site 3 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:0.5 occ:1.00 OP1 I:DC84 3.3 93.6 1.0 OP1 I:DT6 3.8 0.5 1.0 OP2 I:DC84 4.0 85.3 1.0 P I:DC84 4.1 92.6 1.0 O5' I:DT6 4.2 0.3 1.0 P I:DT6 4.6 0.9 1.0 O3' I:DA83 4.9 82.4 1.0

Manganese binding site 4 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:0.4 occ:1.00 O4' J:DA218 4.4 90.9 1.0 N2 J:DG217 4.4 0.5 1.0 C5' I:DG78 4.5 0.7 1.0 N3 I:DA77 4.6 0.0 1.0 C4' J:DA218 4.6 90.2 1.0 C4' I:DG78 4.8 97.9 1.0 O4' I:DG78 5.0 97.2 1.0

Manganese binding site 5 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:0.4 occ:1.00 N7 I:DA133 2.3 0.5 1.0 MN I:MN204 2.4 0.2 1.0 C8 I:DA133 3.0 0.6 1.0 C5 I:DA133 3.2 0.3 1.0 N7 I:DG134 3.6 0.8 1.0 N6 I:DA133 3.6 0.2 1.0 C6 I:DA133 3.8 0.5 1.0 O6 I:DG134 3.8 0.7 1.0 N9 I:DA133 4.2 0.3 1.0 C4 I:DA133 4.2 0.1 1.0 C5 I:DG134 4.3 0.9 1.0 C6 I:DG134 4.4 1.0 1.0 C8 I:DG134 4.6 0.9 1.0 C6 I:DC132 4.9 0.0 1.0 C5 I:DC132 4.9 1.0 1.0

Manganese binding site 6 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn204 b:0.2 occ:1.00 MN I:MN203 2.4 0.4 1.0 N6 I:DA133 3.4 0.2 1.0 N7 I:DA133 3.6 0.5 1.0 C5 I:DC132 4.1 1.0 1.0 C5 I:DA133 4.3 0.3 1.0 C6 I:DA133 4.3 0.5 1.0 C6 I:DC132 4.5 0.0 1.0 O6 I:DG134 4.5 0.7 1.0 C8 I:DA133 4.7 0.6 1.0 OP2 I:DC132 4.9 1.0 1.0

Manganese binding site 7 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn205 b:96.6 occ:1.00 O4' I:DG87 4.0 0.1 1.0 O2 I:DT86 4.1 99.2 1.0 O4' J:DT208 4.1 72.0 1.0 O4' I:DC88 4.2 89.1 1.0 O2 J:DT208 4.4 92.2 1.0 C2 J:DA207 4.4 86.4 1.0 C4' I:DC88 4.4 89.4 1.0 C5' I:DC88 4.4 94.4 1.0 C4' I:DG87 4.6 91.7 1.0 N3 J:DA207 4.7 81.9 1.0 C1' J:DT208 4.8 76.5 1.0

Manganese binding site 8 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn206 b:0.3 occ:1.00 N7 I:DG121 2.6 0.5 1.0 O6 I:DG121 3.0 0.7 1.0 C5 I:DG121 3.4 0.1 1.0 CL I:CL209 3.5 98.4 1.0 C6 I:DG121 3.5 0.5 1.0 C8 I:DG121 3.8 0.7 1.0 C2' I:DT120 3.8 0.1 1.0 C6 I:DT120 3.8 0.6 1.0 OP2 I:DT120 4.1 0.1 1.0 C5 I:DT120 4.2 1.0 1.0 C7 I:DT120 4.3 0.9 1.0 N1 I:DT120 4.4 0.2 1.0 C4 I:DG121 4.7 0.1 1.0 C1' I:DT120 4.7 0.8 1.0 N9 I:DG121 4.8 0.7 1.0 N1 I:DG121 4.9 0.0 1.0 O6 I:DG122 5.0 0.5 1.0

Manganese binding site 9 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn207 b:0.5 occ:1.00 C7 I:DT136 2.2 0.7 1.0 C5 I:DT136 2.9 0.5 1.0 O6 I:DG137 3.4 1.0 1.0 C6 I:DT136 3.4 0.5 1.0 N7 I:DG137 3.6 0.0 1.0 C4 I:DT136 3.9 0.4 1.0 C6 I:DG137 4.0 0.7 1.0 C5 I:DG137 4.1 0.4 1.0 O4 I:DT136 4.2 0.2 1.0 N1 I:DT136 4.6 0.4 1.0 C8 I:DG137 4.7 0.7 1.0 N3 I:DT136 4.9 0.6 1.0

Manganese binding site 10 out of 15 in the Crystal Structure of Nucleosome Core Particle Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B


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 Consisting of Human Testis-Specific Histone Variants, TH2A and TH2B within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn208 b:0.8 occ:1.00 OP1 I:DA67 4.3 0.6 1.0 OP2 I:DA145 4.9 0.2 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