Manganese in PDB 3x1t: Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA, PDB code: 3x1t 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)	34.96 / 2.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	105.771, 109.597, 181.597, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 26.6

The structure of Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA (pdb code 3x1t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 22 binding sites of Manganese where determined in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA, PDB code: 3x1t:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:0.5 occ:1.00 O6 I:DG68 2.9 78.2 1.0 N4 J:DC225 3.9 85.8 1.0 N7 J:DG224 3.9 82.1 1.0 O6 J:DG224 4.0 81.8 1.0 C6 I:DG68 4.0 77.2 1.0 N7 I:DG68 4.4 74.9 1.0 C5 J:DG224 4.4 82.2 1.0 C6 J:DG224 4.5 78.4 1.0 C5 I:DG68 4.6 73.2 1.0 N7 I:DA67 4.8 73.7 1.0 C8 J:DG224 4.8 82.1 1.0 C4 J:DC225 4.9 85.6 1.0

Manganese binding site 2 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:0.6 occ:1.00 N7 I:DG121 2.6 1.0 1.0 O6 I:DG122 2.7 0.2 1.0 MN I:MN209 2.8 0.7 1.0 N4 J:DC171 3.1 0.7 1.0 O6 I:DG121 3.1 0.9 1.0 C5 I:DG121 3.1 0.8 1.0 C6 I:DG121 3.4 0.4 1.0 C8 I:DG121 3.6 0.6 1.0 C6 I:DG122 3.8 0.5 1.0 C4 I:DG121 4.3 0.5 1.0 N7 I:DG122 4.3 0.7 1.0 C4 J:DC171 4.3 0.8 1.0 C5 I:DG122 4.4 1.0 1.0 N9 I:DG121 4.5 0.9 1.0 N1 I:DG121 4.6 0.2 1.0 N3 J:DC171 4.9 0.3 1.0 N1 I:DG122 4.9 0.6 1.0

Manganese binding site 3 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:98.7 occ:1.00 N7 I:DA133 2.1 97.0 1.0 MN I:MN206 2.4 0.0 1.0 C8 I:DA133 3.0 0.7 1.0 C5 I:DA133 3.2 0.3 1.0 N6 I:DA133 3.6 94.3 1.0 C6 I:DA133 3.8 96.9 1.0 O6 I:DG134 3.9 96.7 1.0 N7 I:DG134 4.1 0.1 1.0 C6 I:DC132 4.1 93.6 1.0 N9 I:DA133 4.3 0.3 1.0 C5 I:DC132 4.4 95.8 1.0 C4 I:DA133 4.4 1.0 1.0 C2' I:DC132 4.6 99.5 1.0 C6 I:DG134 4.6 98.3 1.0 C5 I:DG134 4.7 0.2 1.0

Manganese binding site 4 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn204 b:99.4 occ:1.00 O J:HOH401 2.5 64.2 1.0 O6 I:DG78 2.8 81.0 1.0 C6 I:DG78 3.9 74.8 1.0 N4 J:DC215 4.3 72.5 1.0 N7 I:DG78 4.3 78.9 1.0 N7 J:DG214 4.3 66.8 1.0 C5 I:DG78 4.5 72.4 1.0 O6 J:DG214 4.5 69.6 1.0 N7 I:DA77 4.7 72.9 1.0

Manganese binding site 5 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn205 b:91.5 occ:1.00 O2 I:DT86 3.8 78.0 1.0 O4' J:DT208 4.0 53.4 1.0 O4' I:DG87 4.2 68.9 1.0 O4' I:DC88 4.4 59.8 1.0 C2 J:DA207 4.4 65.2 1.0 O2 J:DT208 4.5 64.1 1.0 N3 J:DA207 4.6 58.8 1.0 N3 I:DG87 4.6 76.3 1.0 C4' I:DG87 4.7 62.7 1.0 C4' I:DC88 4.7 64.2 1.0 C4' J:DT208 4.8 47.2 1.0 C1' I:DG87 4.8 67.3 1.0 C1' J:DT208 4.9 54.9 1.0 C2 I:DT86 4.9 78.5 1.0

Manganese binding site 6 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn206 b:0.0 occ:1.00 MN I:MN203 2.4 98.7 1.0 N6 I:DA133 4.2 94.3 1.0 N7 I:DA133 4.3 97.0 1.0 C5 I:DC132 4.5 95.8 1.0 O6 I:DG134 4.6 96.7 1.0 C6 I:DC132 4.7 93.6 1.0

Manganese binding site 7 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn207 b:0.1 occ:1.00 N7 I:DG100 2.4 93.4 1.0 O I:HOH301 2.9 92.3 1.0 O6 I:DG100 3.0 99.9 1.0 C5 I:DG100 3.2 89.6 1.0 C6 I:DG100 3.4 94.5 1.0 C8 I:DG100 3.5 88.7 1.0 N7 I:DA99 4.0 92.2 1.0 C8 I:DA99 4.0 92.9 1.0 C4 I:DG100 4.5 87.4 1.0 N9 I:DG100 4.6 86.8 1.0 N1 I:DG100 4.8 99.0 1.0 C5 I:DA99 5.0 91.4 1.0 N9 I:DA99 5.0 85.3 1.0

Manganese binding site 8 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn208 b:0.6 occ:1.00 O4' J:DA218 4.5 68.2 1.0 C5' I:DG78 4.5 67.6 1.0 C4' J:DA218 4.6 68.9 1.0 C4' I:DG78 4.6 69.4 1.0 O4' I:DG78 4.6 73.1 1.0 N3 I:DA77 4.7 69.5 1.0 N2 J:DG217 4.8 68.8 1.0

Manganese binding site 9 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn209 b:0.7 occ:1.00 MN I:MN202 2.8 0.6 1.0 MN I:MN210 3.3 0.0 1.0 N7 I:DG121 3.3 1.0 1.0 C2' I:DT120 3.9 99.0 1.0 C8 I:DG121 4.1 0.6 1.0 C6 I:DT120 4.4 0.6 1.0 C5 I:DG121 4.5 0.8 1.0 O6 I:DG121 4.6 0.9 1.0 N1 I:DT120 4.9 0.5 1.0 C5 I:DT120 4.9 0.3 1.0 C3' I:DT120 4.9 0.9 1.0 C6 I:DG121 4.9 0.4 1.0 OP2 I:DG121 4.9 97.4 1.0 C1' I:DT120 5.0 0.1 1.0

Manganese binding site 10 out of 22 in the Crystal Structure of Nucleosome Core Particle Consisting of Mouse Testis Specific Histone Variants H2AA and H2BA


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 Mouse Testis Specific Histone Variants H2AA and H2BA within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn210 b:0.0 occ:1.00 C7 I:DT120 2.5 0.4 1.0 OP2 I:DT120 3.1 92.8 1.0 C6 I:DT120 3.2 0.6 1.0 C5 I:DT120 3.2 0.3 1.0 MN I:MN209 3.3 0.7 1.0 C2' I:DT119 4.3 99.5 1.0 N1 I:DT120 4.4 0.5 1.0 P I:DT120 4.4 94.2 1.0 C4 I:DT120 4.5 0.8 1.0 C2' I:DT120 4.7 99.0 1.0 O5' I:DT120 4.8 98.5 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