Manganese in PDB 5b1l: The Mouse Nucleosome Structure Containing H3T

The structure of The Mouse Nucleosome Structure Containing H3T, PDB code: 5b1l was solved by T.Urahama, S.Machida, N.Horikoshi, A.Osakabe, H.Tachiwana, H.Taguchi, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.83 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	98.968, 107.425, 167.332, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.3

The structure of The Mouse Nucleosome Structure Containing H3T also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Manganese atom in the The Mouse Nucleosome Structure Containing H3T (pdb code 5b1l). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the The Mouse Nucleosome Structure Containing H3T, PDB code: 5b1l:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:36.0 occ:1.00 O D:HOH409 1.8 29.7 1.0 O D:VAL48 2.2 28.2 1.0 O D:HOH402 2.3 33.7 1.0 O C:HOH409 2.4 35.4 1.0 C D:VAL48 3.2 31.2 1.0 CA D:VAL48 3.8 30.3 1.0 OE1 C:GLU64 4.2 40.5 1.0 O C:HOH406 4.3 36.6 1.0 N D:HIS49 4.4 31.5 1.0 O D:GLN47 4.4 36.6 1.0 ND1 D:HIS49 4.6 39.1 1.0 CB D:VAL48 4.6 35.1 1.0 CA D:HIS49 4.7 30.4 1.0 CD D:PRO50 4.8 32.6 1.0 CE1 D:HIS49 4.9 37.3 1.0 N D:VAL48 5.0 37.5 1.0

Manganese binding site 2 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn301 b:55.5 occ:1.00 O I:HOH435 1.9 38.7 1.0 O I:HOH406 2.4 47.9 1.0 N7 I:DG121 2.5 41.4 1.0 C8 I:DG121 3.4 43.3 1.0 C5 I:DG121 3.5 39.1 1.0 O6 I:DG121 3.7 38.3 1.0 C6 I:DG121 4.0 38.6 1.0 C2' I:DT120 4.2 43.8 1.0 O6 I:DG122 4.5 39.0 1.0 N9 I:DG121 4.7 42.4 1.0 C4 I:DG121 4.7 38.3 1.0 C6 I:DT120 4.8 37.8 1.0 N4 J:DC171 4.8 44.5 1.0

Manganese binding site 3 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn302 b:59.1 occ:1.00 O I:HOH414 2.8 43.3 1.0 OP1 I:DA126 4.1 61.4 1.0 O I:HOH424 4.3 46.6 1.0

Manganese binding site 4 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn303 b:72.7 occ:1.00 O I:HOH432 1.8 60.5 1.0 N7 I:DG134 2.5 58.1 1.0 O I:HOH437 2.9 52.7 1.0 C8 I:DG134 3.5 59.3 1.0 C5 I:DG134 3.6 57.5 1.0 O6 I:DG134 3.7 58.5 1.0 C6 I:DG134 4.0 57.3 1.0 C8 I:DA133 4.1 62.9 1.0 N7 I:DA133 4.2 57.6 1.0 O6 I:DG135 4.4 63.2 1.0 N9 I:DG134 4.7 64.6 1.0 C4 I:DG134 4.7 61.5 1.0 N7 I:DG135 5.0 60.9 1.0

Manganese binding site 5 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn304 b:55.7 occ:1.00 O J:HOH517 2.2 43.2 1.0 O I:HOH409 2.2 38.0 1.0 O6 I:DG68 2.3 44.5 1.0 C6 I:DG68 3.3 42.6 1.0 N7 I:DG68 3.7 42.5 1.0 C5 I:DG68 3.8 40.4 1.0 N4 J:DC225 3.9 42.5 1.0 O6 J:DG224 4.1 42.1 1.0 N7 J:DG224 4.4 48.5 1.0 N1 I:DG68 4.5 43.7 1.0 N7 I:DA67 4.7 45.8 1.0 C6 J:DG224 4.9 45.4 1.0 C5 J:DG224 5.0 48.2 1.0

Manganese binding site 6 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn305 b:67.7 occ:1.00 O I:HOH419 2.4 44.4 1.0 O J:HOH540 2.5 44.4 1.0 O J:HOH539 3.5 42.0 1.0 O2 I:DT86 3.9 42.7 1.0 O4' I:DG87 4.3 40.9 1.0 O4' J:DT208 4.3 34.8 1.0 C2 J:DA207 4.4 39.0 1.0 O2 J:DT208 4.4 39.3 1.0 N3 J:DA207 4.6 40.0 1.0 C4' I:DG87 4.6 45.8 1.0 O I:HOH415 4.6 44.4 1.0 O4' I:DC88 4.7 48.1 1.0 C4' J:DT208 4.9 37.5 1.0 N3 I:DG87 4.9 42.2 1.0 C1' J:DT208 4.9 41.8 1.0 C4' I:DC88 4.9 43.9 1.0 C5' I:DC88 5.0 44.4 1.0

Manganese binding site 7 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn306 b:87.2 occ:1.00 N7 I:DA17 2.7 44.8 1.0 C8 I:DA17 3.5 44.9 1.0 C5 I:DA17 3.8 43.0 1.0 N6 I:DA17 4.0 44.5 1.0 OP2 I:DA17 4.2 53.6 1.0 O6 I:DG18 4.3 40.9 1.0 O I:HOH403 4.3 49.3 1.0 C6 I:DA17 4.3 44.0 1.0 C2' I:DC16 4.7 50.0 1.0 N9 I:DA17 4.8 51.3 1.0 C4 I:DA17 4.9 43.2 1.0 N7 I:DG18 5.0 44.1 1.0

Manganese binding site 8 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn401 b:57.7 occ:1.00 O J:HOH532 1.8 51.2 1.0 O J:HOH505 2.1 52.6 1.0 O J:HOH537 2.3 50.1 1.0 N7 J:DG267 2.5 50.3 1.0 O J:HOH545 2.6 42.0 1.0 C8 J:DG267 3.2 47.9 1.0 C5 J:DG267 3.7 47.3 1.0 OP2 J:DG267 3.9 54.9 1.0 O6 J:DG268 4.2 44.2 1.0 O6 J:DG267 4.2 48.4 1.0 O I:HOH426 4.2 41.7 1.0 C6 J:DG267 4.3 47.1 1.0 C2' J:DT266 4.3 45.3 1.0 N9 J:DG267 4.5 45.8 1.0 C4 J:DG267 4.7 44.2 1.0

Manganese binding site 9 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn402 b:56.7 occ:1.00 O J:HOH530 2.1 43.0 1.0 N7 J:DG185 2.3 42.3 1.0 O J:HOH531 2.3 50.6 1.0 O6 J:DG186 2.5 38.0 1.0 O J:HOH522 2.7 44.6 1.0 C8 J:DG185 3.1 41.1 1.0 C5 J:DG185 3.4 41.0 1.0 C6 J:DG186 3.4 42.2 1.0 O6 J:DG185 3.8 47.0 1.0 N7 J:DG186 3.9 38.1 1.0 C6 J:DG185 3.9 46.2 1.0 C5 J:DG186 4.0 41.9 1.0 N4 I:DC107 4.0 44.9 1.0 N9 J:DG185 4.3 45.0 1.0 OP2 J:DG185 4.3 50.0 1.0 C4 J:DG185 4.4 39.0 1.0 N1 J:DG186 4.6 37.9 1.0 C2' J:DT184 4.7 46.5 1.0

Manganese binding site 10 out of 13 in the The Mouse Nucleosome Structure Containing H3T


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Mouse Nucleosome Structure Containing H3T within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn403 b:67.6 occ:1.00 O J:HOH544 2.1 54.0 1.0 O J:HOH519 2.3 54.6 1.0 N7 J:DG280 2.4 57.7 1.0 C8 J:DG280 3.3 61.7 1.0 C5 J:DG280 3.4 56.9 1.0 O6 J:DG280 3.6 53.1 1.0 C8 J:DA279 3.8 52.9 1.0 C6 J:DG280 3.9 55.6 1.0 N7 J:DA279 4.0 50.1 1.0 O6 J:DG281 4.4 57.4 1.0 N9 J:DG280 4.5 60.9 1.0 C4 J:DG280 4.6 56.9 1.0 OP2 J:DA279 4.7 48.1 1.0 N9 J:DA279 4.8 57.3 1.0 C2' J:DA279 4.8 57.7 1.0

J.Ueda, A.Harada, T.Urahama, S.Machida, K.Maehara, M.Hada, Y.Makino, J.Nogami, N.Horikoshi, A.Osakabe, H.Taguchi, H.Tanaka, H.Tachiwana, T.Yao, M.Yamada, T.Iwamoto, A.Isotani, M.Ikawa, T.Tachibana, Y.Okada, H.Kimura, Y.Ohkawa, H.Kurumizaka, K.Yamagata. Testis-Specific Histone Variant H3T Gene Is Essential For Entry Into Spermatogenesis Cell Rep V. 18 593 2017.
ISSN: ESSN 2211-1247
PubMed: 28099840
DOI: 10.1016/J.CELREP.2016.12.065