Manganese in PDB 6kvd: Crystal Structure of Human Nucleosome Containing H2A.J

The structure of Crystal Structure of Human Nucleosome Containing H2A.J, PDB code: 6kvd was solved by H.Tanaka, M.Koyama, S.Sato, T.Kujirai, H.Kurumizaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.84 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	99.640, 108.791, 171.177, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.7

The structure of Crystal Structure of Human Nucleosome Containing H2A.J 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 Crystal Structure of Human Nucleosome Containing H2A.J (pdb code 6kvd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 13 binding sites of Manganese where determined in the Crystal Structure of Human Nucleosome Containing H2A.J, PDB code: 6kvd:
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 Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn201 b:54.0 occ:1.00 N7 I:DG121 2.3 34.1 1.0 C8 I:DG121 3.1 39.2 1.0 C5 I:DG121 3.5 42.8 1.0 O6 I:DG121 3.9 41.4 1.0 C6 I:DG121 4.1 39.6 1.0 O I:HOH306 4.2 43.6 1.0 O6 I:DG122 4.4 39.0 1.0 N9 I:DG121 4.4 37.8 1.0 C2' I:DT120 4.5 49.8 1.0 C4 I:DG121 4.5 36.5 1.0

Manganese binding site 2 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn202 b:86.8 occ:1.00 N7 I:DG134 2.6 74.7 1.0 C8 I:DG134 3.5 71.2 1.0 C5 I:DG134 3.6 72.3 1.0 O6 I:DG134 3.8 70.9 1.0 C6 I:DG134 4.1 72.1 1.0 O6 I:DG135 4.4 66.9 1.0 C8 I:DA133 4.4 75.8 1.0 N7 I:DA133 4.5 74.9 1.0 N9 I:DG134 4.7 73.9 1.0 C4 I:DG134 4.8 73.6 1.0 OP2 I:DA133 4.8 81.1 1.0

Manganese binding site 3 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn203 b:60.9 occ:1.00 N3 I:DA113 4.4 41.6 1.0 C5' J:DT182 4.4 50.5 1.0 N3 J:DA181 4.4 47.6 1.0 C4' J:DT182 4.5 53.2 1.0 O4' J:DT182 4.6 47.2 1.0 C5' I:DC114 4.6 54.7 1.0 O J:HOH415 4.6 46.2 1.0 O4' I:DC114 4.7 52.1 1.0 C4' I:DC114 4.8 53.2 1.0 C2 I:DA113 4.9 39.0 1.0

Manganese binding site 4 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn204 b:82.1 occ:1.00 O6 I:DG68 2.6 62.0 1.0 C6 I:DG68 3.7 59.3 1.0 N7 J:DG224 4.1 63.2 1.0 N4 J:DC225 4.2 61.8 1.0 N7 I:DG68 4.2 55.2 1.0 C5 I:DG68 4.3 54.2 1.0 O6 J:DG224 4.4 58.8 1.0 N1 I:DG68 4.8 59.2 1.0 C5 J:DG224 4.9 63.2 1.0 N7 I:DA67 4.9 58.2 1.0 C6 J:DG224 5.0 60.5 1.0 C8 J:DG224 5.0 65.0 1.0

Manganese binding site 5 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn205 b:82.4 occ:1.00 OP2 I:DA27 2.2 60.8 1.0 P I:DA27 3.5 57.9 1.0 N7 I:DA27 3.7 52.5 1.0 C8 I:DA27 3.8 49.7 1.0 O3' I:DC26 3.8 55.9 1.0 C3' I:DC26 4.3 50.7 1.0 O5' I:DA27 4.4 59.1 1.0 C2' I:DC26 4.6 48.0 1.0 OP1 I:DA27 4.7 53.5 1.0

Manganese binding site 6 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn206 b:78.0 occ:1.00 N7 I:DG100 2.4 48.8 1.0 O6 I:DG100 3.2 56.8 1.0 C5 I:DG100 3.3 43.8 1.0 C8 I:DG100 3.4 46.6 1.0 C6 I:DG100 3.6 47.4 1.0 N7 I:DA99 4.4 47.0 1.0 C8 I:DA99 4.4 54.0 1.0 O6 J:DG192 4.5 53.1 1.0 C4 I:DG100 4.5 46.4 1.0 N9 I:DG100 4.6 48.7 1.0 N4 I:DC101 4.7 52.8 1.0 N1 I:DG100 5.0 43.6 1.0

Manganese binding site 7 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ I:Mn207 b:69.5 occ:1.00 O J:HOH426 2.7 37.2 1.0 O2 I:DT86 4.2 50.2 1.0 C2 J:DA207 4.2 43.1 1.0 N3 J:DA207 4.3 40.5 1.0 O4' J:DT208 4.3 38.1 1.0 O2 J:DT208 4.4 40.9 1.0 O4' I:DG87 4.5 45.2 1.0 O4' I:DC88 4.7 50.4 1.0 C4' J:DT208 4.7 40.8 1.0 C1' J:DT208 4.7 41.8 1.0 C4' I:DC88 4.8 52.6 1.0 C4' I:DG87 4.9 50.7 1.0 C5' I:DC88 4.9 48.4 1.0 N3 I:DG87 4.9 45.8 1.0

Manganese binding site 8 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn301 b:59.6 occ:1.00 O J:HOH427 2.3 46.9 1.0 N7 J:DG267 2.4 46.8 1.0 O J:HOH452 2.4 49.5 1.0 O J:HOH406 2.4 46.2 1.0 C8 J:DG267 3.2 46.8 1.0 C5 J:DG267 3.5 46.8 1.0 O6 J:DG267 3.8 52.3 1.0 C6 J:DG267 4.0 46.7 1.0 OP2 J:DG267 4.1 48.5 1.0 O6 J:DG268 4.1 39.6 1.0 O J:HOH401 4.3 32.4 1.0 C2' J:DT266 4.4 50.2 1.0 N9 J:DG267 4.5 46.1 1.0 C4 J:DG267 4.6 43.3 1.0

Manganese binding site 9 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn302 b:64.2 occ:1.00 N7 J:DG217 2.3 43.1 1.0 C8 J:DG217 3.1 47.0 1.0 C5 J:DG217 3.4 42.8 1.0 O6 J:DG217 3.7 52.8 1.0 C6 J:DG217 3.9 48.4 1.0 N6 J:DA218 4.0 50.3 1.0 C2' J:DT216 4.2 44.7 1.0 OP2 J:DG217 4.3 42.6 1.0 N9 J:DG217 4.4 50.9 1.0 C4 J:DG217 4.5 46.2 1.0 C6 J:DT216 4.9 44.0 1.0 C6 J:DA218 5.0 52.5 1.0 N7 J:DA218 5.0 50.0 1.0

Manganese binding site 10 out of 13 in the Crystal Structure of Human Nucleosome Containing H2A.J


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 Human Nucleosome Containing H2A.J within 5.0Å range: probe atom residue distance (Å) B Occ J:Mn303 b:82.8 occ:1.00 N7 J:DG280 2.4 63.0 1.0 O6 J:DG280 3.2 68.0 1.0 C5 J:DG280 3.3 65.7 1.0 C8 J:DG280 3.5 68.2 1.0 C6 J:DG280 3.6 66.4 1.0 N7 J:DA279 4.0 56.5 1.0 C8 J:DA279 4.1 56.8 1.0 O6 J:DG281 4.3 78.9 1.0 C4 J:DG280 4.6 68.8 1.0 N9 J:DG280 4.7 71.0 1.0

H.Tanaka, S.Sato, M.Koyama, T.Kujirai, H.Kurumizaka. Biochemical and Structural Analyses of the Nucleosome Containing Human Histone H2A.J. J.Biochem. 2019.
ISSN: ISSN 0021-924X
PubMed: 31793981
DOI: 10.1093/JB/MVZ109