Atomistry » Manganese » PDB 6i90-6jr1 » 6jr0
Atomistry »
  Manganese »
    PDB 6i90-6jr1 »
      6jr0 »

Manganese in PDB 6jr0: Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms

Protein crystallography data

The structure of Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms, PDB code: 6jr0 was solved by M.Saotome, N.Horikoshi, K.Urano, T.Kujirai, H.Yuzurihara, H.Kurumizaka, W.Kagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.566, 108.514, 168.935, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.3

Other elements in 6jr0:

The structure of Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms (pdb code 6jr0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms, PDB code: 6jr0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 1 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn201

b:29.6
occ:1.00
O E:HOH319 2.0 22.3 1.0
OD1 E:ASP77 2.1 31.3 1.0
O E:HOH312 2.2 19.7 1.0
CG E:ASP77 3.1 27.2 1.0
OD2 E:ASP77 3.6 23.9 1.0
O F:HOH206 3.8 15.6 1.0
CA E:ASP77 4.3 24.6 1.0
CG E:GLN76 4.3 26.1 1.0
O F:HOH216 4.3 21.9 1.0
CB E:ASP77 4.3 27.6 1.0
N E:ASP77 4.3 24.7 1.0
O E:GLU73 4.6 24.8 1.0
C E:GLN76 4.6 30.3 1.0
CB E:GLN76 4.8 24.1 1.0
O E:GLN76 4.8 29.0 1.0

Manganese binding site 2 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 2 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn201

b:0.8
occ:1.00
N7 I:DG100 2.7 46.5 1.0
O I:HOH328 3.5 52.1 1.0
C8 I:DG100 3.6 48.4 1.0
O6 I:DG100 3.6 53.4 1.0
C5 I:DG100 3.7 45.9 1.0
C6 I:DG100 4.0 50.8 1.0
O I:HOH318 4.4 42.1 1.0
C8 I:DA99 4.8 52.8 1.0
N9 I:DG100 4.8 48.9 1.0
C4 I:DG100 4.9 42.6 1.0
N4 I:DC101 5.0 47.9 1.0
N7 I:DA99 5.0 49.3 1.0

Manganese binding site 3 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 3 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn202

b:83.5
occ:1.00
N7 I:DG134 2.5 54.3 1.0
C8 I:DG134 3.4 55.1 1.0
C5 I:DG134 3.5 49.9 1.0
O6 I:DG134 3.6 51.8 1.0
O I:HOH341 3.9 45.3 1.0
C6 I:DG134 3.9 50.3 1.0
O6 I:DG135 4.1 58.7 1.0
N9 I:DG134 4.6 50.9 1.0
C4 I:DG134 4.6 50.5 1.0
N7 I:DA133 4.6 51.1 1.0
C8 I:DA133 4.6 54.1 1.0
N7 I:DG135 4.8 53.1 1.0
C6 I:DG135 5.0 52.4 1.0

Manganese binding site 4 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 4 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mn203

b:46.6
occ:1.00
O I:HOH354 1.9 41.2 1.0
O I:HOH391 2.0 64.2 1.0
N7 I:DG121 2.5 30.1 1.0
O6 I:DG121 3.3 27.5 1.0
C5 I:DG121 3.4 28.6 1.0
C8 I:DG121 3.5 38.3 1.0
C6 I:DG121 3.7 31.0 1.0
C2' I:DT120 4.2 43.0 1.0
O6 I:DG122 4.3 32.4 1.0
C4 I:DG121 4.6 32.7 1.0
N9 I:DG121 4.7 37.3 1.0
N4 J:DC171 4.8 30.6 1.0
C6 I:DT120 4.9 34.6 1.0

Manganese binding site 5 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 5 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn301

b:87.1
occ:1.00
N7 J:DG280 2.5 65.8 1.0
C8 J:DG280 3.4 68.2 1.0
C5 J:DG280 3.5 63.2 1.0
O6 J:DG280 3.7 70.2 1.0
C6 J:DG280 4.0 63.8 1.0
O6 J:DG281 4.2 75.1 1.0
C8 J:DA279 4.5 56.0 1.0
N7 J:DA279 4.5 54.4 1.0
N9 J:DG280 4.6 64.7 1.0
OP2 J:DA279 4.6 55.4 1.0
C4 J:DG280 4.7 64.7 1.0
N7 J:DG281 4.8 76.1 1.0

Manganese binding site 6 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 6 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn302

b:67.8
occ:1.00
O J:HOH425 1.9 66.8 1.0
O J:HOH475 2.2 37.3 1.0
N7 J:DG267 2.6 48.5 1.0
C8 J:DG267 3.5 47.2 1.0
C5 J:DG267 3.7 46.6 1.0
O6 J:DG267 4.0 48.1 1.0
OP2 J:DG267 4.1 54.4 1.0
C6 J:DG267 4.2 47.1 1.0
C2' J:DT266 4.4 49.8 1.0
O6 J:DG268 4.4 45.6 1.0
O J:HOH428 4.6 34.9 1.0
N9 J:DG267 4.7 46.8 1.0
C4 J:DG267 4.8 45.6 1.0
N4 I:DC25 5.0 44.8 1.0

Manganese binding site 7 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 7 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn303

b:67.9
occ:1.00
N7 J:DG185 2.3 38.0 1.0
O6 J:DG186 2.9 36.8 1.0
C8 J:DG185 3.1 38.3 1.0
C5 J:DG185 3.4 37.8 1.0
C6 J:DG186 3.7 35.9 1.0
OP2 J:DG185 3.9 53.9 1.0
O6 J:DG185 4.0 38.6 1.0
C6 J:DG185 4.1 40.3 1.0
N7 J:DG186 4.1 33.6 1.0
C5 J:DG186 4.2 36.0 1.0
N9 J:DG185 4.3 40.1 1.0
N4 I:DC107 4.4 36.4 1.0
C4 J:DG185 4.5 37.5 1.0
C2' J:DT184 4.5 38.1 1.0
N1 J:DG186 4.7 35.7 1.0

Manganese binding site 8 out of 8 in 6jr0

Go back to Manganese Binding Sites List in 6jr0
Manganese binding site 8 out of 8 in the Crystal Structure of the Human Nucleosome Phased with 12 Selenium Atoms


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 the Human Nucleosome Phased with 12 Selenium Atoms within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn304

b:69.5
occ:1.00
N7 J:DG217 2.4 35.2 1.0
O J:HOH410 2.4 40.6 1.0
O J:HOH495 2.5 35.5 1.0
C8 J:DG217 3.2 35.6 1.0
C5 J:DG217 3.4 34.3 1.0
O J:HOH415 3.5 33.6 1.0
O6 J:DG217 3.8 35.9 1.0
N6 J:DA218 4.0 31.7 1.0
C6 J:DG217 4.0 36.0 1.0
C2' J:DT216 4.2 37.6 1.0
N9 J:DG217 4.4 35.7 1.0
OP2 J:DG217 4.5 29.8 1.0
C4 J:DG217 4.6 34.8 1.0
N7 J:DA218 4.8 36.3 1.0
C6 J:DT216 4.8 37.2 1.0
C6 J:DA218 4.9 34.9 1.0

Reference:

M.Saotome, N.Horikoshi, K.Urano, T.Kujirai, H.Yuzurihara, H.Kurumizaka, W.Kagawa. Structure Determination of the Nucleosome Core Particle By Selenium Sad Phasing. Acta Crystallogr D Struct V. 75 930 2019BIOL.
ISSN: ISSN 2059-7983
PubMed: 31588924
DOI: 10.1107/S2059798319012713
Page generated: Sun Oct 6 05:05:00 2024

Last articles

Mg in 2UU7
Mg in 2UAG
Mg in 2UKD
Mg in 2SHK
Mg in 2TPS
Mg in 2TRT
Mg in 2TRA
Mg in 2RMK
Mg in 2RUS
Mg in 2TCT
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy