Atomistry » Rubidium » PDB 1dge-4z3p » 3mgr
Atomistry »
  Rubidium »
    PDB 1dge-4z3p »
      3mgr »

Rubidium in PDB 3mgr: Binding of Rubidium Ions to the Nucleosome Core Particle

Protein crystallography data

The structure of Binding of Rubidium Ions to the Nucleosome Core Particle, PDB code: 3mgr was solved by K.Mohideen, R.Muhammad, C.A.Davey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.462, 109.681, 182.213, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 26.7

Other elements in 3mgr:

The structure of Binding of Rubidium Ions to the Nucleosome Core Particle also contains other interesting chemical elements:

Manganese (Mn) 14 atoms
Chlorine (Cl) 4 atoms

Rubidium Binding Sites:

The binding sites of Rubidium atom in the Binding of Rubidium Ions to the Nucleosome Core Particle (pdb code 3mgr). This binding sites where shown within 5.0 Angstroms radius around Rubidium atom.
In total 5 binding sites of Rubidium where determined in the Binding of Rubidium Ions to the Nucleosome Core Particle, PDB code: 3mgr:
Jump to Rubidium binding site number: 1; 2; 3; 4; 5;

Rubidium binding site 1 out of 5 in 3mgr

Go back to Rubidium Binding Sites List in 3mgr
Rubidium binding site 1 out of 5 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 1 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Rb123

b:0.0
occ:1.00
O D:LEU99 2.1 36.4 1.0
O D:ARG96 2.4 36.6 1.0
C D:LEU99 3.2 36.3 1.0
O D:LEU97 3.4 35.2 1.0
C D:ARG96 3.4 36.1 1.0
N D:LEU99 3.6 35.1 1.0
C D:LEU97 3.6 35.4 1.0
C D:LEU98 3.9 35.2 1.0
CA D:LEU99 4.0 35.7 1.0
N D:LEU98 4.0 35.0 1.0
CA D:LEU97 4.0 35.1 1.0
N D:LEU97 4.1 35.2 1.0
N D:PRO100 4.2 37.1 1.0
CA D:PRO100 4.4 37.7 1.0
O D:LEU98 4.4 35.2 1.0
CA D:LEU98 4.5 34.7 1.0
CA D:ARG96 4.5 37.3 1.0
O D:VAL95 4.6 35.0 1.0
C D:PRO100 4.9 37.9 1.0
CB D:ALA104 4.9 38.2 1.0

Rubidium binding site 2 out of 5 in 3mgr

Go back to Rubidium Binding Sites List in 3mgr
Rubidium binding site 2 out of 5 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 2 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Rb123

b:0.0
occ:1.00
O H:LEU99 3.2 36.6 1.0
O H:ARG96 3.3 34.4 1.0
O H:LEU97 4.0 33.3 1.0
C H:LEU99 4.1 36.6 1.0
C H:LEU97 4.4 33.8 1.0
CA H:PRO100 4.5 38.1 1.0
C H:ARG96 4.5 34.2 1.0
N H:GLY101 4.6 40.8 1.0
CD F:ARG67 4.6 34.6 1.0
N H:PRO100 4.6 37.7 1.0
N H:LEU99 4.8 34.9 1.0
C H:PRO100 4.8 39.0 1.0
CA H:LEU97 4.9 33.7 1.0

Rubidium binding site 3 out of 5 in 3mgr

Go back to Rubidium Binding Sites List in 3mgr
Rubidium binding site 3 out of 5 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 3 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Rb74

b:0.0
occ:1.00
O4' I:DC-25 2.9 65.9 1.0
O2 I:DC-25 3.1 68.5 1.0
O2 I:DT-26 3.3 76.4 1.0
C4' I:DC-25 3.5 64.8 1.0
C1' I:DC-25 3.5 67.4 1.0
O4' I:DC-24 3.5 54.7 1.0
C2 J:DA26 3.8 75.9 1.0
C2 I:DC-25 3.9 68.4 1.0
N1 I:DC-25 4.2 68.4 1.0
C5' I:DC-24 4.2 54.8 1.0
C4' I:DC-24 4.3 54.0 1.0
O3' I:DC-25 4.3 60.6 1.0
C2 I:DT-26 4.3 76.3 1.0
N3 J:DA26 4.4 76.3 1.0
N2 J:DG25 4.4 83.2 1.0
C3' I:DC-25 4.5 63.8 1.0
C5' I:DC-25 4.5 64.9 1.0
C1' I:DC-24 4.7 54.8 1.0
N1 I:DC-24 4.7 55.5 1.0
N1 J:DA26 4.8 75.8 1.0
C2' I:DC-25 4.8 65.8 1.0
N3 I:DT-26 5.0 76.3 1.0
C2 I:DC-24 5.0 54.6 1.0

Rubidium binding site 4 out of 5 in 3mgr

Go back to Rubidium Binding Sites List in 3mgr
Rubidium binding site 4 out of 5 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 4 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Rb74

b:0.0
occ:1.00
O2 J:DT67 2.8 81.8 1.0
O4' J:DA68 2.8 71.7 1.0
O2 I:DT-66 3.1 56.1 1.0
O4' I:DC-65 3.4 71.6 1.0
C4' J:DA68 3.4 72.2 1.0
C4' I:DC-65 3.8 72.4 1.0
C5' J:DA68 3.8 76.1 1.0
C2 J:DT67 4.0 81.8 1.0
C1' J:DA68 4.0 69.3 1.0
C5' I:DC-65 4.0 71.4 1.0
C2 I:DT-66 4.2 56.6 1.0
C1' I:DT-66 4.3 58.7 1.0
C1' I:DC-65 4.4 70.8 1.0
N9 J:DA68 4.5 69.0 1.0
C2 I:DA-67 4.6 55.2 1.0
O5' J:DA68 4.6 79.7 1.0
O4' I:DT-66 4.7 60.2 1.0
N1 I:DT-66 4.8 57.4 1.0
C1' J:DT67 4.8 82.6 1.0
N3 J:DT67 4.8 81.3 1.0
C2 J:DA66 4.8 88.6 1.0
C3' J:DA68 4.8 70.4 1.0
O3' I:DT-66 4.9 65.5 1.0
N1 J:DT67 4.9 82.5 1.0
C4 J:DA68 4.9 69.0 1.0

Rubidium binding site 5 out of 5 in 3mgr

Go back to Rubidium Binding Sites List in 3mgr
Rubidium binding site 5 out of 5 in the Binding of Rubidium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Rubidium with other atoms in the Rb binding site number 5 of Binding of Rubidium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Rb75

b:0.0
occ:1.00
O2 J:DT-66 2.5 62.1 1.0
O4' J:DC-65 3.1 65.6 1.0
O2 I:DT67 3.4 65.7 1.0
O4' I:DA68 3.6 60.5 1.0
C2 J:DT-66 3.6 62.5 1.0
C4' J:DC-65 3.9 66.6 1.0
C1' J:DT-66 4.0 63.2 1.0
C1' J:DC-65 4.1 64.1 1.0
C4' I:DA68 4.1 62.5 1.0
O4' J:DT-66 4.2 64.0 1.0
C5' J:DC-65 4.3 66.4 1.0
C2 I:DA66 4.3 65.7 1.0
N1 J:DT-66 4.3 63.4 1.0
C5' I:DA68 4.4 64.5 1.0
N1 J:DC-65 4.4 63.0 1.0
C2 I:DT67 4.5 66.0 1.0
C2 J:DA-67 4.5 57.7 1.0
N3 J:DT-66 4.7 62.0 1.0
O2 J:DC-65 4.8 63.2 1.0
C2 J:DC-65 4.8 62.3 1.0
C1' I:DA68 4.8 57.7 1.0
O3' J:DT-66 4.8 66.0 1.0
N1 I:DA66 4.9 65.5 1.0
N3 J:DA-67 5.0 57.4 1.0
C4' J:DT-66 5.0 63.4 1.0

Reference:

K.Mohideen, R.Muhammad, C.A.Davey. Perturbations in Nucleosome Structure From Heavy Metal Association. Nucleic Acids Res. V. 38 6301 2010.
ISSN: ISSN 0305-1048
PubMed: 20494975
DOI: 10.1093/NAR/GKQ420
Page generated: Wed Dec 16 02:06:48 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy