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Caesium in PDB 3mgs: Binding of Cesium Ions to the Nucleosome Core Particle

Protein crystallography data

The structure of Binding of Cesium Ions to the Nucleosome Core Particle, PDB code: 3mgs 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) 94.07 / 3.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.510, 109.668, 182.609, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 23.8

Other elements in 3mgs:

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

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

Caesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Caesium atom in the Binding of Cesium Ions to the Nucleosome Core Particle (pdb code 3mgs). This binding sites where shown within 5.0 Angstroms radius around Caesium atom.
In total 12 binding sites of Caesium where determined in the Binding of Cesium Ions to the Nucleosome Core Particle, PDB code: 3mgs:
Jump to Caesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Caesium binding site 1 out of 12 in 3mgs

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Caesium binding site 1 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 1 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cs120

b:0.0
occ:1.00
CE2 C:TYR39 3.4 51.0 1.0
O C:GLY37 3.4 58.6 1.0
CZ C:TYR39 3.6 51.3 1.0
OH C:TYR39 3.8 51.6 1.0
CD2 C:TYR39 4.0 51.5 1.0
CE1 C:TYR39 4.4 50.6 1.0
C C:GLY37 4.5 58.3 1.0
CG C:TYR39 4.7 52.3 1.0
O C:ASN38 4.7 56.4 1.0
CD1 C:TYR39 4.9 50.6 1.0
OG H:SER75 5.0 50.0 1.0

Caesium binding site 2 out of 12 in 3mgs

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Caesium binding site 2 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 2 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cs123

b:0.0
occ:1.00
O D:LEU99 3.1 50.4 1.0
O D:ARG96 3.3 48.4 1.0
O D:LEU97 3.5 49.3 1.0
C D:LEU99 4.1 49.9 1.0
C D:LEU97 4.1 48.8 1.0
C D:ARG96 4.4 48.4 1.0
OD1 B:ASP68 4.5 46.7 1.0
CA D:PRO100 4.6 51.0 1.0
CA D:LEU97 4.6 48.4 1.0
CD B:ARG67 4.6 49.7 1.0
C D:LEU98 4.7 49.2 1.0
N D:LEU99 4.7 49.2 1.0
N D:PRO100 4.7 50.6 1.0
N D:LEU98 4.8 48.9 1.0
O D:LEU98 4.8 49.3 1.0
CA D:LEU99 5.0 49.4 1.0
N D:LEU97 5.0 48.4 1.0

Caesium binding site 3 out of 12 in 3mgs

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Caesium binding site 3 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


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Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 3 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cs123

b:0.0
occ:1.00
O H:ARG96 3.2 47.6 1.0
O H:LEU99 3.3 49.7 1.0
O H:LEU97 3.5 47.9 1.0
C H:LEU97 3.9 47.9 1.0
C H:LEU99 4.1 49.8 1.0
C H:ARG96 4.3 47.5 1.0
CA H:LEU97 4.5 47.5 1.0
N H:LEU99 4.5 49.3 1.0
N H:LEU98 4.5 48.5 1.0
C H:LEU98 4.6 49.2 1.0
CD F:ARG67 4.7 39.8 1.0
N H:PRO100 4.7 50.4 1.0
OD1 F:ASP68 4.8 39.4 1.0
CA H:PRO100 4.9 50.9 1.0
N H:LEU97 4.9 47.5 1.0
CA H:LEU99 4.9 49.2 1.0
CA H:LEU98 4.9 49.2 1.0

Caesium binding site 4 out of 12 in 3mgs

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Caesium binding site 4 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 4 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs74

b:0.0
occ:1.00
O2 I:DT-66 2.8 76.1 1.0
O4' J:DA68 2.9 90.3 1.0
O2 J:DT67 3.1 0.8 1.0
O4' I:DC-65 3.2 90.6 1.0
C4' J:DA68 3.5 90.6 1.0
C4' I:DC-65 3.7 91.0 1.0
C1' I:DT-66 3.7 77.0 1.0
C2 I:DT-66 3.8 76.1 1.0
C5' I:DC-65 3.8 89.0 1.0
C5' J:DA68 3.9 94.4 1.0
O4' I:DT-66 4.1 78.2 1.0
C1' J:DA68 4.1 89.5 1.0
C2 J:DT67 4.2 0.3 1.0
C1' I:DC-65 4.3 90.8 1.0
N1 I:DT-66 4.3 76.1 1.0
C2 I:DA-67 4.3 74.2 1.0
C4' I:DT-66 4.6 78.7 1.0
N9 J:DA68 4.6 89.3 1.0
O3' I:DT-66 4.6 81.8 1.0
O5' J:DA68 4.7 98.8 1.0
C2' I:DT-66 4.8 78.7 1.0
C2 J:DA66 4.8 0.6 1.0
O5' I:DC-65 4.8 85.9 1.0
N1 I:DC-65 4.8 90.7 1.0
C3' J:DA68 4.9 88.0 1.0
N3 I:DA-67 4.9 74.0 1.0
N3 J:DT67 5.0 0.7 1.0
C3' I:DT-66 5.0 79.8 1.0

Caesium binding site 5 out of 12 in 3mgs

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Caesium binding site 5 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 5 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs75

b:0.0
occ:1.00
MN J:MN3136 2.7 87.9 0.7
O4' I:DC15 3.2 80.1 1.0
CS J:CS74 3.3 0.0 1.0
N3 J:DA-13 3.4 64.8 1.0
N2 I:DG14 3.4 88.8 1.0
N3 I:DG14 3.5 89.2 1.0
C2 J:DA-13 3.5 65.4 1.0
O2 I:DC15 3.6 83.9 1.0
C2 I:DG14 3.9 89.0 1.0
C4' I:DC15 4.0 78.7 1.0
C2 I:DC15 4.1 83.4 1.0
C1' I:DC15 4.3 81.5 1.0
N1 I:DC15 4.5 82.5 1.0
C5' I:DC15 4.5 79.2 1.0
C4 J:DA-13 4.6 64.6 1.0
O4' I:DG14 4.6 84.9 1.0
C4 I:DG14 4.7 88.9 1.0
N1 J:DA-13 4.7 65.8 1.0
O2 I:DT13 4.8 85.4 1.0
O4' J:DT-12 4.8 64.3 1.0
C1' I:DG14 4.8 87.4 1.0
N3 I:DC15 4.9 83.6 1.0

Caesium binding site 6 out of 12 in 3mgs

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Caesium binding site 6 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 6 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs76

b:0.0
occ:1.00
O2 I:DT-26 2.8 93.0 1.0
O4' I:DC-25 2.8 82.5 1.0
O2 I:DC-25 2.9 84.8 1.0
C2 J:DA26 3.5 94.4 1.0
C2 I:DC-25 3.6 84.7 1.0
C1' I:DC-25 3.7 83.5 1.0
C4' I:DC-25 3.8 81.2 1.0
C2 I:DT-26 3.8 92.7 1.0
O4' I:DC-24 3.9 72.4 1.0
N1 I:DC-25 4.0 84.5 1.0
N3 J:DA26 4.1 94.3 1.0
N2 J:DG25 4.2 100.0 1.0
N3 I:DT-26 4.3 92.9 1.0
N1 J:DA26 4.3 94.2 1.0
C5' I:DC-25 4.5 82.4 1.0
N3 I:DC-25 4.6 85.0 1.0
C5' I:DC-24 4.7 72.5 1.0
C4' I:DC-24 4.8 72.3 1.0
N1 I:DT-26 4.8 92.8 1.0
C3' I:DC-25 4.9 80.0 1.0
O3' I:DC-25 4.9 76.9 1.0
N1 I:DC-24 4.9 72.8 1.0
N2 J:DG27 5.0 85.6 1.0
C1' I:DC-24 5.0 72.8 1.0

Caesium binding site 7 out of 12 in 3mgs

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Caesium binding site 7 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 7 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs77

b:0.0
occ:1.00
O2 J:DT-66 2.4 79.4 1.0
O2 I:DT67 2.7 85.5 1.0
O4' I:DA68 3.4 76.2 1.0
O4' J:DC-65 3.5 78.0 1.0
C2 J:DT-66 3.5 79.1 1.0
C2 I:DT67 3.7 85.5 1.0
C2 I:DA66 3.7 91.3 1.0
C4' I:DA68 4.0 77.7 1.0
C2 J:DA-67 4.1 73.4 1.0
C5' I:DA68 4.2 80.5 1.0
C1' J:DC-65 4.4 76.9 1.0
N3 J:DT-66 4.4 79.1 1.0
N3 I:DT67 4.4 85.0 1.0
C4' J:DC-65 4.4 78.9 1.0
N3 I:DA66 4.4 91.3 1.0
C1' J:DT-66 4.5 79.2 1.0
N1 I:DA66 4.5 91.4 1.0
N1 J:DT-66 4.5 79.6 1.0
O4' I:DT67 4.5 86.7 1.0
N1 I:DT67 4.6 85.5 1.0
C1' I:DT67 4.6 85.5 1.0
N1 J:DC-65 4.6 76.0 1.0
C1' I:DA68 4.6 75.0 1.0
O4' J:DT-66 4.6 78.3 1.0
O2 J:DC-65 4.7 75.9 1.0
N9 I:DA68 4.8 74.8 1.0
C2 J:DC-65 4.8 75.8 1.0
C5' J:DC-65 4.8 79.7 1.0
N1 J:DA-67 4.8 74.0 1.0
N3 J:DA-67 4.8 72.9 1.0

Caesium binding site 8 out of 12 in 3mgs

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Caesium binding site 8 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 8 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs78

b:0.0
occ:1.00
N2 J:DG-15 2.7 87.0 1.0
O2 I:DC16 2.9 69.8 1.0
O4' I:DC16 3.4 67.5 1.0
O2 I:DC15 3.5 83.9 1.0
C2 I:DC16 3.8 70.2 1.0
O4' I:DT17 3.9 61.9 1.0
C2 J:DG-15 3.9 87.1 1.0
C1' I:DC16 4.0 68.5 1.0
N2 J:DG-16 4.0 91.1 1.0
C4' I:DC16 4.2 67.2 1.0
N1 I:DC16 4.3 69.8 1.0
N3 J:DG-15 4.4 87.6 1.0
C2 I:DC15 4.5 83.4 1.0
C4' I:DT17 4.6 61.3 1.0
N3 I:DC16 4.8 70.8 1.0
C1' I:DT17 4.8 65.1 1.0
O2 J:DC-14 4.9 71.8 1.0
C5' I:DT17 4.9 61.6 1.0
C2 J:DG-16 5.0 91.3 1.0
N1 J:DG-15 5.0 87.0 1.0

Caesium binding site 9 out of 12 in 3mgs

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Caesium binding site 9 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 9 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs79

b:0.0
occ:1.00
O2 J:DT-10 2.5 84.7 1.0
O2 I:DC11 2.8 80.3 1.0
C2 J:DT-10 3.7 84.0 1.0
C2 I:DA10 3.8 69.2 1.0
N2 J:DG-11 3.8 73.6 1.0
C2 I:DC11 3.9 80.1 1.0
O4' J:DT-9 4.0 83.8 1.0
O2 J:DT-9 4.3 84.5 1.0
N3 I:DA10 4.3 68.8 1.0
O4' I:DC11 4.4 78.3 1.0
C1' J:DT-10 4.5 83.3 1.0
N1 I:DA10 4.6 69.3 1.0
N3 I:DC11 4.6 80.1 1.0
N1 J:DT-10 4.6 83.6 1.0
N3 J:DT-10 4.6 83.5 1.0
C2 J:DT-9 4.6 85.0 1.0
C1' I:DC11 4.7 79.3 1.0
N1 I:DC11 4.7 79.7 1.0
C2 J:DG-11 4.8 74.1 1.0
C4' J:DT-9 4.9 83.2 1.0
C1' J:DT-9 4.9 84.2 1.0
N1 J:DT-9 5.0 84.8 1.0

Caesium binding site 10 out of 12 in 3mgs

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Caesium binding site 10 out of 12 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Caesium with other atoms in the Cs binding site number 10 of Binding of Cesium Ions to the Nucleosome Core Particle within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cs80

b:0.0
occ:1.00
O2 I:DT-60 2.9 0.1 1.0
O4' I:DG-59 2.9 0.5 1.0
C1' I:DG-59 3.7 0.1 1.0
N9 I:DG-59 3.8 0.0 1.0
C1' I:DT-60 3.9 0.7 1.0
C2 I:DT-60 3.9 0.0 1.0
C4' I:DG-59 4.0 0.5 1.0
O4' I:DT-60 4.0 0.1 1.0
C4 I:DG-59 4.0 0.9 1.0
N3 I:DG-59 4.1 0.8 1.0
N2 J:DG61 4.2 92.2 1.0
N1 I:DT-60 4.5 0.4 1.0
O3' I:DT-60 4.5 0.8 1.0
C8 I:DG-59 4.5 0.9 1.0
C2 J:DA60 4.6 85.8 1.0
C5' I:DG-59 4.6 0.8 1.0
C4' I:DT-60 4.8 0.8 1.0
C5 I:DG-59 4.8 0.8 1.0
C2 I:DG-59 4.9 1.0 1.0

Reference:

K.Mohideen, R.Muhammad, C.A.Davey. Perturbations in Nucleosome Structure From Heavy Metal Association. Nucleic Acids Res. 2010.
ISSN: ESSN 1362-4962
PubMed: 20494975
DOI: 10.1093/NAR/GKQ420
Page generated: Sun Dec 13 10:56:04 2020

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