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Manganese 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:

Caesium (Cs) 12 atoms
Chlorine (Cl) 4 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese 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 Manganese atom.
In total 14 binding sites of Manganese where determined in the Binding of Cesium Ions to the Nucleosome Core Particle, PDB code: 3mgs:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in 3mgs

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Manganese binding site 1 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
E:Mn3132

b:52.6
occ:1.00
OD1 E:ASP77 2.3 48.3 1.0
CG E:ASP77 3.2 46.3 1.0
OD2 E:ASP77 3.4 47.4 1.0
OE1 E:GLN76 4.2 47.2 1.0
O F:LEU22 4.2 55.0 1.0
O E:GLU73 4.5 38.3 1.0
CB E:ASP77 4.5 45.4 1.0
N E:ASP77 4.8 45.0 1.0
CA E:ASP77 4.8 45.7 1.0
CG E:GLU73 5.0 36.4 1.0

Manganese binding site 2 out of 14 in 3mgs

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Manganese binding site 2 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
I:Mn3137

b:0.7
occ:1.00
N7 I:DG48 2.3 94.2 1.0
C8 I:DG48 3.2 94.1 1.0
C5 I:DG48 3.4 94.2 1.0
O6 I:DG48 3.7 94.0 1.0
C6 I:DG48 4.0 94.0 1.0
C2' I:DT47 4.1 95.2 1.0
O6 I:DG49 4.3 88.7 1.0
N9 I:DG48 4.5 94.0 1.0
C4 I:DG48 4.6 94.5 1.0
OP2 I:DG48 4.9 90.8 1.0

Manganese binding site 3 out of 14 in 3mgs

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Manganese binding site 3 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
I:Mn3138

b:96.7
occ:0.90
N7 I:DG61 2.4 94.3 1.0
C8 I:DG61 3.4 94.4 1.0
C5 I:DG61 3.4 94.4 1.0
O6 I:DG61 3.5 94.5 1.0
C6 I:DG61 3.9 94.3 1.0
C8 I:DA60 4.2 92.2 1.0
N7 I:DA60 4.3 92.4 1.0
O6 I:DG62 4.3 0.5 1.0
N9 I:DG61 4.6 94.7 1.0
C4 I:DG61 4.6 94.4 1.0
N9 I:DA60 4.9 92.0 1.0

Manganese binding site 4 out of 14 in 3mgs

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Manganese binding site 4 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn3140

b:0.6
occ:0.72
N7 I:DG27 2.6 79.3 1.0
C8 I:DG27 3.4 79.3 1.0
C5 I:DG27 3.7 78.9 1.0
O6 I:DG27 4.0 78.9 1.0
C8 I:DA26 4.0 93.3 1.0
N7 I:DA26 4.2 93.5 1.0
C6 I:DG27 4.2 78.8 1.0
N9 I:DA26 4.7 93.2 1.0
N9 I:DG27 4.7 78.8 1.0
C2' I:DA26 4.7 90.8 1.0
C4 I:DG27 4.9 78.9 1.0

Manganese binding site 5 out of 14 in 3mgs

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Manganese binding site 5 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn3141

b:0.2
occ:0.63
O6 I:DG5 2.9 82.3 1.0
C6 I:DG5 3.8 82.1 1.0
O6 J:DG-6 3.9 72.7 1.0
N7 I:DG5 4.0 82.3 1.0
N7 J:DG-6 4.2 72.7 1.0
N4 J:DC-5 4.2 62.8 1.0
C5 I:DG5 4.3 82.2 1.0
C6 J:DG-6 4.7 72.3 1.0
N7 I:DA4 4.8 80.4 1.0
C5 J:DG-6 4.8 72.4 1.0

Manganese binding site 6 out of 14 in 3mgs

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Manganese binding site 6 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn3142

b:0.6
occ:0.64
N7 I:DG-3 2.3 62.5 1.0
C5 I:DG-3 3.2 62.4 1.0
C8 I:DG-3 3.3 62.5 1.0
O6 I:DG-3 3.3 62.5 1.0
O6 I:DG-2 3.4 73.0 1.0
C6 I:DG-3 3.6 62.4 1.0
C6 I:DG-2 4.2 73.0 1.0
C4 I:DG-3 4.4 62.5 1.0
N7 I:DG-2 4.4 72.7 1.0
N9 I:DG-3 4.4 62.5 1.0
C2' I:DT-4 4.5 63.8 1.0
C5 I:DG-2 4.6 72.5 1.0
N4 J:DC2 4.8 98.8 1.0
C6 I:DT-4 4.9 64.5 1.0
N1 I:DG-3 5.0 62.7 1.0
OP2 I:DG-3 5.0 59.2 1.0

Manganese binding site 7 out of 14 in 3mgs

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Manganese binding site 7 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn3143

b:0.4
occ:1.00
N7 I:DG-35 2.3 82.5 1.0
O6 I:DG-34 2.8 76.2 1.0
C8 I:DG-35 3.1 82.2 1.0
C5 I:DG-35 3.4 82.3 1.0
C6 I:DG-34 3.5 76.3 1.0
N7 I:DG-34 3.7 75.7 1.0
O6 I:DG-35 3.7 82.0 1.0
C5 I:DG-34 3.9 76.2 1.0
C6 I:DG-35 3.9 81.9 1.0
C2' I:DT-36 4.2 83.9 1.0
N4 J:DC34 4.3 1.0 1.0
N9 I:DG-35 4.4 82.0 1.0
C4 I:DG-35 4.5 82.3 1.0
N1 I:DG-34 4.7 76.2 1.0
O3' I:DT-36 4.7 81.2 1.0
OP2 I:DG-35 4.7 78.0 1.0
C8 I:DG-34 4.9 75.9 1.0
C3' I:DT-36 4.9 83.8 1.0

Manganese binding site 8 out of 14 in 3mgs

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Manganese binding site 8 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
J:Mn3131

b:94.5
occ:1.00
N7 J:DG61 2.5 90.2 1.0
C8 J:DG61 3.4 90.9 1.0
C5 J:DG61 3.6 90.5 1.0
O6 J:DG61 3.8 89.9 1.0
C6 J:DG61 4.1 90.7 1.0
O6 J:DG62 4.2 0.5 1.0
C8 J:DA60 4.2 85.1 1.0
N7 J:DA60 4.3 86.0 1.0
N9 J:DG61 4.6 91.4 1.0
C4 J:DG61 4.7 91.2 1.0
N9 J:DA60 5.0 84.0 1.0

Manganese binding site 9 out of 14 in 3mgs

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Manganese binding site 9 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
J:Mn3133

b:0.5
occ:0.97
N7 J:DG27 2.5 86.0 1.0
C8 J:DG27 3.4 86.0 1.0
C5 J:DG27 3.5 85.6 1.0
O6 J:DG27 3.6 85.7 1.0
C6 J:DG27 3.9 85.9 1.0
O6 I:DG-28 4.2 0.2 1.0
C8 J:DA26 4.6 94.3 1.0
N9 J:DG27 4.6 85.8 1.0
C4 J:DG27 4.7 85.5 1.0
N7 J:DA26 4.7 94.7 1.0
C7 I:DT-29 4.9 0.4 1.0
N4 J:DC28 4.9 81.0 1.0

Manganese binding site 10 out of 14 in 3mgs

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Manganese binding site 10 out of 14 in the Binding of Cesium Ions to the Nucleosome Core Particle


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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
J:Mn3134

b:0.8
occ:1.00
N7 J:DG-3 2.3 59.0 1.0
C8 J:DG-3 3.2 59.2 1.0
C5 J:DG-3 3.4 59.2 1.0
O6 J:DG-3 3.6 59.4 1.0
C6 J:DG-3 3.9 59.0 1.0
O6 J:DG-2 4.0 74.5 1.0
C2' J:DT-4 4.0 58.0 1.0
C6 J:DT-4 4.3 61.1 1.0
N9 J:DG-3 4.4 59.0 1.0
C4 J:DG-3 4.5 59.5 1.0
C5 J:DT-4 4.7 62.0 1.0
N1 J:DT-4 4.7 61.2 1.0
C6 J:DG-2 4.8 74.4 1.0
N4 I:DC2 4.8 87.2 1.0
C7 J:DT-4 4.9 62.5 1.0
C1' J:DT-4 4.9 60.5 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: Tue Dec 15 04:12:29 2020

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