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Barium in PDB 2yn6: Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium

Protein crystallography data

The structure of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium, PDB code: 2yn6 was solved by I.Zimmermann, A.Marabelli, C.Bertozzi, L.G.Sivilotti, R.Dutzler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.986 / 3.31
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 100.473, 100.473, 263.951, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 25.78

Barium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Barium atom in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium (pdb code 2yn6). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 12 binding sites of Barium where determined in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium, PDB code: 2yn6:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 12 in 2yn6

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Barium binding site 1 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1318

b:0.1
occ:1.00
OD1 B:ASP113 3.5 0.2 1.0
CG2 A:THR149 3.9 0.4 1.0
OD2 B:ASP113 4.3 0.5 1.0
CG B:ASP113 4.3 92.8 1.0
OE1 A:GLU150 4.3 0.9 1.0
O A:GLU150 4.6 0.3 1.0
N A:GLU150 4.7 1.0 1.0

Barium binding site 2 out of 12 in 2yn6

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Barium binding site 2 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba1319

b:0.9
occ:1.00
O A:THR87 3.3 87.5 1.0
N A:THR87 4.2 74.9 1.0
C A:THR87 4.3 75.5 1.0
OD1 A:ASP86 4.4 75.5 1.0
CB A:THR87 4.5 71.6 1.0
CA A:THR87 4.6 68.3 1.0
OG B:SER84 4.8 91.6 1.0

Barium binding site 3 out of 12 in 2yn6

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Barium binding site 3 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba1318

b:0.6
occ:1.00
O B:THR87 3.5 90.8 1.0
OD1 B:ASP86 4.2 79.8 1.0
OG C:SER84 4.2 80.5 1.0
C B:THR87 4.7 71.8 1.0
N B:THR87 4.9 75.5 1.0

Barium binding site 4 out of 12 in 2yn6

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Barium binding site 4 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba1319

b:0.4
occ:1.00
ND2 B:ASN251 4.1 81.8 1.0
ND2 A:ASN251 4.5 75.0 1.0
ND2 D:ASN251 4.5 86.1 1.0
ND2 C:ASN251 4.5 92.6 1.0
ND2 E:ASN251 4.6 94.8 1.0

Barium binding site 5 out of 12 in 2yn6

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Barium binding site 5 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba1318

b:0.4
occ:1.00
OD1 C:ASP113 2.6 0.8 1.0
CG C:ASP113 3.6 97.5 1.0
OE2 B:GLU150 3.8 0.8 1.0
OD2 C:ASP113 3.9 0.9 1.0
CD B:GLU150 4.5 0.5 1.0
CG2 B:THR149 4.5 0.2 1.0
OD1 B:ASP158 4.6 0.7 1.0
OD2 B:ASP158 4.6 0.7 1.0
OE1 B:GLU150 4.9 0.6 1.0
CB C:ASP113 4.9 76.6 1.0

Barium binding site 6 out of 12 in 2yn6

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Barium binding site 6 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba1319

b:0.1
occ:1.00
OE2 C:GLU150 3.0 1.0 1.0
OD1 D:ASP113 3.5 81.7 1.0
CD C:GLU150 3.6 0.8 1.0
OE1 C:GLU150 4.1 0.3 1.0
OD2 C:ASP158 4.2 0.5 1.0
CG2 C:THR149 4.3 0.1 1.0
O C:GLU150 4.3 0.6 1.0
CG C:GLU150 4.4 0.8 1.0
CG D:ASP113 4.4 80.3 1.0
OD2 D:ASP113 4.6 97.3 1.0
OD1 C:ASP158 4.7 0.1 1.0
CG C:ASP158 4.9 0.8 1.0
OD1 C:ASN154 5.0 0.5 1.0

Barium binding site 7 out of 12 in 2yn6

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Barium binding site 7 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba1320

b:0.7
occ:1.00
O C:THR87 3.6 85.4 1.0
OD1 C:ASP86 4.0 84.7 1.0
N C:THR87 4.3 67.5 1.0
OG D:SER84 4.3 87.9 1.0
C C:THR87 4.6 71.4 1.0
CA C:THR87 4.8 59.1 1.0
CB C:THR87 4.9 65.1 1.0
CG C:ASP86 5.0 74.4 1.0

Barium binding site 8 out of 12 in 2yn6

Go back to Barium Binding Sites List in 2yn6
Barium binding site 8 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba1318

b:0.5
occ:1.00
O D:THR87 3.6 64.5 1.0
OD1 D:ASP86 3.9 76.5 1.0
N D:THR87 4.2 55.2 1.0
C D:THR87 4.5 47.1 1.0
OG E:SER84 4.7 83.2 1.0
CA D:THR87 4.8 43.4 1.0
CG D:ASP86 4.8 70.3 1.0
CB D:THR87 4.9 55.8 1.0
C D:ASP86 5.0 64.2 1.0

Barium binding site 9 out of 12 in 2yn6

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Barium binding site 9 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ba1318

b:0.9
occ:1.00
OD1 E:ASP113 2.6 0.9 1.0
OE2 D:GLU150 3.2 0.5 1.0
CG E:ASP113 3.5 0.9 1.0
OD2 E:ASP113 3.7 0.4 1.0
CD D:GLU150 4.0 0.9 1.0
OE1 D:GLU150 4.5 0.7 1.0
OD2 D:ASP158 4.6 0.5 1.0
CG2 D:THR149 4.7 0.5 1.0
OD1 D:ASP158 4.8 0.0 1.0
CB E:ASP113 4.9 90.7 1.0
OD1 D:ASN154 4.9 0.3 1.0
CG D:GLU150 4.9 0.5 1.0

Barium binding site 10 out of 12 in 2yn6

Go back to Barium Binding Sites List in 2yn6
Barium binding site 10 out of 12 in the Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Pentameric Ligand-Gated Ion Channel Elic in Complex with Barium within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ba1319

b:1.0
occ:1.00
CG2 E:THR149 3.9 0.7 1.0
OD2 A:ASP113 4.2 0.3 1.0
OE1 E:GLU150 4.2 0.4 1.0
OE2 E:GLU150 4.2 0.5 1.0
OD1 A:ASP113 4.5 0.3 1.0
CD E:GLU150 4.6 0.3 1.0
CG A:ASP113 4.8 0.6 1.0

Reference:

I.Zimmermann, A.Marabelli, C.Bertozzi, L.G.Sivilotti, R.Dutzler. Inhibition of the Prokaryotic Pentameric Ligand-Gated Ion Channel Elic By Divalent Cations. Plos Biol. V. 10 1429 2012.
ISSN: ISSN 1544-9173
PubMed: 23185134
DOI: 10.1371/JOURNAL.PBIO.1001429
Page generated: Sat Dec 12 01:55:39 2020

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