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Calcium in PDB 1i9b: X-Ray Structure of Acetylcholine Binding Protein (Achbp)

Protein crystallography data

The structure of X-Ray Structure of Acetylcholine Binding Protein (Achbp), PDB code: 1i9b was solved by K.Brejc, W.J.Van Dijk, R.Klaassen, M.Schuurmans, J.Van Der Oost, A.B.Smit, T.K.Sixma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.70
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.660, 141.660, 120.870, 90.00, 90.00, 90.00
R / Rfree (%) 26 / 29.7

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Acetylcholine Binding Protein (Achbp) (pdb code 1i9b). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the X-Ray Structure of Acetylcholine Binding Protein (Achbp), PDB code: 1i9b:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 1i9b

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Calcium binding site 1 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:83.4
occ:1.00
 O A:VAL176 2.5 63.5 1.0
OD2 A:ASP161 2.6 70.0 1.0
OD1 A:ASP161 3.0 65.1 1.0
CG A:ASP161 3.1 68.7 1.0
OD1 A:ASP175 3.4 59.9 1.0
C A:VAL176 3.7 65.6 1.0
O A:GLU157 4.1 0.7 1.0
N A:VAL176 4.2 71.8 1.0
CG A:ASP175 4.3 68.8 1.0
CG2 A:THR177 4.4 69.3 1.0
CA A:VAL176 4.5 68.2 1.0
CB A:ASP161 4.6 63.4 1.0
OD2 A:ASP175 4.6 64.7 1.0
N A:THR177 4.7 65.9 1.0
CA A:THR177 4.8 66.9 1.0
CB A:VAL176 4.8 68.4 1.0

Calcium binding site 2 out of 10 in 1i9b

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Calcium binding site 2 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:52.6
occ:0.50
 CA A:CA307 0.0 52.6 0.5
OD1 B:ASP2 2.9 74.1 1.0
CA A:CA307 3.3 55.0 0.5
CG B:ASP2 4.0 67.9 1.0
CB B:ASP2 4.5 52.6 1.0

Calcium binding site 3 out of 10 in 1i9b

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Calcium binding site 3 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:55.0
occ:0.50
 CA A:CA307 0.0 55.0 0.5
OD1 B:ASP2 2.5 74.1 1.0
OD2 B:ASP5 2.9 63.8 1.0
OD1 B:ASP5 3.2 68.6 1.0
CG B:ASP2 3.2 67.9 1.0
CA A:CA307 3.3 52.6 0.5
CG B:ASP5 3.4 66.1 1.0
OD2 B:ASP2 3.5 71.8 1.0
CB B:ASP2 4.4 52.6 1.0
CB B:ASP5 4.9 49.6 1.0
N B:ASP2 4.9 47.4 1.0

Calcium binding site 4 out of 10 in 1i9b

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Calcium binding site 4 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:83.9
occ:1.00
 OD2 B:ASP161 2.2 71.1 1.0
O B:VAL176 2.7 71.7 1.0
OD1 B:ASP175 2.8 76.6 1.0
CG B:ASP161 2.9 63.3 1.0
OD1 B:ASP161 3.0 64.3 1.0
C B:VAL176 3.8 64.8 1.0
CG B:ASP175 3.8 76.1 1.0
N B:VAL176 3.9 65.2 1.0
OD2 B:ASP175 4.3 67.8 1.0
CB B:ASP161 4.3 62.3 1.0
CA B:VAL176 4.4 58.7 1.0
O B:GLU157 4.5 0.7 1.0
CG2 B:THR177 4.6 67.9 1.0
CB B:VAL176 4.8 59.6 1.0
N B:THR177 4.9 67.0 1.0
C B:ASP175 5.0 70.6 1.0

Calcium binding site 5 out of 10 in 1i9b

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Calcium binding site 5 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:85.9
occ:1.00
 O C:VAL176 2.5 63.6 1.0
OD2 C:ASP161 2.8 74.4 1.0
OD1 C:ASP161 2.8 71.7 1.0
CG C:ASP161 3.1 69.7 1.0
O C:GLU157 3.7 0.1 1.0
C C:VAL176 3.8 63.9 1.0
OD1 C:ASP175 3.9 77.6 1.0
N C:VAL176 4.5 60.2 1.0
CA C:VAL176 4.6 58.9 1.0
CB C:ASP161 4.6 66.7 1.0
CG2 C:THR177 4.7 65.3 1.0
C C:GLU157 4.7 0.4 1.0
N C:THR177 4.7 67.5 1.0
CB C:VAL176 4.8 66.7 1.0
CA C:THR177 4.8 69.1 1.0
CA C:GLU157 4.8 0.4 1.0
CG C:ASP175 4.8 74.3 1.0

Calcium binding site 6 out of 10 in 1i9b

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Calcium binding site 6 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca304

b:71.0
occ:1.00
 O D:VAL176 2.4 64.0 1.0
OD1 D:ASP161 2.6 66.6 1.0
OD2 D:ASP161 3.1 71.7 1.0
CG D:ASP161 3.2 57.9 1.0
C D:VAL176 3.6 64.2 1.0
O D:GLU157 3.8 0.5 1.0
CB D:VAL176 4.5 57.7 1.0
CA D:GLU157 4.5 0.8 1.0
CA D:VAL176 4.5 58.5 1.0
N D:THR177 4.5 67.4 1.0
C D:GLU157 4.5 0.7 1.0
CA D:THR177 4.5 66.3 1.0
OD1 D:ASP175 4.6 71.9 1.0
N D:VAL176 4.7 64.0 1.0
CB D:ASP161 4.7 56.8 1.0
CB D:GLU157 4.8 0.6 1.0
CG2 D:THR177 4.9 53.7 1.0
CG1 D:VAL176 4.9 57.6 1.0

Calcium binding site 7 out of 10 in 1i9b

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Calcium binding site 7 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca305

b:84.7
occ:1.00
 OD2 E:ASP161 2.4 73.1 1.0
O E:VAL176 2.5 60.1 1.0
OD1 E:ASP161 2.8 71.4 1.0
CG E:ASP161 3.0 69.6 1.0
OD1 E:ASP175 3.5 63.5 1.0
C E:VAL176 3.7 64.5 1.0
O E:GLU157 4.0 0.2 1.0
N E:VAL176 4.2 61.3 1.0
CG E:ASP175 4.4 71.3 1.0
CA E:VAL176 4.4 65.0 1.0
CB E:ASP161 4.4 62.8 1.0
CG2 E:THR177 4.6 71.5 1.0
CB E:VAL176 4.7 67.9 1.0
N E:THR177 4.7 66.4 1.0
OD2 E:ASP175 4.8 66.4 1.0
CA E:THR177 4.9 71.8 1.0

Calcium binding site 8 out of 10 in 1i9b

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Calcium binding site 8 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca306

b:75.5
occ:0.50
 CA E:CA306 0.0 75.5 0.5
CA E:CA306 1.9 58.9 0.5
OD1 A:ASP2 2.4 76.3 1.0
OD2 A:ASP5 3.0 70.3 1.0
OD1 A:ASP5 3.2 69.4 1.0
CG A:ASP2 3.2 72.8 1.0
CG A:ASP5 3.4 67.0 1.0
OD2 A:ASP2 3.5 76.3 1.0
CB A:ASP2 4.4 62.3 1.0
CB A:ASP5 4.9 56.2 1.0

Calcium binding site 9 out of 10 in 1i9b

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Calcium binding site 9 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca306

b:58.9
occ:0.50
 CA E:CA306 0.0 58.9 0.5
CA E:CA306 1.9 75.5 0.5
OD1 A:ASP2 2.5 76.3 1.0
CG A:ASP2 3.6 72.8 1.0
CB A:ASP2 4.3 62.3 1.0
OD2 A:ASP5 4.4 70.3 1.0
OD2 A:ASP2 4.5 76.3 1.0

Calcium binding site 10 out of 10 in 1i9b

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Calcium binding site 10 out of 10 in the X-Ray Structure of Acetylcholine Binding Protein (Achbp)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of X-Ray Structure of Acetylcholine Binding Protein (Achbp) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca310

b:84.2
occ:0.50
 OD1 E:ASP2 2.3 75.6 1.0
OD2 E:ASP2 2.4 66.1 1.0
CG E:ASP2 2.6 67.6 1.0
OD2 E:ASP5 3.3 73.3 1.0
OD1 E:ASP5 3.5 69.8 1.0
CG E:ASP5 3.8 65.2 1.0
CB E:ASP2 4.1 57.0 1.0
N E:ASP2 4.9 63.3 1.0

Reference:

K.Brejc, W.J.Van Dijk, R.V.Klaassen, M.Schuurmans, J.Van Der Oost, A.B.Smit, T.K.Sixma. Crystal Structure of An Ach-Binding Protein Reveals the Ligand-Binding Domain of Nicotinic Receptors. Nature V. 411 269 2001.
ISSN: ISSN 0028-0836
PubMed: 11357122
DOI: 10.1038/35077011
Page generated: Mon Jul 7 15:48:29 2025

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