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Calcium in PDB 1r1z: The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding

Protein crystallography data

The structure of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding, PDB code: 1r1z was solved by L.M.Velloso, K.Svensson, R.F.Pettersson, Y.Lindqvist, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 44.351, 81.068, 82.306, 91.05, 94.14, 94.99
R / Rfree (%) 22.3 / 24.1

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding (pdb code 1r1z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding, PDB code: 1r1z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1r1z

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Calcium binding site 1 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca285

b:32.6
occ:1.00
 OD1 A:ASN164 2.3 18.0 1.0
OD2 A:ASP160 2.3 18.2 1.0
OD2 A:ASP189 2.4 21.8 1.0
O A:PHE162 2.4 14.0 1.0
OD1 A:ASP160 2.5 18.7 1.0
O A:HOH303 2.6 37.3 1.0
O A:HOH308 2.6 34.8 1.0
CG A:ASP160 2.8 17.5 1.0
CG A:ASP189 3.4 21.9 1.0
CG A:ASN164 3.4 17.6 1.0
C A:PHE162 3.5 14.4 1.0
N A:ASN164 4.1 15.3 1.0
CB A:ASN164 4.1 16.0 1.0
OD1 A:ASP189 4.2 21.7 1.0
CA A:PHE162 4.2 14.8 1.0
N A:PHE162 4.2 15.4 1.0
CB A:PHE162 4.3 14.4 1.0
CB A:ASP189 4.3 22.5 1.0
CB A:ASP160 4.3 16.5 1.0
O A:HIS186 4.4 25.8 1.0
ND2 A:ASN164 4.5 17.6 1.0
CA A:ASP189 4.5 22.6 1.0
N A:ASP163 4.6 14.7 1.0
ND2 A:ASN170 4.6 18.9 1.0
CE1 A:HIS186 4.6 32.1 1.0
CA A:ASN164 4.8 16.1 1.0
CD2 A:PHE162 4.8 15.3 1.0
CA A:ASP163 4.9 14.9 1.0
O A:ASP129 4.9 23.4 1.0
OH A:TYR184 4.9 30.4 1.0
NE2 A:HIS186 4.9 32.5 1.0
O A:HOH311 5.0 42.0 1.0
C A:ASP163 5.0 14.9 1.0

Calcium binding site 2 out of 8 in 1r1z

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Calcium binding site 2 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca286

b:34.8
occ:1.00
 O A:HOH329 2.0 29.8 1.0
OD1 A:ASN169 2.3 19.9 1.0
OD1 A:ASP163 2.3 15.7 1.0
OD1 A:ASP189 2.4 21.7 1.0
OD1 A:ASP165 2.4 23.4 1.0
OD1 A:ASN170 2.5 19.7 1.0
O A:HOH297 2.7 36.9 1.0
CG A:ASN169 3.4 20.2 1.0
CG A:ASP165 3.4 20.6 1.0
CG A:ASP163 3.4 15.6 1.0
CG A:ASP189 3.5 21.9 1.0
CG A:ASN170 3.6 19.4 1.0
OD2 A:ASP165 3.7 22.2 1.0
ND2 A:ASN169 3.9 19.9 1.0
CB A:ASP189 4.0 22.5 1.0
CA A:ASP163 4.0 14.9 1.0
ND2 A:ASN170 4.1 18.9 1.0
CB A:ASP163 4.1 14.5 1.0
OD2 A:ASP163 4.3 16.1 1.0
N A:ASN169 4.5 20.8 1.0
N A:ASP165 4.5 17.6 1.0
CB A:LYS167 4.5 21.4 1.0
O A:ASN169 4.5 19.8 1.0
C A:ASN169 4.5 20.0 1.0
C A:ASP163 4.5 14.9 1.0
OD2 A:ASP189 4.5 21.8 1.0
N A:LYS167 4.5 21.1 1.0
O A:HOH364 4.6 57.4 1.0
CB A:ASN169 4.6 20.4 1.0
N A:ASN164 4.7 15.3 1.0
CB A:ASP165 4.8 19.3 1.0
CA A:ASN169 4.8 20.4 1.0
N A:ASN170 4.9 19.4 1.0
CB A:ASN170 4.9 18.8 1.0
N A:GLY166 4.9 20.2 1.0
CA A:LYS167 4.9 21.4 1.0
CA A:ASP165 5.0 19.0 1.0

Calcium binding site 3 out of 8 in 1r1z

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Calcium binding site 3 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca310

b:45.6
occ:1.00
 OD1 B:ASN164 2.3 18.0 1.0
O B:PHE162 2.3 13.8 1.0
OD2 B:ASP189 2.3 21.8 1.0
O B:HOH341 2.3 44.0 1.0
OD2 B:ASP160 2.4 18.3 1.0
OD1 B:ASP160 2.5 18.6 1.0
O B:HOH332 2.5 46.9 1.0
CG B:ASP160 2.9 17.5 1.0
CG B:ASP189 3.3 22.0 1.0
CG B:ASN164 3.4 17.5 1.0
C B:PHE162 3.4 14.4 1.0
CB B:ASN164 4.0 16.1 1.0
OD1 B:ASP189 4.0 21.8 1.0
N B:ASN164 4.0 15.3 1.0
CA B:PHE162 4.2 14.8 1.0
CB B:ASP189 4.2 22.4 1.0
N B:PHE162 4.3 15.3 1.0
CB B:PHE162 4.4 14.6 1.0
CB B:ASP160 4.4 16.4 1.0
O B:HIS186 4.4 25.9 1.0
CA B:ASP189 4.5 22.5 1.0
N B:ASP163 4.5 14.8 1.0
ND2 B:ASN164 4.5 18.0 1.0
ND2 B:ASN170 4.5 18.9 1.0
CA B:ASN164 4.6 16.3 1.0
CE1 B:HIS186 4.7 32.2 1.0
CA B:ASP163 4.8 15.0 1.0
CD2 B:PHE162 4.8 15.3 1.0
C B:ASP163 4.9 15.1 1.0
OH B:TYR184 5.0 30.0 1.0
NE2 B:HIS186 5.0 32.7 1.0

Calcium binding site 4 out of 8 in 1r1z

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Calcium binding site 4 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca315

b:59.3
occ:1.00
 OD1 B:ASP189 2.3 21.8 1.0
OD1 B:ASN169 2.4 19.7 1.0
OD1 B:ASP163 2.4 15.3 1.0
OD1 B:ASN170 2.4 20.1 1.0
OD1 B:ASP165 2.6 23.0 1.0
CG B:ASP189 3.4 22.0 1.0
CG B:ASN169 3.4 20.1 1.0
CG B:ASN170 3.5 19.4 1.0
CG B:ASP163 3.6 15.5 1.0
CG B:ASP165 3.6 20.4 1.0
OD2 B:ASP165 3.7 21.8 1.0
CB B:ASP189 3.9 22.4 1.0
ND2 B:ASN169 3.9 19.7 1.0
ND2 B:ASN170 4.0 18.9 1.0
CA B:ASP163 4.1 15.0 1.0
CB B:ASP163 4.2 14.6 1.0
O B:ASN169 4.4 19.8 1.0
OD2 B:ASP189 4.4 21.8 1.0
OD2 B:ASP163 4.5 15.9 1.0
C B:ASN169 4.5 19.9 1.0
C B:ASP163 4.6 15.1 1.0
N B:ASN169 4.6 20.8 1.0
CB B:LYS167 4.6 21.6 1.0
N B:ASP165 4.6 17.7 1.0
N B:ASN164 4.6 15.3 1.0
CB B:ASN169 4.7 20.4 1.0
N B:LYS167 4.7 21.1 1.0
CB B:ASN170 4.8 19.1 1.0
CA B:ASN169 4.8 20.4 1.0
N B:ASN170 4.9 19.4 1.0
CB B:ASP165 4.9 19.3 1.0

Calcium binding site 5 out of 8 in 1r1z

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Calcium binding site 5 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca410

b:60.0
occ:1.00
 O C:HOH426 2.2 57.9 1.0
O C:PHE162 2.3 14.2 1.0
OD2 C:ASP189 2.3 21.6 1.0
OD1 C:ASN164 2.3 18.0 1.0
OD2 C:ASP160 2.4 18.7 1.0
OD1 C:ASP160 2.4 18.4 1.0
CG C:ASP160 2.8 17.6 1.0
CG C:ASP189 3.3 21.9 1.0
C C:PHE162 3.4 14.6 1.0
CG C:ASN164 3.4 17.5 1.0
OD1 C:ASP189 4.0 21.8 1.0
N C:ASN164 4.1 15.7 1.0
CB C:ASN164 4.1 16.1 1.0
CA C:PHE162 4.2 14.8 1.0
CB C:ASP189 4.2 22.5 1.0
N C:PHE162 4.2 15.5 1.0
CB C:ASP160 4.3 16.5 1.0
CB C:PHE162 4.4 14.5 1.0
O C:HIS186 4.4 25.8 1.0
CA C:ASP189 4.5 22.6 1.0
N C:ASP163 4.5 14.6 1.0
ND2 C:ASN170 4.5 19.0 1.0
ND2 C:ASN164 4.5 17.9 1.0
CE1 C:HIS186 4.7 32.1 1.0
CA C:ASN164 4.7 16.3 1.0
CA C:ASP163 4.8 15.0 1.0
CD2 C:PHE162 4.8 15.3 1.0
C C:ASP163 4.9 15.2 1.0
OH C:TYR184 5.0 30.0 1.0
NE2 C:HIS186 5.0 32.6 1.0

Calcium binding site 6 out of 8 in 1r1z

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Calcium binding site 6 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca415

b:66.6
occ:1.00
 OD1 C:ASP189 2.3 21.8 1.0
OD1 C:ASN169 2.4 19.9 1.0
O C:HOH429 2.4 50.2 1.0
OD1 C:ASN170 2.5 19.8 1.0
OD1 C:ASP165 2.6 23.1 1.0
OD1 C:ASP163 2.6 15.3 1.0
CG C:ASN169 3.4 20.2 1.0
CG C:ASP189 3.4 21.9 1.0
CG C:ASP165 3.5 20.6 1.0
CG C:ASN170 3.6 19.4 1.0
OD2 C:ASP165 3.6 21.9 1.0
CG C:ASP163 3.8 15.5 1.0
ND2 C:ASN169 3.8 19.9 1.0
CB C:ASP189 3.8 22.5 1.0
ND2 C:ASN170 4.0 19.0 1.0
CA C:ASP163 4.2 15.0 1.0
O C:ASN169 4.4 19.8 1.0
CB C:ASP163 4.4 14.7 1.0
OD2 C:ASP189 4.5 21.6 1.0
C C:ASN169 4.5 19.9 1.0
N C:ASN169 4.6 20.9 1.0
CB C:ASN169 4.6 20.4 1.0
OD2 C:ASP163 4.7 16.0 1.0
CB C:LYS167 4.7 21.6 1.0
N C:ASP165 4.7 17.8 1.0
C C:ASP163 4.7 15.2 1.0
N C:ASN164 4.8 15.7 1.0
CA C:ASN169 4.8 20.4 1.0
N C:LYS167 4.8 21.2 1.0
CB C:ASN170 4.9 19.0 1.0
CB C:ASP165 4.9 19.3 1.0
N C:ASN170 4.9 19.4 1.0

Calcium binding site 7 out of 8 in 1r1z

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Calcium binding site 7 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca510

b:48.3
occ:1.00
 OD1 D:ASN164 2.2 17.6 1.0
OD2 D:ASP189 2.3 21.8 1.0
O D:HOH518 2.3 42.5 1.0
OD1 D:ASP160 2.4 18.3 1.0
O D:PHE162 2.4 14.0 1.0
OD2 D:ASP160 2.4 18.5 1.0
CG D:ASP160 2.8 17.4 1.0
CG D:ASP189 3.3 21.9 1.0
CG D:ASN164 3.4 17.6 1.0
C D:PHE162 3.5 14.5 1.0
CB D:ASN164 4.0 16.1 1.0
OD1 D:ASP189 4.1 21.8 1.0
N D:ASN164 4.1 15.4 1.0
CB D:ASP189 4.2 22.4 1.0
CA D:PHE162 4.3 14.7 1.0
CB D:ASP160 4.3 16.5 1.0
O D:HIS186 4.3 25.8 1.0
N D:PHE162 4.3 15.3 1.0
CA D:ASP189 4.4 22.5 1.0
CB D:PHE162 4.4 14.3 1.0
ND2 D:ASN164 4.5 17.9 1.0
N D:ASP163 4.6 14.7 1.0
ND2 D:ASN170 4.6 18.9 1.0
CE1 D:HIS186 4.6 32.0 1.0
CA D:ASN164 4.7 16.1 1.0
OH D:TYR184 4.8 29.8 1.0
O D:HOH531 4.9 74.8 1.0
CD2 D:PHE162 4.9 15.5 1.0
CA D:ASP163 4.9 14.9 1.0
NE2 D:HIS186 4.9 32.4 1.0
C D:ASP163 5.0 15.1 1.0
ND1 D:HIS186 5.0 32.7 1.0

Calcium binding site 8 out of 8 in 1r1z

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Calcium binding site 8 out of 8 in the The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Crystal Structure of the Carbohydrate Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals A Novel Metal Binding Site and Conformational Changes Associated with Calcium Ion Binding within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca515

b:61.9
occ:1.00
 OD1 D:ASP189 2.2 21.8 1.0
O D:HOH529 2.3 56.3 1.0
OD1 D:ASP165 2.4 23.1 1.0
OD1 D:ASP163 2.5 15.3 1.0
OD1 D:ASN169 2.5 19.9 1.0
OD1 D:ASN170 2.6 19.9 1.0
CG D:ASP189 3.3 21.9 1.0
CG D:ASP165 3.3 20.4 1.0
OD2 D:ASP165 3.5 21.6 1.0
CG D:ASN169 3.6 20.1 1.0
CG D:ASP163 3.6 15.6 1.0
CG D:ASN170 3.7 19.4 1.0
CB D:ASP189 3.8 22.4 1.0
ND2 D:ASN169 4.0 19.7 1.0
CA D:ASP163 4.1 14.9 1.0
ND2 D:ASN170 4.1 18.9 1.0
CB D:ASP163 4.2 14.6 1.0
OD2 D:ASP189 4.3 21.8 1.0
N D:ASP165 4.5 17.6 1.0
OD2 D:ASP163 4.5 15.9 1.0
C D:ASP163 4.5 15.1 1.0
O D:ASN169 4.5 19.8 1.0
N D:ASN164 4.6 15.4 1.0
CB D:LYS167 4.6 21.5 1.0
C D:ASN169 4.6 19.9 1.0
CB D:ASP165 4.7 19.2 1.0
N D:LYS167 4.7 21.1 1.0
N D:ASN169 4.7 20.9 1.0
CB D:ASN169 4.8 20.4 1.0
CA D:ASN169 4.9 20.4 1.0
CB D:ASN170 5.0 18.9 1.0
CA D:ASP165 5.0 19.0 1.0

Reference:

L.M.Velloso, K.Svensson, R.F.Pettersson, Y.Lindqvist. The Crystal Structure of the Carbohydrate-Recognition Domain of the Glycoprotein Sorting Receptor P58/Ergic-53 Reveals An Unpredicted Metal-Binding Site and Conformational Changes Associated with Calcium Ion Binding. J.Mol.Biol. V. 334 845 2003.
ISSN: ISSN 0022-2836
PubMed: 14643651
DOI: 10.1016/J.JMB.2003.10.031
Page generated: Thu Jul 11 22:02:27 2024

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