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Calcium in PDB 4bwe: Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity

Protein crystallography data

The structure of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity, PDB code: 4bwe was solved by W.Awad, G.Svensson Birkedal, M.M.G.M.Thunnissen, K.Mani, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.476 / 2.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.230, 166.720, 139.090, 90.00, 90.80, 90.00
R / Rfree (%) 22.87 / 28.04

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity (pdb code 4bwe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity, PDB code: 4bwe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4bwe

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Calcium binding site 1 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:88.9
occ:1.00
 O A:ILE437 2.5 43.5 1.0
O A:HOH2116 2.6 51.1 1.0
OE1 A:GLU443 2.6 99.0 1.0
O A:HOH2115 2.9 42.3 1.0
OE2 A:GLU443 2.9 0.9 1.0
CD A:GLU443 3.0 95.5 1.0
C A:ILE437 3.7 44.3 1.0
CG A:GLU443 4.4 79.6 1.0
CA A:ILE437 4.6 55.9 1.0
N A:ASN438 4.6 48.3 1.0
CA A:GLU443 4.6 59.0 1.0
O A:GLN436 4.6 39.2 1.0
CA A:ASN438 4.7 55.6 1.0
O A:ASN439 4.7 48.1 1.0
N A:VAL444 4.8 46.6 1.0
O A:VAL444 4.8 60.7 1.0
CB A:GLU443 4.9 67.6 1.0
C A:ASN438 4.9 56.6 1.0
N A:ASN439 4.9 46.7 1.0
O A:VAL442 5.0 60.5 1.0

Calcium binding site 2 out of 9 in 4bwe

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Calcium binding site 2 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:49.6
occ:1.00
 O A:ASP388 2.4 31.4 1.0
O A:HOH2104 2.5 43.5 1.0
O A:HOH2106 2.6 64.7 1.0
OD1 A:ASP391 2.6 45.5 1.0
OD2 A:ASP391 3.0 51.3 1.0
O A:HOH2123 3.0 56.8 1.0
CG A:ASP391 3.1 35.3 1.0
OD1 A:ASP388 3.5 56.6 1.0
C A:ASP388 3.5 24.9 1.0
CA A:ASP388 4.1 20.8 1.0
O A:HOH2108 4.2 40.0 1.0
O B:ASP302 4.2 33.0 1.0
CG A:ASP388 4.3 49.4 1.0
CB A:ASP391 4.5 31.1 1.0
N A:VAL389 4.7 20.8 1.0
O A:ARG387 4.7 40.3 1.0
CB A:ASP388 4.9 44.3 1.0
N A:ASP391 5.0 32.5 1.0
CA A:VAL389 5.0 28.1 1.0

Calcium binding site 3 out of 9 in 4bwe

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Calcium binding site 3 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:90.5
occ:1.00
 O B:ILE437 2.5 38.5 1.0
O B:HOH2074 2.7 53.2 1.0
OE1 B:GLU443 2.7 97.8 1.0
OE2 B:GLU443 3.0 93.5 1.0
O B:HOH2073 3.1 43.4 1.0
CD B:GLU443 3.2 88.7 1.0
C B:ILE437 3.7 37.3 1.0
CA B:ILE437 4.6 36.5 1.0
N B:ASN438 4.6 36.8 1.0
CG B:GLU443 4.6 74.0 1.0
CA B:ASN438 4.6 43.2 1.0
O B:VAL444 4.8 47.2 1.0
CG1 B:ILE437 4.8 40.1 1.0
CA B:GLU443 4.9 42.6 1.0
N B:VAL444 4.9 37.0 1.0
O B:ASN439 4.9 37.8 1.0
O B:GLN436 5.0 54.0 1.0

Calcium binding site 4 out of 9 in 4bwe

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Calcium binding site 4 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:83.5
occ:1.00
 O B:ASP388 2.5 39.2 1.0
O B:HOH2067 2.7 49.4 1.0
OD1 B:ASP391 2.8 56.8 1.0
O B:HOH2082 2.8 49.7 1.0
O B:HOH2066 3.0 45.5 1.0
OD2 B:ASP391 3.1 63.7 1.0
O B:HOH2064 3.1 61.3 1.0
CG B:ASP391 3.3 48.2 1.0
C B:ASP388 3.7 37.8 1.0
OD1 B:ASP388 4.2 51.4 1.0
CA B:ASP388 4.4 36.6 1.0
CG B:ASP388 4.5 51.2 1.0
N B:VAL389 4.7 23.1 1.0
CB B:ASP391 4.8 28.9 1.0
OD2 B:ASP388 4.8 61.4 1.0
CA B:VAL389 5.0 21.4 1.0

Calcium binding site 5 out of 9 in 4bwe

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Calcium binding site 5 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:65.0
occ:1.00
 OD1 C:ASP48 2.4 46.5 1.0
O C:HOH2082 2.5 56.0 1.0
O C:HOH2006 2.7 54.5 1.0
OE1 C:GLU72 2.8 53.9 1.0
CG C:ASP48 3.6 49.5 1.0
CD C:GLU72 3.8 62.1 1.0
OE2 C:GLU72 4.0 72.2 1.0
OD2 C:ASP48 4.2 56.5 1.0
CB C:ASP48 4.7 42.7 1.0
CA C:ASP48 4.8 44.0 1.0
OG C:SER45 4.9 54.7 1.0

Calcium binding site 6 out of 9 in 4bwe

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Calcium binding site 6 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:86.4
occ:1.00
 OE1 C:GLU443 2.7 0.3 1.0
O C:HOH2076 2.8 57.6 1.0
O C:ILE437 2.8 53.7 1.0
O C:HOH2083 2.9 77.0 1.0
O C:HOH2077 3.3 57.3 1.0
CD C:GLU443 3.3 0.6 1.0
OE2 C:GLU443 3.4 0.1 1.0
C C:ILE437 4.0 64.1 1.0
O C:VAL444 4.2 72.2 1.0
CA C:ILE437 4.7 65.8 1.0
N C:VAL444 4.7 51.7 1.0
CG C:GLU443 4.7 88.8 1.0
CA C:GLU443 4.9 64.0 1.0
CG1 C:ILE437 4.9 52.2 1.0
O C:GLN436 5.0 44.8 1.0

Calcium binding site 7 out of 9 in 4bwe

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Calcium binding site 7 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca504

b:54.5
occ:1.00
 O C:ASP388 2.6 33.8 1.0
O C:HOH2066 2.6 49.1 1.0
OD1 C:ASP391 2.7 42.5 1.0
O C:HOH2084 2.9 62.5 1.0
OD2 C:ASP391 3.0 62.0 1.0
CG C:ASP391 3.2 45.4 1.0
C C:ASP388 3.7 32.7 1.0
CA C:ASP388 4.3 34.4 1.0
OD1 C:ASP388 4.3 60.3 1.0
CG C:ASP388 4.5 54.0 1.0
CB C:ASP391 4.6 36.1 1.0
OD2 C:ASP388 4.6 56.8 1.0
O D:ASP302 4.6 36.1 1.0
N C:VAL389 4.8 31.8 1.0
O C:ARG387 4.9 46.7 1.0

Calcium binding site 8 out of 9 in 4bwe

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Calcium binding site 8 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:77.4
occ:1.00
 O D:ILE437 2.5 35.6 1.0
O D:HOH2078 2.6 44.2 1.0
O D:HOH2077 2.8 52.1 1.0
OE1 D:GLU443 2.9 69.0 1.0
OE2 D:GLU443 2.9 92.0 1.0
CD D:GLU443 3.2 80.8 1.0
C D:ILE437 3.7 34.9 1.0
CG D:GLU443 4.5 68.7 1.0
N D:ASN438 4.6 42.8 1.0
CA D:ILE437 4.6 34.5 1.0
CA D:ASN438 4.6 40.5 1.0
O D:ASN439 4.6 39.4 1.0
CA D:GLU443 4.7 35.8 1.0
N D:VAL444 4.7 42.4 1.0
O D:VAL444 4.8 45.8 1.0
O D:GLN436 4.8 37.6 1.0
C D:ASN438 4.9 37.5 1.0
N D:ASN439 5.0 35.7 1.0
O D:VAL442 5.0 42.7 1.0
CG1 D:ILE437 5.0 38.3 1.0

Calcium binding site 9 out of 9 in 4bwe

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Calcium binding site 9 out of 9 in the Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of C-Terminally Truncated Glypican-1 After Controlled Dehydration to 86 Percent Relative Humidity within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca503

b:82.3
occ:1.00
 O D:ASP388 2.6 44.6 1.0
O D:HOH2067 2.6 63.8 1.0
OD1 D:ASP391 2.7 57.3 1.0
O D:HOH2066 2.8 54.7 1.0
O D:HOH2065 3.1 57.2 1.0
OD2 D:ASP391 3.4 67.0 1.0
CG D:ASP391 3.4 54.4 1.0
C D:ASP388 3.8 44.0 1.0
OD1 D:ASP388 4.2 49.0 1.0
CG D:ASP388 4.4 52.2 1.0
CA D:ASP388 4.5 34.0 1.0
OD2 D:ASP388 4.6 67.2 1.0
N D:VAL389 4.8 40.7 1.0
CB D:ASP391 4.8 40.5 1.0
CA D:VAL389 5.0 25.9 1.0

Reference:

W.Awad, G.Svensson Birkedal, M.M.G.M.Thunnissen, K.Mani, D.T.Logan. Improvements of the Order, Isotropy and Electron Density of Glypican-1 Crystals By Controlled Dehydration Acta Crystallogr.,Sect.D V. 69 2524 2013.
ISSN: ISSN 0907-4449
PubMed: 24311593
DOI: 10.1107/S0907444913025250
Page generated: Tue Jul 8 19:02:55 2025

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