Calcium in PDB 4ywt: Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity

The structure of Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity, PDB code: 4ywt was solved by W.Awad, K.Mani, D.T.Logan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.780, 166.590, 137.700, 90.00, 90.38, 90.00
R / Rfree (%)	23.9 / 27.3

The binding sites of Calcium atom in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity (pdb code 4ywt). 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity, PDB code: 4ywt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:47.2 occ:1.00 OD1 A:ASP391 2.4 38.6 1.0 O A:ASP388 2.4 39.0 1.0 OD2 A:ASP391 2.4 47.7 1.0 O A:HOH741 2.4 38.2 1.0 O A:HOH731 2.4 56.5 1.0 O A:HOH787 2.4 60.4 1.0 CG A:ASP391 2.7 42.3 1.0 C A:ASP388 3.5 34.1 1.0 OD1 A:ASP388 3.9 52.4 1.0 CB A:ASP391 4.2 40.0 1.0 CA A:ASP388 4.4 35.6 1.0 CG A:ASP388 4.5 51.1 1.0 N A:VAL389 4.5 32.0 1.0 CA A:VAL389 4.6 34.4 1.0 N A:ASP391 4.8 25.5 1.0 CA A:ASP391 5.0 25.9 1.0 OG A:SER395 5.0 42.9 1.0

Calcium binding site 2 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:90.3 occ:1.00 O A:ILE437 2.4 38.9 1.0 O A:HOH766 2.4 60.8 1.0 O A:HOH780 2.4 58.4 1.0 O A:HOH770 2.4 64.6 1.0 CG A:GLU443 3.6 76.3 1.0 C A:ILE437 3.6 37.9 1.0 CD A:GLU443 4.4 86.2 1.0 N A:ASN438 4.4 40.5 1.0 CA A:ASN438 4.5 45.6 1.0 CA A:ILE437 4.5 38.5 1.0 CB A:GLU443 4.6 69.3 1.0 CA A:GLU443 4.6 58.4 1.0 C A:ASN438 4.8 46.5 1.0 O A:GLN436 4.8 36.1 1.0 OE2 A:GLU443 4.8 90.4 1.0 O A:ASN439 4.8 43.1 1.0 N A:ASN439 4.9 42.3 1.0 N A:VAL444 4.9 53.5 1.0 O A:VAL444 4.9 51.5 1.0 CG1 A:ILE437 4.9 39.4 1.0

Calcium binding site 3 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:87.8 occ:1.00 OE2 B:GLU443 2.4 81.4 1.0 OE1 B:GLU443 2.4 82.6 1.0 O B:ILE437 2.4 38.2 1.0 O B:HOH716 2.4 34.1 1.0 O B:HOH707 2.4 45.5 1.0 CD B:GLU443 2.7 80.0 1.0 C B:ILE437 3.6 37.6 1.0 CG B:GLU443 4.2 71.0 1.0 N B:ASN438 4.4 37.3 1.0 CA B:ASN438 4.5 46.1 1.0 CA B:ILE437 4.5 38.8 1.0 O B:ASN439 4.6 37.1 1.0 O B:GLN436 4.6 44.8 1.0 CA B:GLU443 4.6 49.4 1.0 N B:VAL444 4.7 42.2 1.0 O B:VAL444 4.8 43.4 1.0 C B:ASN438 4.8 48.5 1.0 N B:ASN439 4.8 49.7 1.0 CB B:GLU443 4.9 58.2 1.0 CG1 B:ILE437 5.0 38.9 1.0 O B:VAL442 5.0 36.6 1.0

Calcium binding site 4 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:43.1 occ:0.46 OD1 B:ASP391 2.4 61.2 1.0 O B:ASP388 2.4 45.9 1.0 OD2 B:ASP391 2.4 60.0 1.0 O B:HOH731 2.4 43.7 1.0 O B:HOH741 2.4 31.6 1.0 O B:HOH776 2.4 52.4 1.0 O B:HOH702 2.4 52.0 1.0 CG B:ASP391 2.7 53.4 1.0 C B:ASP388 3.5 39.7 1.0 OD1 B:ASP388 4.1 58.9 1.0 CB B:ASP391 4.2 43.6 1.0 CA B:ASP388 4.3 44.7 1.0 N B:VAL389 4.5 35.3 1.0 CG B:ASP388 4.5 55.0 1.0 CA B:VAL389 4.7 28.8 1.0 N B:ASP391 4.7 34.4 1.0 O B:ARG387 4.8 36.5 1.0 OD2 B:ASP388 4.9 58.0 1.0 CA B:ASP391 5.0 30.5 1.0

Calcium binding site 5 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca602 b:71.8 occ:1.00 OE1 C:GLU72 2.4 74.7 1.0 OD1 C:ASP48 2.4 55.2 1.0 OE2 C:GLU72 2.4 75.3 1.0 O C:HOH703 2.4 54.8 1.0 CD C:GLU72 2.6 70.8 1.0 CG C:ASP48 3.3 59.7 1.0 OD2 C:ASP48 3.8 73.8 1.0 O C:HOH707 4.0 38.3 1.0 CG C:GLU72 4.1 65.3 1.0 CB C:ASP48 4.5 56.3 1.0 CB C:GLU72 4.7 60.4 1.0 CA C:ASP48 4.7 55.0 1.0

Calcium binding site 6 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:99.2 occ:1.00 OE2 C:GLU443 2.4 96.6 1.0 O C:ILE437 2.4 50.3 1.0 O C:HOH720 2.4 56.7 1.0 O C:HOH724 2.4 71.5 1.0 CD C:GLU443 3.5 94.2 1.0 C C:ILE437 3.6 51.3 1.0 OE1 C:GLU443 4.2 97.9 1.0 CA C:ASN438 4.2 62.1 1.0 N C:ASN438 4.4 55.0 1.0 CG C:GLU443 4.5 86.8 1.0 C C:ASN438 4.6 61.3 1.0 CA C:ILE437 4.7 60.3 1.0 O C:ASN439 4.8 48.9 1.0 N C:ASN439 4.8 58.8 1.0 O C:VAL444 4.9 68.8 1.0 CG1 C:ILE437 5.0 52.0 1.0 O C:GLN436 5.0 61.0 1.0

Calcium binding site 7 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca604 b:61.0 occ:1.00 OD1 C:ASP391 2.4 59.5 1.0 O C:ASP388 2.4 49.2 1.0 OD2 C:ASP391 2.4 60.5 1.0 O C:HOH717 2.4 55.7 1.0 CG C:ASP391 2.7 57.0 1.0 C C:ASP388 3.5 47.0 1.0 OD1 C:ASP388 4.2 69.6 1.0 CB C:ASP391 4.2 49.9 1.0 O C:HOH745 4.2 53.0 1.0 CA C:ASP388 4.3 55.2 1.0 CG C:ASP388 4.5 67.1 1.0 N C:VAL389 4.5 38.6 1.0 N C:ASP391 4.7 44.6 1.0 CA C:VAL389 4.7 43.2 1.0 O D:ASP302 4.7 41.3 1.0 O C:ARG387 4.8 58.6 1.0 CA C:ASP391 5.0 45.1 1.0 OD2 C:ASP388 5.0 68.1 1.0 OG C:SER395 5.0 56.2 1.0

Calcium binding site 8 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca602 b:93.1 occ:1.00 OE1 D:GLU443 2.4 75.5 1.0 O D:ILE437 2.4 46.7 1.0 O D:HOH712 2.4 56.6 1.0 CD D:GLU443 3.3 73.5 1.0 C D:ILE437 3.6 42.9 1.0 OE2 D:GLU443 3.6 78.3 1.0 O D:ASN439 4.4 51.3 1.0 N D:VAL444 4.4 50.9 1.0 CA D:GLU443 4.4 51.2 1.0 N D:ASN438 4.4 44.7 1.0 CA D:ASN438 4.5 46.6 1.0 CA D:ILE437 4.5 44.5 1.0 O D:GLN436 4.5 52.3 1.0 O D:VAL444 4.5 56.1 1.0 O D:VAL442 4.6 43.8 1.0 CG D:GLU443 4.6 66.1 1.0 C D:ASN438 4.7 47.5 1.0 N D:ASN439 4.7 46.4 1.0 O D:HOH719 4.8 48.4 1.0 CB D:GLU443 4.8 57.6 1.0 C D:GLU443 4.9 52.4 1.0

Calcium binding site 9 out of 9 in the Crystal Structure of Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% 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 Full-Length Glypican-1 Core Protein After Controlled Crystal Dehydration to 87% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca603 b:82.0 occ:1.00 OD1 D:ASP391 2.4 69.5 1.0 OD2 D:ASP391 2.4 69.7 1.0 O D:ASP388 2.4 57.8 1.0 O D:HOH738 2.4 72.4 1.0 CG D:ASP391 2.7 64.0 1.0 C D:ASP388 3.5 54.2 1.0 OD1 D:ASP388 3.9 68.0 1.0 CB D:ASP391 4.2 51.7 1.0 CA D:ASP388 4.3 55.0 1.0 CG D:ASP388 4.4 64.5 1.0 N D:VAL389 4.6 55.1 1.0 N D:ASP391 4.7 46.6 1.0 CA D:VAL389 4.8 47.0 1.0 OD2 D:ASP388 4.9 68.2 1.0 CA D:ASP391 4.9 43.0 1.0 CB D:ASP388 5.0 57.8 1.0 O D:ARG387 5.0 52.8 1.0

W.Awad, B.Adamczyk, J.Ornros, N.G.Karlsson, K.Mani, D.T.Logan. Structural Aspects of N-Glycosylations and the C-Terminal Region in Human Glypican-1. J.Biol.Chem. V. 290 22991 2015.
ISSN: ESSN 1083-351X
PubMed: 26203194
DOI: 10.1074/JBC.M115.660878