Calcium in PDB 1y1a: Crystal Structure of Calcium and Integrin Binding Protein

The structure of Crystal Structure of Calcium and Integrin Binding Protein, PDB code: 1y1a was solved by C.J.Blamey, C.Ceccarelli, U.P.Naik, B.J.Bahnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.25 / 2.30
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	115.222, 115.222, 268.202, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 25.1

The binding sites of Calcium atom in the Crystal Structure of Calcium and Integrin Binding Protein (pdb code 1y1a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Calcium and Integrin Binding Protein, PDB code: 1y1a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Calcium and Integrin Binding Protein


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 Calcium and Integrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:45.0 occ:1.00 OD1 A:ASP116 2.5 33.3 1.0 O A:THR122 2.5 38.7 1.0 OD2 A:ASP127 2.5 42.6 1.0 O A:HOH1077 2.7 52.4 1.0 O A:HOH1029 2.7 45.0 1.0 OD1 A:ASP120 2.8 50.4 1.0 OD2 A:ASP120 2.8 57.1 1.0 CG A:ASP120 3.1 50.6 1.0 CG A:ASP127 3.5 38.1 1.0 CG A:ASP116 3.6 34.7 1.0 C A:THR122 3.7 38.4 1.0 OD1 A:ASP127 3.7 37.2 1.0 CA A:ASP116 4.3 34.5 1.0 OD2 A:ASP116 4.4 35.8 1.0 N A:THR122 4.4 37.8 1.0 OG1 A:THR122 4.5 42.3 1.0 CB A:ASP116 4.5 33.1 1.0 N A:ASP118 4.5 45.8 1.0 CB A:ASP120 4.5 46.6 1.0 N A:ASP120 4.5 44.8 1.0 CA A:LEU123 4.5 35.6 1.0 N A:LEU123 4.6 37.5 1.0 C A:ASP116 4.6 36.9 1.0 CA A:THR122 4.6 38.6 1.0 CB A:ASP118 4.6 51.4 1.0 N A:ASN124 4.7 35.2 1.0 OD1 A:ASN124 4.7 38.9 1.0 N A:PHE117 4.7 40.1 1.0 CB A:ASP127 4.8 38.7 1.0 CG A:ASN124 4.9 39.1 1.0 OD2 A:ASP118 4.9 58.9 1.0 CA A:ASP120 4.9 44.8 1.0 CA A:ASP118 5.0 48.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Calcium and Integrin Binding Protein


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 Calcium and Integrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:41.7 occ:1.00 OD1 A:ASP161 2.4 37.0 1.0 OD1 A:ASP165 2.6 46.5 1.0 OE1 A:GLU172 2.6 42.0 1.0 O A:THR167 2.6 40.6 1.0 O A:HOH1016 2.7 41.8 1.0 OD1 A:ASP163 2.7 53.3 1.0 OE2 A:GLU172 2.7 43.2 1.0 CD A:GLU172 3.0 41.2 1.0 CG A:ASP163 3.3 49.8 1.0 CG A:ASP165 3.3 45.7 1.0 OD2 A:ASP163 3.4 53.0 1.0 CG A:ASP161 3.5 40.3 1.0 C A:THR167 3.6 38.7 1.0 OD2 A:ASP165 3.8 50.2 1.0 OG1 A:THR167 4.1 44.8 1.0 N A:ASP165 4.2 42.7 1.0 CA A:ASP161 4.2 39.3 1.0 N A:THR167 4.3 39.3 1.0 CB A:ASP161 4.3 38.5 1.0 CB A:ASP165 4.3 43.0 1.0 N A:ILE168 4.4 37.0 1.0 OD2 A:ASP161 4.4 42.7 1.0 CA A:ILE168 4.4 35.1 1.0 CA A:THR167 4.5 39.4 1.0 CG A:GLU172 4.5 41.2 1.0 N A:ASP163 4.5 45.5 1.0 N A:ASN169 4.5 35.3 1.0 C A:ASP161 4.6 40.9 1.0 CB A:ASP163 4.6 47.4 1.0 ND2 A:ASN169 4.6 39.5 1.0 N A:ARG164 4.7 43.3 1.0 CA A:ASP165 4.8 42.0 1.0 O A:HOH1059 4.8 50.6 1.0 C A:ASP163 4.8 44.3 1.0 C A:ILE168 4.9 35.7 1.0 CA A:ASP163 4.9 45.2 1.0 N A:GLY166 4.9 41.5 1.0 CG A:ASN169 4.9 38.2 1.0 CB A:THR167 4.9 41.8 1.0 N A:ILE162 4.9 41.4 1.0 O A:ASP161 5.0 39.0 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Calcium and Integrin Binding Protein


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 Calcium and Integrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:68.5 occ:1.00 O A:SER99 2.4 41.2 1.0 O A:SER96 2.4 38.2 1.0 O A:ALA102 2.6 40.6 1.0 O A:HOH1045 2.7 49.1 1.0 C A:SER96 3.1 37.2 1.0 O A:HOH1065 3.2 51.1 1.0 O A:LEU95 3.3 38.2 1.0 C A:SER99 3.5 41.1 1.0 CA A:SER96 3.7 36.8 1.0 C A:ALA102 3.7 39.3 1.0 N A:SER99 3.9 39.5 1.0 N A:VAL97 4.1 37.2 1.0 CA A:SER99 4.2 40.4 1.0 C A:LEU95 4.2 36.9 1.0 O A:VAL97 4.3 39.5 1.0 C A:VAL97 4.3 39.0 1.0 O A:HOH1151 4.4 61.4 1.0 N A:ASP100 4.4 42.3 1.0 CA A:VAL97 4.5 37.0 1.0 N A:SER96 4.5 35.5 1.0 OG1 A:THR103 4.5 41.0 1.0 N A:ALA102 4.5 38.7 1.0 CA A:ASP100 4.5 46.5 1.0 CE B:LYS107 4.5 52.4 1.0 CA A:THR103 4.6 38.5 1.0 N A:THR103 4.6 39.2 1.0 CA A:ALA102 4.6 37.6 1.0 N A:PHE98 4.7 38.6 1.0 C A:PHE98 4.8 39.7 1.0 CB A:ALA102 4.8 31.5 1.0 CB A:SER96 4.9 35.7 1.0 NZ B:LYS107 4.9 54.4 1.0 C A:ASP100 4.9 44.6 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Calcium and Integrin Binding Protein


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 Calcium and Integrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:55.6 occ:1.00 O B:THR122 2.6 48.0 1.0 OD2 B:ASP127 2.6 49.9 1.0 O B:HOH1088 2.7 53.7 1.0 OD2 B:ASP120 2.7 67.1 1.0 OD1 B:ASP116 2.8 55.5 1.0 O B:HOH1171 2.8 63.8 1.0 OD1 B:ASP120 2.9 64.9 1.0 CG B:ASP120 3.1 64.6 1.0 CG B:ASP127 3.6 45.2 1.0 CG B:ASP116 3.6 54.0 1.0 C B:THR122 3.8 48.4 1.0 OD1 B:ASP127 3.8 43.9 1.0 CB B:ASP118 4.2 64.4 1.0 N B:ASP118 4.2 59.0 1.0 OD2 B:ASP116 4.2 54.8 1.0 CA B:ASP116 4.3 51.1 1.0 OD2 B:ASP118 4.3 67.2 1.0 CB B:ASP116 4.5 52.8 1.0 N B:ASP120 4.5 61.7 1.0 C B:ASP116 4.5 50.9 1.0 N B:THR122 4.5 50.5 1.0 CB B:ASP120 4.5 62.3 1.0 OG1 B:THR122 4.6 52.9 1.0 N B:PHE117 4.6 51.8 1.0 CA B:ASP118 4.6 62.5 1.0 CG B:ASP118 4.7 66.7 1.0 N B:LEU123 4.7 46.8 1.0 CA B:LEU123 4.7 45.8 1.0 CA B:THR122 4.7 49.4 1.0 N B:ASP119 4.7 65.2 1.0 C B:ASP118 4.9 64.2 1.0 N B:ASN124 4.9 47.1 1.0 CB B:ASP127 4.9 45.3 1.0 OD1 B:ASN124 4.9 49.3 1.0 CA B:ASP120 5.0 60.0 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Calcium and Integrin Binding Protein


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 Calcium and Integrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:70.8 occ:1.00 OD1 B:ASP165 2.6 57.3 1.0 OD1 B:ASP163 2.6 78.3 1.0 OD1 B:ASP161 2.6 63.8 1.0 OE1 B:GLU172 2.6 58.7 1.0 O B:HOH1126 2.7 58.5 1.0 O B:THR167 2.7 58.1 1.0 OE2 B:GLU172 2.8 59.2 1.0 CD B:GLU172 3.1 58.2 1.0 CG B:ASP163 3.3 75.1 1.0 OD2 B:ASP163 3.4 74.3 1.0 CG B:ASP165 3.5 61.7 1.0 C B:THR167 3.5 57.5 1.0 CG B:ASP161 3.7 65.7 1.0 OG1 B:THR167 3.9 63.8 1.0 OD2 B:ASP165 4.0 61.1 1.0 CA B:ILE168 4.1 52.0 1.0 ND2 B:ASN169 4.2 51.6 1.0 N B:ILE168 4.2 55.5 1.0 N B:ASN169 4.2 50.8 1.0 N B:THR167 4.4 60.0 1.0 OD2 B:ASP161 4.4 65.4 1.0 O B:HOH1145 4.5 60.6 1.0 CA B:THR167 4.5 59.0 1.0 CB B:ASP163 4.5 73.0 1.0 CG B:ASN169 4.5 50.0 1.0 CB B:ASP161 4.5 66.0 1.0 C B:ILE168 4.6 51.1 1.0 CB B:ASP165 4.6 60.9 1.0 CA B:ASP161 4.6 67.5 1.0 CG B:GLU172 4.6 56.9 1.0 N B:ASP165 4.6 62.9 1.0 CB B:THR167 4.8 60.1 1.0 N B:ASP163 4.8 71.6 1.0 CB B:ASN169 4.9 49.4 1.0 C B:ASP161 5.0 69.5 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Calcium and Integrin Binding Protein


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 Calcium and Integrin Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:72.1 occ:1.00 O B:SER99 2.5 49.8 1.0 O B:SER96 2.6 39.4 1.0 O B:ALA102 2.6 45.1 1.0 C B:SER96 3.4 38.7 1.0 C B:SER99 3.4 49.3 1.0 O B:LEU95 3.5 37.3 1.0 C B:ALA102 3.7 45.8 1.0 CA B:SER96 4.0 37.6 1.0 N B:SER99 4.0 44.9 1.0 N B:ASP100 4.2 51.3 1.0 CA B:SER99 4.3 47.9 1.0 CE A:LYS107 4.3 54.7 1.0 N B:VAL97 4.3 38.5 1.0 CA B:ASP100 4.3 54.3 1.0 OG1 B:THR103 4.4 51.8 1.0 NZ A:LYS107 4.4 58.8 1.0 C B:VAL97 4.4 38.7 1.0 N B:ALA102 4.5 46.0 1.0 O B:VAL97 4.5 41.6 1.0 C B:LEU95 4.5 38.2 1.0 N B:THR103 4.6 45.1 1.0 CA B:THR103 4.6 46.1 1.0 CA B:ALA102 4.6 45.2 1.0 CA B:VAL97 4.6 37.4 1.0 N B:PHE98 4.7 39.4 1.0 N B:SER96 4.8 36.0 1.0 C B:ASP100 4.8 53.1 1.0 C B:PHE98 4.8 43.3 1.0 CB B:ALA102 4.9 43.6 1.0 CB B:THR103 5.0 47.1 1.0

C.J.Blamey, C.Ceccarelli, U.P.Naik, B.J.Bahnson. The Crystal Structure of Calcium- and Integrin-Binding Protein 1: Insights Into Redox Regulated Functions Protein Sci. V. 14 1214 2005.
ISSN: ISSN 0961-8368
PubMed: 15840829
DOI: 10.1110/PS.041270805