Atomistry » Calcium » PDB 1xk4-1y1k » 1y1a
Atomistry »
  Calcium »
    PDB 1xk4-1y1k »
      1y1a »

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

Protein crystallography data

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

Calcium Binding Sites:

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 1y1a

Go back to Calcium Binding Sites List in 1y1a
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 1y1a

Go back to Calcium Binding Sites List in 1y1a
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 1y1a

Go back to Calcium Binding Sites List in 1y1a
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 1y1a

Go back to Calcium Binding Sites List in 1y1a
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 1y1a

Go back to Calcium Binding Sites List in 1y1a
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 1y1a

Go back to Calcium Binding Sites List in 1y1a
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

Reference:

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
Page generated: Tue Jul 8 03:42:22 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy