Calcium in PDB 1jv2: Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3

The structure of Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3, PDB code: 1jv2 was solved by J.P.Xiong, T.Stehle, B.Diefenbach, R.Zhang, R.Dunker, D.Scott, A.Joachimiak, S.L.Goodman, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.000, 130.000, 307.300, 90.00, 90.00, 120.00
R / Rfree (%)	25.5 / 33.5

The binding sites of Calcium atom in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3 (pdb code 1jv2). 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 the Extracellular Segment of Integrin ALPHAVBETA3, PDB code: 1jv2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3


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 the Extracellular Segment of Integrin ALPHAVBETA3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:61.9 occ:1.00 OD1 B:ASP127 2.3 87.6 1.0 O B:MET335 2.3 84.0 1.0 OD1 B:ASP126 2.5 77.4 1.0 OD2 B:ASP126 2.6 75.1 1.0 O B:SER123 2.7 63.9 1.0 CG B:ASP126 2.9 73.6 1.0 CG B:ASP127 3.2 84.0 1.0 C B:MET335 3.4 88.2 1.0 OD2 B:ASP127 3.5 98.1 1.0 C B:SER123 3.8 63.2 1.0 CA B:MET335 4.3 88.8 1.0 N B:ASP336 4.4 91.5 1.0 CB B:ASP126 4.4 68.9 1.0 N B:ASP127 4.4 79.4 1.0 CA B:ASP336 4.6 91.9 1.0 CB B:ASP127 4.6 72.3 1.0 CA B:MET124 4.6 46.7 1.0 N B:MET124 4.7 56.5 1.0 OD1 B:ASP251 4.7 78.7 1.0 CA B:SER123 4.8 66.0 1.0 CB B:MET335 4.9 93.0 1.0 CB B:SER123 4.9 71.0 1.0 CA B:ASP127 5.0 69.2 1.0 N B:ASP126 5.0 65.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3


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 the Extracellular Segment of Integrin ALPHAVBETA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4004 b:54.3 occ:1.00 OD1 A:ASP238 2.4 35.4 1.0 O A:ILE236 2.4 58.1 1.0 OD2 A:ASP230 2.7 59.5 1.0 O A:ASN232 3.2 60.5 1.0 CG A:ASP238 3.3 40.1 1.0 OD2 A:ASP238 3.5 47.2 1.0 C A:ILE236 3.5 64.9 1.0 CG A:ASP230 3.9 62.9 1.0 O A:ASP234 4.0 55.5 1.0 N A:ILE236 4.2 69.5 1.0 C A:ASN232 4.2 64.9 1.0 CA A:ILE236 4.3 69.6 1.0 CB A:ASN232 4.3 71.8 1.0 O A:ASP237 4.3 51.2 1.0 C A:ASP237 4.4 52.9 1.0 N A:ASN232 4.5 65.1 1.0 N A:ASP237 4.5 63.7 1.0 C A:GLY235 4.6 66.4 1.0 CA A:ASN232 4.6 65.2 1.0 OD1 A:ASP230 4.6 55.6 1.0 CB A:ASP238 4.7 23.6 1.0 CA A:ASP237 4.7 62.4 1.0 C A:ASP234 4.8 67.0 1.0 N A:ASP238 4.8 43.9 1.0 CB A:ASP230 4.8 52.2 1.0 CA A:ASP230 4.8 39.0 1.0 CB A:ILE236 4.8 76.6 1.0 CD1 A:ILE236 4.9 66.6 1.0 N A:PHE231 5.0 42.8 1.0 O A:GLY235 5.0 61.4 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3


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 the Extracellular Segment of Integrin ALPHAVBETA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4005 b:49.0 occ:1.00 OD2 A:ASP284 2.5 50.1 1.0 OD2 A:ASP288 2.5 51.3 1.0 ND2 A:ASN286 2.6 35.2 1.0 O A:TYR290 2.8 74.3 1.0 OD2 A:ASP292 2.9 53.6 1.0 OD1 A:ASP288 3.1 37.1 1.0 CG A:ASP288 3.2 48.2 1.0 OD1 A:ASP292 3.4 33.3 1.0 CG A:ASN286 3.5 43.6 1.0 CB A:TYR290 3.5 61.4 1.0 OD1 A:ASN286 3.5 55.3 1.0 CG A:ASP292 3.5 46.1 1.0 CG A:ASP284 3.7 60.4 1.0 C A:TYR290 3.8 67.1 1.0 CA A:TYR290 4.1 64.9 1.0 N A:TYR290 4.1 64.4 1.0 O A:GLN320 4.2 46.9 1.0 OD1 A:ASP284 4.4 71.7 1.0 CB A:ASP288 4.6 50.0 1.0 CG A:TYR290 4.7 59.6 1.0 CB A:ASP284 4.7 56.4 1.0 N A:GLN320 4.8 52.6 1.0 CB A:ASN286 4.9 43.3 1.0 C A:ASP288 4.9 57.8 1.0 CD1 A:TYR290 4.9 60.8 1.0 N A:ASN286 5.0 45.8 1.0 CA A:ASP284 5.0 53.6 1.0 C A:ASP289 5.0 66.1 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3


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 the Extracellular Segment of Integrin ALPHAVBETA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4006 b:58.2 occ:1.00 OD2 A:ASP357 2.2 76.5 1.0 O A:PHE355 2.3 45.2 1.0 OD2 A:ASP353 2.8 67.6 1.0 OD2 A:ASP351 2.9 61.9 1.0 OD1 A:ASP351 3.0 66.0 1.0 CG A:ASP357 3.3 76.1 1.0 CG A:ASP351 3.3 64.2 1.0 C A:PHE355 3.4 45.7 1.0 N A:ASP357 3.4 52.8 1.0 ND2 A:ASN377 3.4 51.8 1.0 C A:ASN356 3.4 48.2 1.0 OD1 A:ASP349 3.6 52.5 1.0 CB A:ASP357 3.8 68.7 1.0 O A:ASN356 3.8 53.4 1.0 CA A:ASP357 3.8 58.9 1.0 N A:GLY378 3.8 50.6 1.0 CA A:ASN356 3.9 49.3 1.0 CG A:ASP353 3.9 70.4 1.0 N A:ASN356 4.0 49.7 1.0 CG A:ASP349 4.2 49.5 1.0 CG A:ASN377 4.3 41.0 1.0 OD1 A:ASP357 4.3 82.8 1.0 OD1 A:ASP353 4.3 72.1 1.0 CB A:ASN377 4.4 32.7 1.0 CA A:ASP349 4.4 42.5 1.0 CA A:PHE355 4.5 44.3 1.0 O A:GLY378 4.5 72.2 1.0 CB A:PHE355 4.5 39.2 1.0 CA A:ASN377 4.5 38.2 1.0 O A:GLY348 4.6 45.7 1.0 CA A:GLY378 4.7 56.6 1.0 C A:ASN377 4.7 47.4 1.0 OD2 A:ASP349 4.7 56.8 1.0 N A:PHE355 4.8 51.9 1.0 CB A:ASP349 4.8 44.8 1.0 N A:LEU350 4.8 37.7 1.0 CB A:ASP351 4.9 58.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3


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 the Extracellular Segment of Integrin ALPHAVBETA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4007 b:39.9 occ:1.00 O A:TYR419 2.4 33.7 1.0 OD1 A:ASP413 2.5 73.4 1.0 OD1 A:ASN417 2.5 59.0 1.0 OD2 A:ASP421 2.6 66.8 1.0 O A:PRO420 2.6 20.7 1.0 OD2 A:ASP415 2.7 53.8 1.0 OD1 A:ASP421 2.8 66.7 1.0 CG A:ASP421 3.0 56.6 1.0 OD1 A:ASP415 3.2 54.2 1.0 CG A:ASP415 3.2 59.6 1.0 CG A:ASN417 3.4 60.9 1.0 C A:TYR419 3.5 40.6 1.0 ND2 A:ASN417 3.5 61.8 1.0 CG A:ASP413 3.7 60.4 1.0 C A:PRO420 3.7 28.9 1.0 O A:ALA437 4.0 34.3 1.0 N A:ALA437 4.1 22.1 1.0 N A:PRO420 4.4 29.5 1.0 CB A:ASP421 4.4 42.6 1.0 CB A:ASP413 4.5 45.0 1.0 CA A:TYR419 4.5 50.4 1.0 CA A:PRO420 4.5 27.5 1.0 O A:ASN417 4.5 79.6 1.0 CB A:ALA437 4.6 17.1 1.0 OD2 A:ASP413 4.6 70.8 1.0 CB A:TYR419 4.6 55.9 1.0 CB A:ASP415 4.6 56.6 1.0 N A:TYR419 4.6 60.9 1.0 N A:ASP421 4.6 33.8 1.0 N A:ASP415 4.7 51.9 1.0 CA A:ALA437 4.7 19.2 1.0 CA A:ASP413 4.8 30.9 1.0 CA A:ASP421 4.8 32.9 1.0 CB A:ASN417 4.8 66.3 1.0 C A:ALA437 4.8 30.1 1.0 CA A:ARG436 4.9 28.5 1.0 C A:ARG436 4.9 27.5 1.0 CB A:ARG436 4.9 33.2 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Extracellular Segment of Integrin ALPHAVBETA3


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 the Extracellular Segment of Integrin ALPHAVBETA3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4008 b:72.5 occ:1.00 OE1 A:GLU636 2.1 58.4 1.0 OD1 A:ASP599 2.1 56.7 1.0 O A:VAL601 2.5 52.5 1.0 O A:GLY597 2.5 87.4 1.0 CG A:ASP599 2.8 64.8 1.0 CD A:GLU636 2.9 67.6 1.0 OE2 A:GLU636 3.0 65.7 1.0 OD2 A:ASP599 3.1 54.7 1.0 C A:VAL601 3.3 52.9 1.0 N A:VAL601 3.3 49.0 1.0 N A:GLY597 3.4 93.8 1.0 C A:CYS596 3.5 89.1 1.0 C A:GLY597 3.6 88.1 1.0 N A:ASN600 3.7 64.9 1.0 CA A:CYS596 3.8 82.5 1.0 CA A:VAL601 3.9 48.3 1.0 N A:ASP599 4.0 81.7 1.0 CB A:ASP599 4.0 67.9 1.0 CA A:GLY597 4.0 92.5 1.0 C A:ASN600 4.0 63.0 1.0 O A:CYS596 4.1 91.8 1.0 C A:ASP599 4.2 65.4 1.0 CA A:ASP599 4.3 72.8 1.0 CA A:ASN600 4.3 65.1 1.0 N A:CYS602 4.3 50.7 1.0 CG A:GLU636 4.3 74.5 1.0 O A:ASP595 4.5 57.5 1.0 CB A:CYS596 4.6 87.9 1.0 CA A:CYS602 4.7 42.9 1.0 N A:GLU598 4.7 85.9 1.0 O A:ASN600 5.0 59.5 1.0 CB A:GLU636 5.0 79.0 1.0 C A:GLU598 5.0 79.4 1.0 CB A:GLU598 5.0 82.5 1.0 N A:CYS596 5.0 70.8 1.0

J.P.Xiong, T.Stehle, B.Diefenbach, R.Zhang, R.Dunker, D.L.Scott, A.Joachimiak, S.L.Goodman, M.A.Arnaout. Crystal Structure of the Extracellular Segment of Integrin Alpha VBETA3. Science V. 294 339 2001.
ISSN: ISSN 0036-8075
PubMed: 11546839
DOI: 10.1126/SCIENCE.1064535