Calcium in PDB 3ije: Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment

The structure of Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment, PDB code: 3ije was solved by J.-P.Xiong, B.Mahalingham, X.Rui, B.T.Hyman, 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 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.870, 129.870, 305.900, 90.00, 90.00, 120.00
R / Rfree (%)	24.4 / 28.5

The binding sites of Calcium atom in the Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment (pdb code 3ije). 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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment, PDB code: 3ije:
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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment


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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4004 b:78.1 occ:1.00 OD1 A:ASN232 2.1 52.5 1.0 O A:ILE236 2.3 53.2 1.0 OD1 A:ASP238 2.5 50.8 1.0 OD2 A:ASP230 2.6 51.3 1.0 OD2 A:ASP238 3.0 51.7 1.0 CG A:ASP238 3.1 51.6 1.0 CG A:ASN232 3.2 53.0 1.0 C A:ILE236 3.4 53.3 1.0 N A:ILE236 3.4 53.6 1.0 CG A:ASP230 3.6 51.1 1.0 O A:ASP234 3.6 53.8 1.0 ND2 A:ASN232 3.7 53.5 1.0 O A:ASN232 3.9 53.2 1.0 CA A:ILE236 4.0 53.5 1.0 CG2 A:ILE236 4.0 53.5 1.0 C A:GLY235 4.1 53.6 1.0 OD1 A:ASP230 4.2 51.1 1.0 C A:ASP234 4.3 53.9 1.0 OD1 A:ASP257 4.3 52.0 1.0 N A:ASN232 4.4 52.7 1.0 CA A:GLY235 4.5 53.7 1.0 CB A:ASN232 4.5 53.0 1.0 CB A:ASP230 4.5 51.1 1.0 CB A:ASP238 4.6 51.8 1.0 CA A:ASP230 4.6 51.0 1.0 N A:ASP237 4.6 53.2 1.0 N A:PHE231 4.6 51.7 1.0 C A:ASN232 4.6 53.2 1.0 N A:ASP238 4.7 52.3 1.0 CB A:ILE236 4.7 53.6 1.0 N A:GLY235 4.7 53.7 1.0 CA A:ASN232 4.8 53.0 1.0 C A:ASP237 4.8 52.7 1.0 O A:GLY235 4.8 53.3 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment


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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4005 b:46.6 occ:1.00 OD1 A:ASN286 2.2 51.5 1.0 OD1 A:ASP288 2.4 51.5 1.0 O A:TYR290 2.4 49.7 1.0 OD2 A:ASP284 2.5 50.3 1.0 OD1 A:ASP292 2.5 47.9 1.0 OD2 A:ASP292 2.8 47.3 1.0 CG A:ASP292 3.0 48.2 1.0 CG A:ASP288 3.2 51.3 1.0 CG A:ASN286 3.2 51.2 1.0 C A:TYR290 3.4 49.7 1.0 OD2 A:ASP288 3.4 52.0 1.0 CB A:TYR290 3.6 49.8 1.0 CG A:ASP284 3.6 50.7 1.0 ND2 A:ASN286 3.7 51.4 1.0 CA A:TYR290 3.8 49.8 1.0 N A:TYR290 4.0 50.0 1.0 O A:GLN320 4.3 51.7 1.0 N A:ASN286 4.4 51.4 1.0 OD1 A:ASP284 4.4 50.4 1.0 CB A:ASP284 4.5 50.9 1.0 CA A:ASP284 4.5 50.9 1.0 CB A:ASP292 4.5 48.4 1.0 CB A:ASN286 4.6 51.4 1.0 N A:ALA291 4.6 49.3 1.0 CB A:ASP288 4.6 51.0 1.0 N A:ILE285 4.6 51.3 1.0 N A:GLN320 4.7 50.8 1.0 C A:ALA291 4.7 48.9 1.0 O A:ALA291 4.7 49.0 1.0 N A:ASP288 4.7 51.0 1.0 C A:ASP284 4.8 51.1 1.0 CG A:TYR290 4.9 49.9 1.0 CA A:ASN286 4.9 51.3 1.0 N A:ASP292 4.9 48.7 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment


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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4006 b:59.2 occ:1.00 OD1 A:ASP351 2.2 47.5 1.0 OD2 A:ASP353 2.3 48.0 1.0 O A:PHE355 2.4 47.4 1.0 OD2 A:ASP357 2.4 47.6 1.0 OD2 A:ASP349 2.6 48.2 1.0 OD1 A:ASP357 2.6 47.7 1.0 CG A:ASP357 2.9 47.8 1.0 CG A:ASP353 2.9 47.6 1.0 OD1 A:ASP353 3.2 48.5 1.0 CG A:ASP351 3.3 47.7 1.0 C A:PHE355 3.5 47.3 1.0 CG A:ASP349 3.7 48.4 1.0 ND2 A:ASN377 3.8 55.6 1.0 OD2 A:ASP351 3.8 48.7 1.0 N A:PHE355 4.2 47.3 1.0 CB A:ASP353 4.2 47.2 1.0 CA A:PHE355 4.2 47.3 1.0 O A:ASN356 4.2 47.4 1.0 N A:ASP353 4.3 47.2 1.0 C A:ASN356 4.3 47.5 1.0 OD1 A:ASP349 4.3 48.6 1.0 N A:ASP351 4.3 47.5 1.0 CB A:ASP357 4.4 47.7 1.0 CB A:PHE355 4.4 47.2 1.0 CA A:ASP349 4.4 47.9 1.0 N A:ASN356 4.5 47.3 1.0 N A:LEU350 4.5 47.9 1.0 O A:GLY378 4.5 55.0 1.0 CB A:ASP351 4.6 47.5 1.0 N A:GLY378 4.6 54.5 1.0 CB A:ASP349 4.6 47.9 1.0 N A:ASP357 4.7 47.6 1.0 CA A:ASN356 4.7 47.4 1.0 C A:ASP349 4.7 47.9 1.0 N A:GLN352 4.7 47.3 1.0 CA A:ASP353 4.7 47.3 1.0 CG A:ASN377 4.7 54.8 1.0 CB A:ASN377 4.8 54.3 1.0 CA A:ASP351 4.9 47.5 1.0 CA A:ASP357 5.0 47.7 1.0 N A:GLY354 5.0 47.3 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment


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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4007 b:34.5 occ:1.00 OD1 A:ASP415 2.3 48.6 1.0 O A:TYR419 2.3 47.1 1.0 OD1 A:ASP413 2.4 47.9 1.0 ND2 A:ASN417 2.4 49.2 1.0 OD2 A:ASP421 2.6 47.5 1.0 OD1 A:ASP421 2.9 47.7 1.0 CG A:ASP421 3.1 47.6 1.0 CG A:ASN417 3.3 48.9 1.0 O A:ASN417 3.3 48.9 1.0 CG A:ASP415 3.4 48.5 1.0 OD1 A:ASN417 3.4 49.0 1.0 CG A:ASP413 3.4 47.9 1.0 C A:TYR419 3.5 47.3 1.0 OD2 A:ASP415 3.8 48.6 1.0 CA A:ASP413 4.0 48.0 1.0 CB A:ASP413 4.1 48.0 1.0 N A:TYR419 4.1 47.7 1.0 CA A:TYR419 4.2 47.5 1.0 C A:ASN417 4.3 48.6 1.0 CB A:TYR419 4.3 47.5 1.0 N A:ASP415 4.3 48.2 1.0 OD2 A:ASP413 4.4 47.6 1.0 C A:ASP413 4.4 48.0 1.0 N A:ILE414 4.4 48.0 1.0 O A:ALA437 4.5 43.8 1.0 C A:PRO420 4.5 47.5 1.0 CB A:ASP421 4.5 47.5 1.0 N A:PRO420 4.6 47.3 1.0 CB A:ASN417 4.6 48.7 1.0 CB A:ASP415 4.7 48.2 1.0 N A:ALA437 4.7 44.4 1.0 N A:ASP421 4.7 47.6 1.0 O A:PRO420 4.7 47.7 1.0 CA A:PRO420 4.7 47.4 1.0 CA A:ASN417 4.8 48.7 1.0 N A:ASN417 4.8 48.8 1.0 C A:ASP415 4.8 48.5 1.0 O A:ASP415 4.8 48.7 1.0 CA A:ASP415 4.8 48.3 1.0 CB A:ALA437 5.0 43.9 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment


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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4008 b:32.4 occ:1.00 O A:VAL601 2.3 51.6 1.0 O A:CYS596 2.4 49.6 1.0 OD1 A:ASP599 2.5 50.5 1.0 OE1 A:GLU636 2.5 47.6 1.0 OE2 A:GLU636 2.9 47.7 1.0 OD2 A:ASP599 3.0 50.4 1.0 CD A:GLU636 3.1 47.6 1.0 CG A:ASP599 3.1 50.4 1.0 C A:CYS596 3.5 49.8 1.0 C A:VAL601 3.5 51.5 1.0 CE A:LYS603 3.6 53.0 1.0 CG1 A:VAL601 4.1 51.3 1.0 N A:VAL601 4.3 51.2 1.0 N A:GLY597 4.3 49.9 1.0 CA A:GLY597 4.4 50.0 1.0 CA A:CYS596 4.4 49.8 1.0 N A:LYS603 4.4 52.4 1.0 CA A:VAL601 4.4 51.3 1.0 N A:CYS602 4.5 51.7 1.0 CA A:CYS602 4.5 51.8 1.0 NZ A:LYS603 4.5 52.9 1.0 CG A:GLU636 4.5 47.6 1.0 CG A:LYS603 4.6 52.7 1.0 CB A:ASP599 4.6 50.4 1.0 OE2 A:GLU598 4.7 51.9 1.0 CD A:LYS603 4.7 52.7 1.0 CB A:LYS603 4.8 52.6 1.0 CB A:CYS596 4.8 49.9 1.0 CB A:VAL601 4.8 51.3 1.0 C A:GLY597 4.9 50.0 1.0 C A:CYS602 4.9 52.1 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of the Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment


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 Complete Integrin ALHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:55.7 occ:1.00 OD1 B:ASP127 2.3 52.4 1.0 O B:MET335 2.4 54.6 1.0 O B:SER123 2.4 49.4 1.0 OD2 B:ASP126 2.4 52.2 1.0 CG B:ASP126 3.2 51.6 1.0 OD1 B:ASP126 3.3 52.0 1.0 CG B:ASP127 3.5 52.0 1.0 C B:SER123 3.5 49.3 1.0 C B:MET335 3.6 54.8 1.0 OD2 B:ASP127 4.0 52.5 1.0 CA B:MET124 4.1 50.0 1.0 N B:MET124 4.2 49.7 1.0 N B:ASP127 4.4 51.5 1.0 N B:ASP336 4.5 54.7 1.0 CA B:MET335 4.5 55.0 1.0 CA B:ASP336 4.5 54.7 1.0 OD2 B:ASP251 4.5 46.5 1.0 CA B:SER123 4.6 49.0 1.0 CB B:ASP126 4.7 51.2 1.0 CB B:ASP127 4.7 51.6 1.0 C B:MET124 4.7 50.3 1.0 CB B:SER123 4.8 48.9 1.0 SD B:MET124 4.8 51.3 1.0 CB B:MET335 4.9 55.4 1.0 N B:ASP126 4.9 50.9 1.0

J.P.Xiong, B.Mahalingham, J.L.Alonso, L.A.Borrelli, X.Rui, S.Anand, B.T.Hyman, T.Rysiok, D.Muller-Pompalla, S.L.Goodman, M.A.Arnaout. Crystal Structure of the Complete Integrin ALPHAVBETA3 Ectodomain Plus An Alpha/Beta Transmembrane Fragment. J.Cell Biol. V. 186 589 2009.
ISSN: ISSN 0021-9525
PubMed: 19704023
DOI: 10.1083/JCB.200905085