Calcium in PDB 1u8c: A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure

The structure of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure, PDB code: 1u8c was solved by J.P.Xiong, T.Stehle, 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 (%)	29.3 / 36.7

The binding sites of Calcium atom in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure (pdb code 1u8c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure, PDB code: 1u8c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca4002 b:61.9 occ:1.00 O B:MET1335 2.3 68.3 1.0 OD1 B:ASP1126 2.5 54.2 1.0 OD1 B:ASP1127 2.6 50.7 1.0 O B:SER1123 2.7 51.0 1.0 OD2 B:ASP1126 3.2 55.6 1.0 C B:MET1335 3.2 68.3 1.0 CG B:ASP1126 3.2 54.7 1.0 CG B:ASP1127 3.5 51.3 1.0 CA B:MET1335 3.5 67.7 1.0 OD2 B:ASP1127 3.7 51.9 1.0 CB B:MET1335 3.7 70.0 1.0 C B:SER1123 3.8 51.4 1.0 CG B:MET1335 4.2 72.2 1.0 N B:ASP1336 4.4 68.4 1.0 CA B:MET1124 4.5 50.6 1.0 N B:MET1124 4.5 51.5 1.0 OD2 B:ASP1251 4.6 42.8 1.0 SD B:MET1124 4.6 44.3 1.0 CB B:ASP1126 4.7 52.9 1.0 CA B:SER1123 4.7 50.8 1.0 N B:ASP1127 4.8 53.8 1.0 CB B:SER1123 4.9 51.7 1.0 CB B:ASP1127 4.9 51.5 1.0 N B:MET1335 4.9 65.8 1.0

Calcium binding site 2 out of 6 in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4004 b:72.0 occ:1.00 OD1 A:ASN232 2.4 47.1 1.0 OD2 A:ASP230 2.5 39.8 1.0 O A:ILE236 2.6 49.0 1.0 OD1 A:ASP238 2.7 42.5 1.0 O A:ASP234 3.3 55.5 1.0 CG A:ASP238 3.5 42.6 1.0 CG A:ASP230 3.6 39.7 1.0 CG A:ASN232 3.6 46.7 1.0 N A:ILE236 3.6 51.7 1.0 OD2 A:ASP238 3.6 44.9 1.0 C A:ILE236 3.7 49.4 1.0 C A:GLY235 4.0 53.5 1.0 CA A:GLY235 4.1 55.2 1.0 C A:ASP234 4.1 57.2 1.0 OD1 A:ASP230 4.2 42.4 1.0 ND2 A:ASN232 4.2 46.5 1.0 CA A:ILE236 4.2 49.9 1.0 O A:ASN232 4.4 47.8 1.0 N A:GLY235 4.5 55.2 1.0 OD1 A:ASP257 4.6 49.2 1.0 CB A:ASP230 4.6 35.9 1.0 CG2 A:ILE236 4.7 47.4 1.0 CA A:ASP230 4.7 33.7 1.0 N A:ASN232 4.7 45.3 1.0 CB A:ASN232 4.7 46.5 1.0 N A:PHE231 4.7 35.6 1.0 O A:GLY235 4.8 52.2 1.0 N A:ASP237 4.8 48.5 1.0 C A:ASP237 4.9 45.0 1.0 N A:ASP238 4.9 43.0 1.0 CB A:ASP238 5.0 40.7 1.0

Calcium binding site 3 out of 6 in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4005 b:45.0 occ:1.00 OD2 A:ASP292 2.1 32.9 1.0 OD1 A:ASP288 2.2 54.5 1.0 O A:TYR290 2.6 47.2 1.0 OD1 A:ASN286 2.6 39.2 1.0 OD1 A:ASP284 2.8 40.5 1.0 CG A:ASP292 2.9 33.5 1.0 OD1 A:ASP292 2.9 34.1 1.0 CG A:ASP288 3.1 53.6 1.0 OD2 A:ASP288 3.3 53.4 1.0 CG A:ASN286 3.5 40.7 1.0 C A:TYR290 3.6 47.2 1.0 ND2 A:ASN286 3.6 40.3 1.0 CB A:TYR290 3.7 51.6 1.0 O A:GLN320 3.9 54.2 1.0 CG A:ASP284 4.0 41.6 1.0 CA A:TYR290 4.1 49.6 1.0 O A:ALA291 4.1 37.4 1.0 N A:TYR290 4.3 51.7 1.0 CB A:ASP292 4.3 33.5 1.0 C A:ALA291 4.4 38.2 1.0 CB A:ASP288 4.5 52.6 1.0 N A:GLN320 4.6 48.7 1.0 N A:ALA291 4.6 44.3 1.0 OD2 A:ASP284 4.6 43.1 1.0 CG A:LEU319 4.7 43.7 1.0 N A:ASN286 4.8 44.2 1.0 N A:ASP292 4.8 36.4 1.0 CB A:ASN286 4.8 42.4 1.0 C A:GLN320 4.9 53.9 1.0 N A:ASP288 4.9 49.5 1.0 CA A:ASP292 4.9 33.7 1.0 CB A:ASP284 4.9 40.4 1.0 CA A:ALA291 5.0 40.5 1.0 N A:ILE285 5.0 41.0 1.0

Calcium binding site 4 out of 6 in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4006 b:68.0 occ:1.00 OD2 A:ASP353 2.0 50.9 1.0 O A:PHE355 2.2 39.7 1.0 OD1 A:ASP357 2.2 43.3 1.0 OD2 A:ASP349 2.6 50.0 1.0 OD2 A:ASP357 2.6 43.8 1.0 OD1 A:ASP351 2.7 48.3 1.0 CG A:ASP357 2.7 41.8 1.0 CG A:ASP353 3.1 50.0 1.0 C A:PHE355 3.2 39.0 1.0 OD1 A:ASP353 3.6 51.7 1.0 CG A:ASP349 3.7 50.5 1.0 CG A:ASP351 3.7 49.7 1.0 C A:ASN356 3.9 39.2 1.0 OD2 A:ASP351 4.0 51.5 1.0 O A:ASN356 4.0 40.5 1.0 CA A:PHE355 4.1 38.9 1.0 N A:ASN356 4.1 39.6 1.0 CB A:ASP357 4.1 39.8 1.0 N A:ASP357 4.2 38.9 1.0 CA A:ASP349 4.2 47.0 1.0 CB A:PHE355 4.2 37.4 1.0 CA A:ASN356 4.2 40.2 1.0 N A:PHE355 4.2 39.1 1.0 N A:GLY378 4.2 43.1 1.0 O A:GLY378 4.3 49.3 1.0 OD1 A:ASN377 4.3 41.3 1.0 CB A:ASP353 4.3 47.7 1.0 OD1 A:ASP349 4.4 52.3 1.0 N A:LEU350 4.5 45.4 1.0 CB A:ASP349 4.5 48.6 1.0 CA A:ASP357 4.6 38.7 1.0 C A:ASP349 4.6 46.6 1.0 N A:ASP353 4.6 46.9 1.0 N A:ASP351 4.6 45.4 1.0 CB A:ASN377 4.7 39.0 1.0 CA A:ASN377 4.8 40.0 1.0 CG A:ASN377 4.9 40.3 1.0

Calcium binding site 5 out of 6 in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4007 b:34.6 occ:1.00 O A:TYR419 2.2 32.2 1.0 O A:PRO420 2.5 28.1 1.0 OD2 A:ASP421 2.6 38.6 1.0 OD1 A:ASP413 2.6 38.7 1.0 OD2 A:ASP415 2.6 53.3 1.0 OD1 A:ASN417 2.7 52.0 1.0 OD1 A:ASP421 2.8 39.0 1.0 CG A:ASP421 3.0 37.2 1.0 C A:TYR419 3.3 34.3 1.0 CG A:ASN417 3.4 53.2 1.0 CG A:ASP415 3.4 53.4 1.0 ND2 A:ASN417 3.5 52.6 1.0 CG A:ASP413 3.5 39.1 1.0 C A:PRO420 3.5 28.5 1.0 OD1 A:ASP415 3.7 53.7 1.0 O A:ASN417 3.7 50.3 1.0 CB A:ASP413 3.9 36.9 1.0 CA A:ASP413 4.0 35.1 1.0 N A:PRO420 4.2 31.3 1.0 CA A:PRO420 4.3 29.7 1.0 CA A:TYR419 4.3 38.6 1.0 CB A:ASP421 4.3 32.0 1.0 C A:ASP413 4.4 34.4 1.0 N A:TYR419 4.4 42.2 1.0 OD2 A:ASP413 4.5 40.4 1.0 N A:ASP421 4.5 29.0 1.0 N A:ASP415 4.6 44.3 1.0 CB A:TYR419 4.6 43.1 1.0 N A:ILE414 4.7 35.2 1.0 N A:ALA437 4.7 32.5 1.0 CB A:ASP415 4.7 50.4 1.0 C A:ASN417 4.7 49.6 1.0 CA A:ASP421 4.8 29.4 1.0 O A:ALA437 4.8 34.0 1.0 CB A:ASN417 4.8 53.8 1.0 CB A:ALA437 4.9 32.7 1.0 O A:ASP413 4.9 32.4 1.0

Calcium binding site 6 out of 6 in the A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca4008 b:66.2 occ:1.00 O A:VAL601 2.3 62.5 1.0 OE1 A:GLU636 2.4 65.5 1.0 OE2 A:GLU636 2.6 66.2 1.0 O A:CYS596 2.7 67.0 1.0 CD A:GLU636 2.8 64.4 1.0 OD2 A:ASP599 2.9 76.0 1.0 C A:CYS596 2.9 66.6 1.0 CA A:GLY597 3.0 71.9 1.0 N A:GLY597 3.1 69.4 1.0 C A:VAL601 3.6 63.5 1.0 OD1 A:ASP599 3.7 75.9 1.0 CG A:ASP599 3.7 75.5 1.0 CA A:CYS596 4.0 63.4 1.0 N A:VAL601 4.2 66.4 1.0 C A:GLY597 4.2 73.5 1.0 CG1 A:VAL601 4.3 63.8 1.0 N A:GLU598 4.3 74.7 1.0 CG A:GLU636 4.4 61.9 1.0 CB A:CYS596 4.5 63.7 1.0 CA A:VAL601 4.5 64.5 1.0 N A:CYS602 4.5 62.0 1.0 OE2 A:GLU598 4.5 85.2 1.0 CA A:CYS602 4.5 60.9 1.0 CD A:LYS603 4.7 67.6 1.0 CG A:LYS603 4.8 65.8 1.0 N A:ASP599 4.9 75.8 1.0 N A:LYS603 4.9 60.2 1.0 N A:ASN600 5.0 71.8 1.0

J.P.Xiong, T.Stehle, S.L.Goodman, M.A.Arnaout. A Novel Adaptation of the Integrin Psi Domain Revealed From Its Crystal Structure. J.Biol.Chem. V. 279 40252 2004.
ISSN: ISSN 0021-9258
PubMed: 15299032
DOI: 10.1074/JBC.C400362200