Calcium in PDB 3k72: Structure of Integrin Alphax BETA2

The structure of Structure of Integrin Alphax BETA2, PDB code: 3k72 was solved by C.Xie, J.Zhu, X.Chen, L.Mi, N.Nishida, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.48 / 3.70
Space group	I 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	160.962, 165.549, 536.178, 90.00, 90.00, 90.00
R / Rfree (%)	31.5 / 33.5

The binding sites of Calcium atom in the Structure of Integrin Alphax BETA2 (pdb code 3k72). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structure of Integrin Alphax BETA2, PDB code: 3k72:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:0.4 occ:1.00 O A:SER453 2.6 0.5 1.0 CG A:ASP455 2.8 0.0 1.0 OD1 A:ASP447 2.8 0.7 1.0 CG A:ASP447 2.9 0.8 1.0 OD1 A:ASP449 2.9 0.5 1.0 OD2 A:ASP455 2.9 0.1 1.0 CB A:ASP455 3.1 0.6 1.0 OD1 A:ASP451 3.1 0.3 1.0 OD1 A:ASP455 3.2 0.0 1.0 OD2 A:ASP447 3.2 0.3 1.0 N A:ASP455 3.3 0.5 1.0 CA A:ASP447 3.4 0.7 1.0 CB A:ASP447 3.6 0.2 1.0 C A:ASP447 3.7 0.1 1.0 N A:VAL448 3.7 0.9 1.0 C A:SER453 3.7 0.3 1.0 CA A:ASP455 3.7 0.4 1.0 CG A:ASP449 3.9 0.2 1.0 C A:THR454 4.0 0.3 1.0 CG A:ASP451 4.1 0.2 1.0 N A:ASP449 4.2 0.8 1.0 CA A:THR454 4.2 0.3 1.0 CG1 A:VAL448 4.2 0.9 1.0 OD2 A:ASP449 4.4 0.6 1.0 OD2 A:ASP451 4.4 0.6 1.0 N A:THR454 4.4 0.5 1.0 O A:ASP447 4.5 0.6 1.0 O A:VAL446 4.6 0.8 1.0 N A:ASP447 4.7 0.8 1.0 N A:SER453 4.8 0.5 1.0 CA A:VAL448 4.8 0.6 1.0 CA A:SER453 4.8 0.7 1.0 O A:THR454 4.9 0.6 1.0 CA A:ASP449 4.9 0.9 1.0 C A:ASP449 5.0 0.6 1.0

Calcium binding site 2 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:0.4 occ:1.00 O A:LEU517 2.6 0.3 1.0 OD1 A:ASN513 3.0 0.8 1.0 OD1 A:ASP515 3.1 0.1 1.0 C A:LEU517 3.2 0.3 1.0 CA A:ASP511 3.3 0.5 1.0 CG A:ASP511 3.4 0.7 1.0 N A:VAL512 3.5 0.3 1.0 OD2 A:ASP511 3.5 0.2 1.0 N A:LEU517 3.5 1.0 1.0 OD2 A:ASP519 3.7 0.3 1.0 CB A:ASP511 3.7 1.0 1.0 C A:ASP511 3.8 0.3 1.0 N A:GLY514 3.8 0.3 1.0 N A:THR518 3.8 0.1 1.0 OD1 A:ASP511 3.9 0.7 1.0 CA A:LEU517 3.9 0.9 1.0 CG A:ASN513 3.9 0.9 1.0 N A:ASN513 3.9 0.6 1.0 CG A:ASP519 4.0 0.1 1.0 OD1 A:ASP519 4.0 0.1 1.0 N A:ASP515 4.0 0.1 1.0 O A:GLY510 4.1 0.8 1.0 CA A:THR518 4.1 0.5 1.0 CG A:ASP515 4.2 0.7 1.0 N A:LYS516 4.3 0.3 1.0 N A:ASP511 4.3 0.0 1.0 C A:THR518 4.4 0.6 1.0 C A:LYS516 4.5 0.9 1.0 C A:ASN513 4.5 0.4 1.0 CB A:LEU517 4.5 0.6 1.0 ND2 A:ASN513 4.5 0.9 1.0 CA A:GLY514 4.6 0.6 1.0 CA A:ASN513 4.6 0.9 1.0 N A:ASP519 4.6 0.8 1.0 C A:GLY510 4.6 0.9 1.0 C A:ASP515 4.7 0.6 1.0 CA A:VAL512 4.7 0.9 1.0 C A:GLY514 4.7 0.1 1.0 C A:VAL512 4.7 0.3 1.0 CA A:ASP515 4.8 0.7 1.0 CA A:LYS516 4.8 0.9 1.0 CG2 A:VAL512 4.9 0.3 1.0 CB A:ASN513 4.9 0.7 1.0 O A:ASP511 4.9 0.8 1.0 OD2 A:ASP515 5.0 0.9 1.0

Calcium binding site 3 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:0.6 occ:1.00 O A:LEU580 2.5 0.1 1.0 OD1 A:ASP578 2.5 0.3 1.0 OD2 A:ASP582 2.7 0.8 1.0 O A:ASP578 2.7 0.6 1.0 OD1 A:ASP582 2.8 0.8 1.0 OD1 A:ASP574 2.9 0.1 1.0 CG A:ASP582 3.0 0.1 1.0 OG1 A:THR576 3.2 0.9 1.0 CG A:ASP574 3.7 0.7 1.0 C A:LEU580 3.7 0.4 1.0 CG A:ASP578 3.7 0.8 1.0 C A:ASP578 3.8 0.0 1.0 CA A:ASP574 3.9 0.9 1.0 N A:THR576 3.9 0.6 1.0 CB A:ASP574 4.0 0.4 1.0 O A:VAL581 4.0 0.8 1.0 N A:LEU575 4.0 0.2 1.0 N A:GLN577 4.0 0.4 1.0 C A:VAL581 4.1 0.8 1.0 CB A:ASP582 4.2 0.9 1.0 CB A:THR576 4.3 0.9 1.0 N A:ASP578 4.3 0.7 1.0 C A:ASP574 4.3 0.7 1.0 N A:LEU580 4.3 0.1 1.0 C A:GLY579 4.4 0.5 1.0 O A:GLY579 4.4 0.2 1.0 OD2 A:ASP578 4.4 0.7 1.0 N A:ASP582 4.4 0.4 1.0 CA A:THR576 4.5 0.8 1.0 CA A:ASP578 4.5 1.0 1.0 C A:THR576 4.5 0.3 1.0 CA A:VAL581 4.6 0.0 1.0 N A:VAL581 4.6 0.0 1.0 CG2 A:THR576 4.6 0.0 1.0 CA A:LEU580 4.6 0.7 1.0 OD2 A:ASP574 4.7 0.9 1.0 CB A:ASP578 4.7 0.3 1.0 CA A:ASP582 4.8 0.0 1.0 N A:GLY579 4.8 0.6 1.0 CA A:GLN577 4.9 0.9 1.0 C A:LEU575 4.9 0.9 1.0 C A:GLN577 4.9 0.6 1.0

Calcium binding site 4 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:0.3 occ:1.01 OD1 B:ASP120 2.1 0.9 1.0 OD1 B:ASP119 2.3 0.9 1.0 OE2 B:GLU325 2.3 0.4 1.0 O B:SER116 2.5 0.1 1.0 O B:GLU325 2.7 0.6 1.0 CG B:ASP120 2.8 0.9 1.0 CD B:GLU325 3.2 0.2 1.0 OD2 B:ASP120 3.2 0.9 1.0 CG B:ASP119 3.4 0.9 1.0 CG B:GLU325 3.5 0.9 1.0 C B:SER116 3.7 0.6 1.0 CA B:MET117 3.8 0.5 1.0 CB B:ASP120 3.9 0.5 1.0 N B:ASP120 3.9 0.4 1.0 OD2 B:ASP119 3.9 0.7 1.0 C B:GLU325 3.9 0.1 1.0 OD2 B:ASP242 4.2 0.1 1.0 N B:MET117 4.2 0.6 1.0 N B:LEU118 4.3 0.0 1.0 OE1 B:GLU325 4.3 0.3 1.0 C B:MET117 4.3 0.5 1.0 CA B:ASP120 4.4 0.5 1.0 N B:ASP119 4.4 0.9 1.0 C B:ASP119 4.6 0.9 1.0 CB B:GLU325 4.6 0.7 1.0 CA B:GLU325 4.7 0.7 1.0 CB B:ASP119 4.7 0.9 1.0 SD B:MET117 4.7 0.9 1.0 CA B:ASP119 4.8 0.1 1.0 N B:ASP326 4.9 0.1 1.0 CA B:SER116 4.9 0.2 1.0 CB B:MET117 5.0 0.9 1.0

Calcium binding site 5 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2005 b:0.4 occ:1.00 O C:SER453 2.6 0.3 1.0 OD1 C:ASP447 2.8 0.4 1.0 CG C:ASP455 2.8 0.2 1.0 OD1 C:ASP449 2.9 1.0 1.0 CG C:ASP447 2.9 0.7 1.0 OD2 C:ASP455 2.9 0.3 1.0 CB C:ASP455 3.1 0.7 1.0 OD1 C:ASP451 3.1 0.3 1.0 OD1 C:ASP455 3.2 0.3 1.0 OD2 C:ASP447 3.2 0.9 1.0 CA C:ASP447 3.4 0.3 1.0 N C:ASP455 3.4 0.3 1.0 CB C:ASP447 3.6 0.9 1.0 C C:ASP447 3.7 0.4 1.0 N C:VAL448 3.7 0.4 1.0 CA C:ASP455 3.8 0.6 1.0 C C:SER453 3.8 0.3 1.0 CG C:ASP449 3.9 0.9 1.0 C C:THR454 4.0 0.3 1.0 CG C:ASP451 4.1 0.3 1.0 N C:ASP449 4.2 0.6 1.0 CG1 C:VAL448 4.2 0.0 1.0 CA C:THR454 4.2 0.2 1.0 OD2 C:ASP449 4.3 0.6 1.0 OD2 C:ASP451 4.3 0.1 1.0 N C:THR454 4.5 0.9 1.0 O C:ASP447 4.5 0.8 1.0 O C:VAL446 4.6 0.9 1.0 N C:ASP447 4.7 0.7 1.0 N C:SER453 4.8 0.3 1.0 CA C:VAL448 4.8 0.8 1.0 CA C:SER453 4.8 0.7 1.0 CA C:ASP449 4.9 0.5 1.0 O C:THR454 5.0 0.1 1.0 C C:ASP449 5.0 0.5 1.0

Calcium binding site 6 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2006 b:0.2 occ:1.00 O C:LEU517 2.6 1.0 1.0 OD1 C:ASN513 3.1 1.0 1.0 OD1 C:ASP515 3.1 0.5 1.0 C C:LEU517 3.1 0.4 1.0 CA C:ASP511 3.3 0.9 1.0 CG C:ASP511 3.4 0.5 1.0 OD2 C:ASP511 3.4 0.5 1.0 N C:LEU517 3.4 0.8 1.0 N C:VAL512 3.6 0.1 1.0 CB C:ASP511 3.6 0.2 1.0 OD2 C:ASP519 3.8 0.6 1.0 N C:GLY514 3.8 0.3 1.0 CA C:LEU517 3.8 1.0 1.0 N C:THR518 3.8 0.4 1.0 OD1 C:ASP511 3.8 0.8 1.0 C C:ASP511 3.9 0.6 1.0 N C:ASP515 3.9 0.0 1.0 CG C:ASN513 4.0 0.7 1.0 N C:ASN513 4.0 0.3 1.0 CA C:THR518 4.1 0.3 1.0 OD1 C:ASP519 4.1 0.0 1.0 CG C:ASP519 4.1 1.0 1.0 N C:LYS516 4.1 0.9 1.0 O C:GLY510 4.2 0.6 1.0 CG C:ASP515 4.2 0.1 1.0 C C:LYS516 4.3 0.8 1.0 N C:ASP511 4.4 0.3 1.0 C C:THR518 4.5 0.3 1.0 CB C:LEU517 4.5 0.1 1.0 CA C:GLY514 4.5 0.3 1.0 C C:ASP515 4.5 0.7 1.0 C C:ASN513 4.5 0.6 1.0 ND2 C:ASN513 4.6 0.5 1.0 C C:GLY514 4.6 0.9 1.0 CA C:ASN513 4.7 0.7 1.0 C C:GLY510 4.7 0.1 1.0 CA C:LYS516 4.7 0.3 1.0 CA C:ASP515 4.7 0.3 1.0 N C:ASP519 4.7 0.8 1.0 CA C:VAL512 4.8 0.8 1.0 C C:VAL512 4.8 0.3 1.0 CB C:ASN513 4.9 0.6 1.0 OD2 C:ASP515 5.0 0.3 1.0 O C:ASP511 5.0 0.7 1.0 CG2 C:VAL512 5.0 1.0 1.0

Calcium binding site 7 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2007 b:0.5 occ:1.00 OD1 C:ASP578 2.5 0.6 1.0 O C:LEU580 2.5 0.6 1.0 OD2 C:ASP582 2.7 0.3 1.0 O C:ASP578 2.7 0.1 1.0 OD1 C:ASP582 2.8 0.7 1.0 OD1 C:ASP574 2.9 0.7 1.0 CG C:ASP582 3.0 0.5 1.0 OG1 C:THR576 3.1 0.4 1.0 CG C:ASP578 3.7 0.5 1.0 CG C:ASP574 3.7 0.7 1.0 C C:LEU580 3.7 0.0 1.0 C C:ASP578 3.8 0.3 1.0 CA C:ASP574 3.9 0.1 1.0 N C:THR576 3.9 0.2 1.0 N C:LEU575 4.0 0.4 1.0 CB C:ASP574 4.0 0.6 1.0 O C:VAL581 4.0 0.3 1.0 N C:GLN577 4.0 0.1 1.0 C C:VAL581 4.1 0.8 1.0 CB C:THR576 4.2 0.8 1.0 CB C:ASP582 4.3 0.1 1.0 N C:ASP578 4.3 0.8 1.0 C C:ASP574 4.3 0.1 1.0 N C:LEU580 4.4 0.2 1.0 OD2 C:ASP578 4.4 0.7 1.0 CA C:THR576 4.4 0.7 1.0 C C:GLY579 4.4 0.6 1.0 O C:GLY579 4.4 0.2 1.0 N C:ASP582 4.5 0.9 1.0 C C:THR576 4.5 0.5 1.0 CA C:ASP578 4.5 0.4 1.0 CG2 C:THR576 4.6 0.9 1.0 CA C:VAL581 4.6 0.5 1.0 N C:VAL581 4.6 0.3 1.0 CA C:LEU580 4.7 0.4 1.0 OD2 C:ASP574 4.7 0.9 1.0 CB C:ASP578 4.7 0.7 1.0 CA C:ASP582 4.8 0.9 1.0 N C:GLY579 4.8 0.5 1.0 CA C:GLN577 4.8 0.4 1.0 C C:LEU575 4.9 0.9 1.0 C C:GLN577 4.9 0.3 1.0

Calcium binding site 8 out of 8 in the Structure of Integrin Alphax BETA2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of Integrin Alphax BETA2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2002 b:0.8 occ:1.01 OD1 D:ASP120 2.1 0.4 1.0 OE2 D:GLU325 2.3 0.5 1.0 OD1 D:ASP119 2.4 0.9 1.0 O D:SER116 2.5 0.1 1.0 O D:GLU325 2.7 0.4 1.0 CG D:ASP120 2.8 0.9 1.0 CD D:GLU325 3.2 0.5 1.0 OD2 D:ASP120 3.2 0.6 1.0 CG D:ASP119 3.5 0.4 1.0 CG D:GLU325 3.5 0.6 1.0 C D:SER116 3.6 0.6 1.0 CA D:MET117 3.8 1.0 1.0 CB D:ASP120 3.8 0.1 1.0 N D:ASP120 3.9 0.5 1.0 C D:GLU325 3.9 0.9 1.0 OD2 D:ASP119 3.9 0.2 1.0 OD2 D:ASP242 4.1 0.8 1.0 N D:MET117 4.2 0.9 1.0 N D:LEU118 4.3 0.5 1.0 OE1 D:GLU325 4.3 0.9 1.0 C D:MET117 4.3 0.0 1.0 CA D:ASP120 4.4 0.1 1.0 N D:ASP119 4.4 0.3 1.0 CB D:GLU325 4.6 0.6 1.0 C D:ASP119 4.6 0.8 1.0 CA D:GLU325 4.7 0.3 1.0 SD D:MET117 4.7 0.2 1.0 CB D:ASP119 4.7 0.8 1.0 CA D:ASP119 4.8 0.5 1.0 CA D:SER116 4.9 0.7 1.0 N D:ASP326 4.9 0.9 1.0 CB D:MET117 4.9 0.3 1.0

C.Xie, J.Zhu, X.Chen, L.Mi, N.Nishida, T.A.Springer. Structure of An Integrin with An Alphai Domain, Complement Receptor Type 4. Embo J. V. 29 666 2010.
ISSN: ISSN 0261-4189
PubMed: 20033057
DOI: 10.1038/EMBOJ.2009.367