Calcium in PDB 3k6s: Structure of Integrin ALPHAXBETA2 Ectodomain

The structure of Structure of Integrin ALPHAXBETA2 Ectodomain, PDB code: 3k6s 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)	48.61 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	132.095, 163.561, 536.911, 90.00, 90.00, 90.00
R / Rfree (%)	29.7 / 33.5

The structure of Structure of Integrin ALPHAXBETA2 Ectodomain also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure of Integrin ALPHAXBETA2 Ectodomain (pdb code 3k6s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure of Integrin ALPHAXBETA2 Ectodomain, PDB code: 3k6s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2005 b:0.5 occ:1.00 O A:SER453 2.9 0.3 1.0 CG A:ASP447 2.9 0.3 1.0 OD1 A:ASP447 2.9 0.2 1.0 CG A:ASP455 2.9 0.8 1.0 OD1 A:ASP451 3.0 87.3 1.0 N A:ASP455 3.1 0.7 1.0 OD2 A:ASP447 3.1 47.2 1.0 OD1 A:ASP449 3.1 0.1 1.0 OD1 A:ASP455 3.2 0.5 1.0 OD2 A:ASP455 3.2 0.2 1.0 CB A:ASP455 3.3 63.8 1.0 C A:SER453 3.4 77.6 1.0 CA A:ASP447 3.5 65.1 1.0 CB A:ASP447 3.6 0.7 1.0 C A:THR454 3.7 63.6 1.0 CA A:ASP455 3.8 0.4 1.0 CA A:THR454 3.8 0.9 1.0 N A:THR454 3.8 0.7 1.0 C A:ASP447 4.0 0.6 1.0 CG A:ASP451 4.0 65.2 1.0 N A:SER453 4.2 0.8 1.0 N A:VAL448 4.2 0.5 1.0 CG A:ASP449 4.2 55.1 1.0 CA A:SER453 4.3 97.5 1.0 OD2 A:ASP451 4.4 90.9 1.0 O A:VAL446 4.5 50.1 1.0 N A:ASP449 4.6 0.8 1.0 OD2 A:ASP449 4.6 0.5 1.0 O A:THR454 4.6 75.6 1.0 N A:ASP447 4.7 0.6 1.0 O A:ASP447 4.8 0.6 1.0 CG1 A:VAL448 4.8 0.9 1.0 N A:GLY452 4.9 84.3 1.0 N A:ASP451 5.0 35.4 1.0 C A:GLY452 5.0 0.3 1.0

Calcium binding site 2 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2006 b:0.8 occ:1.00 O A:LEU517 2.8 0.7 1.0 OD1 A:ASN513 3.0 80.0 1.0 OD1 A:ASP515 3.1 1.0 1.0 CG A:ASP511 3.2 0.4 1.0 OD2 A:ASP511 3.2 0.5 1.0 CA A:ASP511 3.3 66.3 1.0 C A:LEU517 3.4 0.5 1.0 N A:LEU517 3.5 1.0 1.0 OD1 A:ASP511 3.5 0.2 1.0 N A:GLY514 3.5 0.3 1.0 CB A:ASP511 3.6 0.5 1.0 N A:VAL512 3.6 32.3 1.0 OD2 A:ASP519 3.7 0.4 1.0 N A:ASP515 3.7 51.2 1.0 C A:ASP511 3.8 0.4 1.0 N A:ASN513 3.9 47.4 1.0 CA A:LEU517 4.0 20.9 1.0 CG A:ASN513 4.0 0.0 1.0 N A:LYS516 4.1 0.1 1.0 N A:THR518 4.1 0.6 1.0 CA A:GLY514 4.1 63.9 1.0 CG A:ASP515 4.2 43.1 1.0 CG A:ASP519 4.3 0.8 1.0 C A:ASN513 4.3 25.4 1.0 C A:GLY514 4.3 0.8 1.0 C A:LYS516 4.4 0.6 1.0 OD1 A:ASP519 4.4 0.9 1.0 CA A:THR518 4.4 0.4 1.0 O A:GLY510 4.4 77.7 1.0 C A:ASP515 4.5 51.9 1.0 N A:ASP511 4.5 0.6 1.0 CA A:ASN513 4.5 0.7 1.0 CA A:ASP515 4.6 0.6 1.0 CB A:LEU517 4.6 0.7 1.0 CA A:LYS516 4.7 59.2 1.0 ND2 A:ASN513 4.7 0.3 1.0 C A:VAL512 4.7 0.6 1.0 CA A:VAL512 4.7 0.1 1.0 C A:THR518 4.8 0.7 1.0 CB A:ASN513 4.9 0.7 1.0 C A:GLY510 4.9 0.3 1.0 O A:ASP511 4.9 0.2 1.0

Calcium binding site 3 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2007 b:0.3 occ:1.00 O A:ASP578 2.6 0.0 1.0 OG1 A:THR576 2.7 0.9 1.0 O A:LEU580 2.7 0.0 1.0 OD2 A:ASP582 2.8 91.9 1.0 OD1 A:ASP582 2.8 0.9 1.0 OD1 A:ASP574 3.0 0.9 1.0 OD2 A:ASP578 3.0 0.8 1.0 CG A:ASP582 3.1 0.7 1.0 CG A:ASP578 3.4 0.7 1.0 C A:ASP578 3.7 0.3 1.0 OD1 A:ASP578 3.7 0.4 1.0 N A:ASP578 3.7 0.4 1.0 CB A:THR576 3.9 0.8 1.0 N A:GLN577 3.9 0.0 1.0 C A:LEU580 3.9 0.1 1.0 N A:THR576 3.9 0.8 1.0 CG A:ASP574 4.0 0.1 1.0 CA A:ASP578 4.1 0.4 1.0 CB A:ASP578 4.2 0.1 1.0 CA A:THR576 4.2 0.7 1.0 C A:THR576 4.3 40.3 1.0 CG2 A:THR576 4.3 0.1 1.0 O A:VAL581 4.3 46.5 1.0 N A:LEU580 4.4 92.9 1.0 N A:LEU575 4.4 72.9 1.0 CA A:ASP574 4.4 51.2 1.0 C A:VAL581 4.5 0.6 1.0 CB A:ASP574 4.5 0.2 1.0 CB A:ASP582 4.5 87.7 1.0 C A:GLN577 4.6 0.2 1.0 C A:GLY579 4.7 0.3 1.0 CA A:GLN577 4.7 0.2 1.0 CD A:ARG595 4.7 0.4 1.0 C A:ASP574 4.7 0.5 1.0 CA A:LEU580 4.7 0.5 1.0 N A:ASP582 4.8 0.6 1.0 N A:GLY579 4.8 75.4 1.0 O A:GLY579 4.9 0.7 1.0 N A:VAL581 4.9 60.1 1.0 CG A:ARG595 5.0 0.6 1.0 OD2 A:ASP574 5.0 0.5 1.0

Calcium binding site 4 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:0.8 occ:1.01 OD1 B:ASP120 2.1 0.8 1.0 OE2 B:GLU325 2.3 0.3 1.0 OD1 B:ASP119 2.4 0.5 1.0 O B:SER116 2.4 0.4 1.0 O B:GLU325 2.7 0.9 1.0 CG B:ASP120 3.0 0.5 1.0 CD B:GLU325 3.2 0.1 1.0 CG B:GLU325 3.4 0.3 1.0 CG B:ASP119 3.5 0.5 1.0 OD2 B:ASP120 3.5 0.6 1.0 C B:SER116 3.6 0.6 1.0 OD2 B:ASP119 3.9 0.2 1.0 CA B:MET117 3.9 0.6 1.0 C B:GLU325 3.9 0.6 1.0 N B:ASP120 4.0 0.5 1.0 CB B:ASP120 4.0 0.9 1.0 OD2 B:ASP242 4.1 0.0 1.0 N B:MET117 4.2 0.8 1.0 OE1 B:GLU325 4.3 0.7 1.0 N B:LEU118 4.3 0.8 1.0 C B:MET117 4.4 0.4 1.0 N B:ASP119 4.5 1.0 1.0 CA B:ASP120 4.5 0.3 1.0 CB B:GLU325 4.6 0.5 1.0 CA B:GLU325 4.7 0.6 1.0 C B:ASP119 4.7 0.7 1.0 SD B:MET117 4.7 0.1 1.0 CB B:ASP119 4.7 92.9 1.0 CA B:SER116 4.8 0.8 1.0 CA B:ASP119 4.9 0.4 1.0 N B:ASP326 4.9 0.0 1.0

Calcium binding site 5 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2005 b:0.5 occ:1.00 O C:SER453 2.8 0.9 1.0 CG C:ASP447 2.9 0.9 1.0 OD1 C:ASP447 2.9 0.5 1.0 CG C:ASP455 2.9 0.3 1.0 OD1 C:ASP451 3.0 0.3 1.0 N C:ASP455 3.1 0.1 1.0 OD1 C:ASP455 3.1 0.4 1.0 OD1 C:ASP449 3.1 0.6 1.0 OD2 C:ASP447 3.2 0.1 1.0 OD2 C:ASP455 3.2 0.5 1.0 CB C:ASP455 3.3 0.6 1.0 C C:SER453 3.4 0.5 1.0 CA C:ASP447 3.5 0.6 1.0 CB C:ASP447 3.6 0.3 1.0 C C:THR454 3.7 0.6 1.0 CA C:ASP455 3.7 0.3 1.0 CA C:THR454 3.8 0.4 1.0 N C:THR454 3.8 0.2 1.0 C C:ASP447 4.0 0.6 1.0 CG C:ASP451 4.0 0.2 1.0 N C:SER453 4.2 0.1 1.0 N C:VAL448 4.2 0.7 1.0 CG C:ASP449 4.2 0.6 1.0 CA C:SER453 4.3 0.0 1.0 OD2 C:ASP451 4.4 0.7 1.0 O C:VAL446 4.6 84.1 1.0 N C:ASP449 4.6 0.4 1.0 OD2 C:ASP449 4.6 0.2 1.0 O C:THR454 4.6 0.1 1.0 N C:ASP447 4.7 0.9 1.0 O C:ASP447 4.8 0.2 1.0 CG1 C:VAL448 4.8 0.2 1.0 N C:GLY452 4.9 0.1 1.0 N C:ASP451 5.0 0.1 1.0

Calcium binding site 6 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2006 b:0.5 occ:1.00 O C:LEU517 2.8 0.1 1.0 OD1 C:ASN513 3.0 0.0 1.0 OD1 C:ASP515 3.1 0.6 1.0 CG C:ASP511 3.2 0.7 1.0 OD2 C:ASP511 3.2 91.5 1.0 CA C:ASP511 3.3 66.2 1.0 C C:LEU517 3.4 0.6 1.0 N C:LEU517 3.5 0.5 1.0 N C:GLY514 3.5 0.9 1.0 OD1 C:ASP511 3.5 0.8 1.0 N C:VAL512 3.6 77.8 1.0 CB C:ASP511 3.6 0.2 1.0 OD2 C:ASP519 3.7 0.7 1.0 N C:ASP515 3.7 85.8 1.0 N C:ASN513 3.9 0.1 1.0 C C:ASP511 3.9 0.6 1.0 CG C:ASN513 3.9 0.5 1.0 CA C:LEU517 4.0 88.8 1.0 N C:LYS516 4.1 97.6 1.0 N C:THR518 4.1 0.9 1.0 CA C:GLY514 4.1 0.4 1.0 CG C:ASP515 4.2 0.6 1.0 CG C:ASP519 4.3 0.6 1.0 C C:ASN513 4.3 71.2 1.0 C C:GLY514 4.3 0.4 1.0 OD1 C:ASP519 4.4 0.2 1.0 C C:LYS516 4.4 0.8 1.0 CA C:THR518 4.4 0.1 1.0 O C:GLY510 4.4 89.0 1.0 C C:ASP515 4.5 0.6 1.0 N C:ASP511 4.5 0.6 1.0 CA C:ASN513 4.5 0.7 1.0 CA C:ASP515 4.6 0.5 1.0 CB C:LEU517 4.6 0.2 1.0 ND2 C:ASN513 4.6 0.6 1.0 CA C:LYS516 4.7 72.6 1.0 C C:VAL512 4.7 0.0 1.0 CA C:VAL512 4.7 0.8 1.0 C C:THR518 4.8 0.1 1.0 CB C:ASN513 4.8 0.8 1.0 C C:GLY510 4.9 0.5 1.0 O C:ASP511 4.9 1.0 1.0

Calcium binding site 7 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2007 b:0.7 occ:1.00 O C:ASP578 2.6 0.5 1.0 OG1 C:THR576 2.7 0.8 1.0 O C:LEU580 2.7 0.3 1.0 OD2 C:ASP582 2.8 95.0 1.0 OD1 C:ASP582 2.8 0.6 1.0 OD1 C:ASP574 3.0 0.1 1.0 OD2 C:ASP578 3.1 0.2 1.0 CG C:ASP582 3.1 0.1 1.0 CG C:ASP578 3.4 0.7 1.0 C C:ASP578 3.7 0.3 1.0 OD1 C:ASP578 3.7 0.3 1.0 N C:ASP578 3.8 0.8 1.0 CB C:THR576 3.9 0.1 1.0 C C:LEU580 3.9 0.6 1.0 N C:GLN577 3.9 0.4 1.0 N C:THR576 4.0 0.8 1.0 CG C:ASP574 4.0 0.9 1.0 CA C:ASP578 4.1 0.7 1.0 CB C:ASP578 4.2 0.8 1.0 CA C:THR576 4.2 0.0 1.0 C C:THR576 4.3 0.6 1.0 O C:VAL581 4.3 96.3 1.0 CG2 C:THR576 4.3 1.0 1.0 N C:LEU580 4.4 0.7 1.0 N C:LEU575 4.4 58.5 1.0 CA C:ASP574 4.4 0.8 1.0 C C:VAL581 4.5 0.2 1.0 CB C:ASP574 4.5 0.0 1.0 CB C:ASP582 4.5 81.6 1.0 C C:GLN577 4.6 0.1 1.0 C C:GLY579 4.7 0.3 1.0 CD C:ARG595 4.7 0.9 1.0 CA C:GLN577 4.7 0.9 1.0 C C:ASP574 4.7 0.9 1.0 CA C:LEU580 4.7 0.3 1.0 N C:ASP582 4.8 1.0 1.0 N C:GLY579 4.8 0.8 1.0 O C:GLY579 4.9 0.3 1.0 N C:VAL581 4.9 0.3 1.0 CG C:ARG595 5.0 0.3 1.0 OD2 C:ASP574 5.0 0.5 1.0 CA C:VAL581 5.0 0.7 1.0

Calcium binding site 8 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


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 ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2002 b:0.5 occ:1.01 OD1 D:ASP120 2.1 0.5 1.0 OE2 D:GLU325 2.3 0.3 1.0 OD1 D:ASP119 2.4 0.5 1.0 O D:SER116 2.4 0.2 1.0 O D:GLU325 2.7 0.3 1.0 CG D:ASP120 3.0 0.2 1.0 CD D:GLU325 3.2 0.7 1.0 CG D:GLU325 3.4 0.7 1.0 CG D:ASP119 3.5 0.1 1.0 OD2 D:ASP120 3.5 0.6 1.0 C D:SER116 3.6 0.8 1.0 OD2 D:ASP119 3.9 0.0 1.0 C D:GLU325 3.9 0.3 1.0 CA D:MET117 3.9 0.6 1.0 N D:ASP120 4.0 0.1 1.0 CB D:ASP120 4.0 0.5 1.0 OD2 D:ASP242 4.1 0.3 1.0 N D:MET117 4.2 1.0 1.0 OE1 D:GLU325 4.3 0.1 1.0 N D:LEU118 4.3 0.8 1.0 C D:MET117 4.4 0.6 1.0 N D:ASP119 4.5 0.0 1.0 CA D:ASP120 4.5 0.4 1.0 CB D:GLU325 4.6 0.8 1.0 CA D:GLU325 4.7 0.8 1.0 C D:ASP119 4.7 0.3 1.0 SD D:MET117 4.7 0.5 1.0 CB D:ASP119 4.7 0.5 1.0 CA D:SER116 4.8 0.1 1.0 CA D:ASP119 4.9 0.6 1.0 N D:ASP326 4.9 0.8 1.0

Calcium binding site 9 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of Integrin ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2005 b:0.9 occ:1.00 O E:SER453 2.8 0.1 1.0 CG E:ASP447 2.9 0.2 1.0 OD1 E:ASP447 2.9 0.9 1.0 CG E:ASP455 2.9 0.7 1.0 OD1 E:ASP451 3.0 0.7 1.0 N E:ASP455 3.1 0.8 1.0 OD1 E:ASP455 3.1 0.8 1.0 OD1 E:ASP449 3.1 0.1 1.0 OD2 E:ASP447 3.2 76.4 1.0 OD2 E:ASP455 3.2 0.3 1.0 CB E:ASP455 3.3 0.3 1.0 C E:SER453 3.4 74.6 1.0 CA E:ASP447 3.5 0.9 1.0 CB E:ASP447 3.6 0.4 1.0 C E:THR454 3.7 0.9 1.0 CA E:ASP455 3.7 0.5 1.0 CA E:THR454 3.8 0.1 1.0 N E:THR454 3.8 0.2 1.0 C E:ASP447 4.0 0.2 1.0 CG E:ASP451 4.0 92.8 1.0 N E:SER453 4.2 0.8 1.0 N E:VAL448 4.2 0.2 1.0 CG E:ASP449 4.2 64.7 1.0 CA E:SER453 4.3 0.6 1.0 OD2 E:ASP451 4.4 93.4 1.0 O E:VAL446 4.6 27.6 1.0 N E:ASP449 4.6 1.0 1.0 OD2 E:ASP449 4.6 0.4 1.0 O E:THR454 4.6 62.8 1.0 N E:ASP447 4.7 0.5 1.0 O E:ASP447 4.8 0.8 1.0 CG1 E:VAL448 4.8 0.6 1.0 N E:GLY452 4.9 0.4 1.0 N E:ASP451 5.0 46.2 1.0 C E:GLY452 5.0 0.7 1.0

Calcium binding site 10 out of 16 in the Structure of Integrin ALPHAXBETA2 Ectodomain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of Integrin ALPHAXBETA2 Ectodomain within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca2006 b:0.7 occ:1.00 O E:LEU517 2.8 0.4 1.0 OD1 E:ASN513 3.0 70.7 1.0 OD1 E:ASP515 3.1 0.6 1.0 CG E:ASP511 3.2 0.3 1.0 OD2 E:ASP511 3.2 0.0 1.0 CA E:ASP511 3.3 82.9 1.0 C E:LEU517 3.4 0.4 1.0 N E:LEU517 3.5 0.4 1.0 N E:GLY514 3.5 0.7 1.0 OD1 E:ASP511 3.5 1.0 1.0 CB E:ASP511 3.6 0.2 1.0 N E:VAL512 3.6 68.2 1.0 N E:ASP515 3.7 0.1 1.0 OD2 E:ASP519 3.7 0.1 1.0 C E:ASP511 3.9 0.0 1.0 N E:ASN513 3.9 80.9 1.0 CG E:ASN513 3.9 0.4 1.0 CA E:LEU517 3.9 67.0 1.0 N E:LYS516 4.1 1.0 1.0 N E:THR518 4.1 0.8 1.0 CA E:GLY514 4.1 0.4 1.0 CG E:ASP515 4.2 63.5 1.0 CG E:ASP519 4.3 0.7 1.0 C E:ASN513 4.3 8.7 1.0 C E:GLY514 4.3 0.8 1.0 C E:LYS516 4.4 0.4 1.0 OD1 E:ASP519 4.4 0.9 1.0 CA E:THR518 4.4 0.2 1.0 C E:ASP515 4.4 47.1 1.0 O E:GLY510 4.5 93.4 1.0 CA E:ASN513 4.5 0.6 1.0 N E:ASP511 4.5 0.5 1.0 CA E:ASP515 4.6 70.5 1.0 CB E:LEU517 4.6 0.5 1.0 CA E:LYS516 4.7 65.8 1.0 ND2 E:ASN513 4.7 0.3 1.0 C E:VAL512 4.7 0.7 1.0 CA E:VAL512 4.7 0.0 1.0 C E:THR518 4.8 0.6 1.0 CB E:ASN513 4.9 0.8 1.0 C E:GLY510 4.9 0.8 1.0 O E:ASP511 4.9 0.1 1.0 OD2 E:ASP515 5.0 0.1 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