Calcium in PDB 5e6s: Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand

The structure of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand, PDB code: 5e6s was solved by T.A.Springer, M.Sen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.45 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	151.900, 118.877, 150.967, 90.00, 118.52, 90.00
R / Rfree (%)	19.4 / 23.4

The structure of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Calcium atom in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand (pdb code 5e6s). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 15 binding sites of Calcium where determined in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand, PDB code: 5e6s:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2002 b:48.5 occ:1.00 OD1 A:ASP443 2.3 35.7 1.0 O A:HOH4126 2.4 23.3 1.0 O A:GLU449 2.4 37.2 1.0 OD1 A:ASP447 2.4 36.7 1.0 OE1 A:GLU451 2.5 34.1 1.0 O A:HOH4218 2.5 33.9 1.0 OD2 A:ASP447 3.0 37.6 1.0 CG A:ASP447 3.0 34.5 1.0 CD A:GLU451 3.3 27.0 1.0 CG A:ASP443 3.4 34.0 1.0 C A:GLU449 3.6 29.9 1.0 OE2 A:GLU451 3.9 29.0 1.0 CB A:GLU449 4.0 24.9 1.0 OD2 A:ASP443 4.1 43.1 1.0 CA A:GLU449 4.1 26.9 1.0 N A:GLU449 4.1 19.2 1.0 CA A:ASP443 4.2 24.3 1.0 CB A:ASP443 4.3 23.8 1.0 CG A:GLU451 4.3 18.1 1.0 CB A:ASP447 4.3 28.3 1.0 N A:VAL444 4.4 17.1 1.0 CB A:GLU451 4.5 17.2 1.0 N A:ASP447 4.5 20.1 1.0 C A:ASP443 4.5 24.1 1.0 N A:GLU451 4.5 23.3 1.0 N A:ASP445 4.5 30.2 1.0 N A:THR450 4.7 25.8 1.0 CB A:ASP445 4.8 32.2 1.0 OD2 A:ASP445 4.8 49.1 1.0 CA A:ASP447 4.9 21.8 1.0 N A:GLN446 4.9 28.7 1.0 CA A:THR450 5.0 27.6 1.0

Calcium binding site 2 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:27.9 occ:1.00 O A:HOH4101 2.3 16.6 1.0 OD1 A:ASN507 2.3 39.5 1.0 O A:LEU511 2.3 22.9 1.0 OD1 A:ASP513 2.5 23.9 1.0 OD1 A:ASP505 2.5 44.3 1.0 OD1 A:ASP509 2.5 39.4 1.0 OD2 A:ASP513 2.5 18.6 1.0 CG A:ASP513 2.8 22.2 1.0 CG A:ASN507 3.4 34.7 1.0 C A:LEU511 3.5 24.2 1.0 CG A:ASP509 3.5 36.9 1.0 CG A:ASP505 3.6 45.8 1.0 OD2 A:ASP509 3.8 39.9 1.0 ND2 A:ASN507 4.0 34.4 1.0 N A:LEU511 4.0 33.3 1.0 CA A:LEU511 4.1 23.0 1.0 CB A:LEU511 4.1 22.7 1.0 CA A:ASP505 4.3 43.6 1.0 CB A:ASP513 4.3 19.2 1.0 ND2 A:ASN530 4.4 43.4 1.0 N A:ASN507 4.4 36.1 1.0 CB A:ASP505 4.4 41.2 1.0 OD2 A:ASP505 4.4 45.2 1.0 N A:ILE506 4.4 30.8 1.0 C A:VAL512 4.5 18.8 1.0 N A:GLY531 4.5 28.6 1.0 N A:ASP513 4.5 18.1 1.0 N A:VAL512 4.6 21.1 1.0 O A:VAL512 4.6 28.3 1.0 O A:GLY531 4.7 41.9 1.0 N A:ASP509 4.7 29.9 1.0 CB A:ASN507 4.7 36.8 1.0 CB A:ASP509 4.8 35.1 1.0 C A:ASP505 4.8 38.0 1.0 CA A:VAL512 4.9 23.6 1.0 N A:GLY508 4.9 31.6 1.0 CA A:ASP513 4.9 22.6 1.0 CA A:ASN507 4.9 39.3 1.0

Calcium binding site 3 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2004 b:0.1 occ:1.00 OD1 A:ASP565 2.4 67.1 1.0 O A:HOH4134 2.5 47.7 1.0 OD1 A:ASP569 2.6 81.3 1.0 OD2 A:ASP573 2.7 57.0 1.0 CG A:ASP569 3.2 71.2 1.0 O A:HOH4106 3.2 54.0 1.0 OD2 A:ASP569 3.3 67.9 1.0 CG A:ASP573 3.4 50.0 1.0 OD1 A:ASP573 3.4 50.2 1.0 O A:LEU571 3.5 32.2 1.0 N A:GLU567 3.6 56.6 1.0 CG A:ASP565 3.6 63.0 1.0 N A:LEU566 3.8 50.3 1.0 CB A:GLU567 4.0 60.5 1.0 C A:ASP565 4.2 50.6 1.0 CA A:GLU567 4.2 58.1 1.0 N A:GLY568 4.3 60.8 1.0 CA A:ASP565 4.4 57.1 1.0 N A:ASP569 4.4 69.2 1.0 OD2 A:ASP565 4.4 61.0 1.0 C A:LEU571 4.5 38.7 1.0 C A:GLU567 4.5 60.0 1.0 C A:LEU566 4.6 57.5 1.0 CB A:ASP565 4.6 60.5 1.0 CB A:ASP569 4.6 64.2 1.0 CA A:LEU566 4.6 51.8 1.0 CG A:GLU567 4.6 70.0 1.0 OE1 A:GLU567 4.7 91.4 1.0 CB A:ASP573 4.8 41.6 1.0 CB A:LEU566 4.9 42.9 1.0 CB A:LEU571 4.9 34.8 1.0 O A:ASP565 4.9 50.3 1.0 N A:LEU571 4.9 35.2 1.0

Calcium binding site 4 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2002 b:33.6 occ:1.00 O B:GLU325 2.3 25.1 1.0 OD1 B:ASP120 2.3 32.6 1.0 O B:SER116 2.4 19.3 1.0 O B:HOH4220 2.4 35.1 1.0 O B:HOH4114 2.5 25.1 1.0 OD1 B:ASP119 2.6 61.0 1.0 CG B:ASP119 3.4 53.5 1.0 CG B:ASP120 3.4 26.8 1.0 OD2 B:ASP119 3.5 57.9 1.0 C B:GLU325 3.5 24.0 1.0 C B:SER116 3.6 20.2 1.0 OD2 B:ASP120 3.9 22.2 1.0 O B:HOH4042 4.0 32.4 1.0 CA B:MET117 4.1 14.9 1.0 O B:HOH4111 4.2 28.9 1.0 N B:MET117 4.3 18.1 1.0 CA B:GLU325 4.3 29.1 1.0 N B:ASP120 4.4 25.9 1.0 O B:HOH4157 4.4 52.5 1.0 N B:ASP326 4.5 16.3 1.0 CA B:ASP326 4.6 22.6 1.0 CB B:ASP120 4.6 23.9 1.0 C B:MET117 4.6 18.1 1.0 CB B:GLU325 4.7 37.9 1.0 CA B:SER116 4.7 20.9 1.0 OE1 B:GLU325 4.8 67.6 1.0 SD B:MET117 4.8 27.0 1.0 CB B:ASP119 4.8 36.0 1.0 OD2 B:ASP242 4.8 22.3 1.0 N B:ASP119 4.9 26.0 1.0 N B:LEU118 4.9 22.2 1.0 CB B:SER116 5.0 8.3 1.0

Calcium binding site 5 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2003 b:48.9 occ:1.00 OD1 B:ASN207 2.2 28.2 1.0 O B:PRO211 2.2 21.2 1.0 OD1 B:ASP209 2.3 29.2 1.0 OD2 B:ASP151 2.4 28.0 1.0 O B:ASP209 2.7 23.8 1.0 CG B:ASP209 3.3 20.2 1.0 CG B:ASN207 3.4 26.3 1.0 CG B:ASP151 3.4 26.3 1.0 C B:PRO211 3.4 21.9 1.0 CB B:ASP151 3.6 20.8 1.0 C B:ASP209 3.7 23.1 1.0 CA B:GLU212 3.7 18.9 1.0 CG B:GLU212 3.8 23.9 1.0 O B:PHE157 3.8 27.5 1.0 OD2 B:ASP209 4.0 23.5 1.0 N B:GLU212 4.0 21.9 1.0 N B:ASP209 4.1 23.3 1.0 NE2 B:HIS246 4.1 28.3 1.0 CB B:ASN207 4.2 17.5 1.0 CA B:ASP209 4.2 17.5 1.0 CB B:GLU212 4.3 24.4 1.0 ND2 B:ASN207 4.4 33.8 1.0 CB B:ASP209 4.4 19.5 1.0 CD2 B:HIS246 4.4 21.4 1.0 C B:ALA210 4.5 25.2 1.0 O B:ALA210 4.5 29.7 1.0 N B:PRO211 4.5 21.2 1.0 OD1 B:ASP151 4.6 21.7 1.0 CA B:PRO211 4.6 18.3 1.0 N B:ALA210 4.7 21.3 1.0 C B:PHE157 4.7 23.6 1.0 CB B:PHE157 4.7 11.7 1.0 CA B:PHE157 4.7 19.2 1.0 C B:GLU212 4.9 18.2 1.0 N B:LEU208 4.9 24.3 1.0

Calcium binding site 6 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2002 b:44.6 occ:1.00 OE1 C:GLU451 2.3 38.5 1.0 O C:HOH4037 2.4 38.7 1.0 OD1 C:ASP447 2.4 51.8 1.0 O C:HOH4006 2.5 15.4 1.0 O C:GLU449 2.5 24.9 1.0 OD1 C:ASP443 2.6 35.2 1.0 OD2 C:ASP447 2.7 42.3 1.0 CG C:ASP447 2.8 42.8 1.0 CD C:GLU451 3.2 38.3 1.0 CG C:ASP443 3.6 37.2 1.0 C C:GLU449 3.6 26.9 1.0 OE2 C:GLU451 3.9 40.5 1.0 CB C:GLU449 4.1 26.2 1.0 CG C:GLU451 4.2 32.8 1.0 CB C:GLU451 4.2 28.6 1.0 CA C:GLU449 4.2 27.2 1.0 CB C:ASP447 4.2 32.8 1.0 OD2 C:ASP443 4.2 36.4 1.0 N C:GLU449 4.3 24.7 1.0 N C:GLU451 4.3 22.7 1.0 CA C:ASP443 4.4 33.3 1.0 OD2 C:ASP445 4.4 53.3 1.0 CB C:ASP443 4.4 36.0 1.0 N C:VAL444 4.6 30.8 1.0 N C:ASP447 4.7 28.2 1.0 N C:THR450 4.7 26.1 1.0 C C:ASP443 4.7 29.1 1.0 N C:ASP445 4.9 40.3 1.0 CA C:GLU451 4.9 26.6 1.0 CA C:THR450 4.9 26.4 1.0 CA C:ASP447 4.9 27.1 1.0

Calcium binding site 7 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2003 b:36.6 occ:1.00 OD1 C:ASN507 2.2 39.6 1.0 OD1 C:ASP505 2.4 33.4 1.0 O C:LEU511 2.4 37.2 1.0 O C:HOH4040 2.4 18.5 1.0 OD1 C:ASP509 2.4 39.6 1.0 OD1 C:ASP513 2.4 32.4 1.0 OD2 C:ASP513 2.7 30.9 1.0 CG C:ASP513 2.9 30.8 1.0 CG C:ASP509 3.3 42.5 1.0 CG C:ASN507 3.3 36.1 1.0 OD2 C:ASP509 3.4 49.5 1.0 C C:LEU511 3.5 34.3 1.0 CG C:ASP505 3.5 37.8 1.0 ND2 C:ASN507 3.8 39.4 1.0 CB C:LEU511 4.1 30.1 1.0 CA C:LEU511 4.1 30.9 1.0 N C:LEU511 4.1 29.8 1.0 N C:GLY531 4.3 35.8 1.0 OD2 C:ASP505 4.3 32.5 1.0 ND2 C:ASN530 4.3 33.5 1.0 N C:ASN507 4.3 32.8 1.0 CB C:ASP513 4.4 27.4 1.0 C C:VAL512 4.5 26.3 1.0 CB C:ASP505 4.5 39.1 1.0 N C:ASP513 4.5 31.5 1.0 CA C:ASP505 4.5 43.9 1.0 N C:ILE506 4.6 34.5 1.0 CB C:ASN507 4.6 36.0 1.0 N C:VAL512 4.6 31.9 1.0 N C:ASP509 4.6 34.3 1.0 O C:VAL512 4.6 23.8 1.0 CB C:ASP509 4.6 32.7 1.0 CA C:GLY531 4.8 37.5 1.0 CA C:ASN507 4.8 38.1 1.0 N C:GLY508 4.9 43.5 1.0 O C:GLY531 4.9 33.0 1.0 CA C:ASP513 4.9 29.5 1.0 C C:ASN507 4.9 45.3 1.0 CA C:VAL512 4.9 21.7 1.0 CB C:ASN530 5.0 24.7 1.0

Calcium binding site 8 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2004 b:88.1 occ:1.00 OD1 C:ASP565 2.5 72.0 1.0 OD1 C:ASP569 2.6 95.1 1.0 O C:HOH4291 2.6 68.1 1.0 OD2 C:ASP573 2.9 44.8 1.0 OD1 C:ASP573 2.9 46.8 1.0 O C:LEU571 3.1 52.5 1.0 CG C:ASP573 3.2 45.0 1.0 CG C:ASP569 3.4 92.1 1.0 OD2 C:ASP569 3.5 89.1 1.0 CG C:ASP565 3.6 75.9 1.0 CB C:LEU571 3.9 57.2 1.0 C C:LEU571 4.0 52.2 1.0 OG C:SER586 4.1 32.8 0.4 OD2 C:ASP565 4.3 77.5 1.0 OG C:SER586 4.3 36.1 0.6 CA C:LEU571 4.4 59.8 1.0 N C:LEU566 4.4 62.4 1.0 N C:LEU571 4.5 65.6 1.0 N C:GLU567 4.5 72.9 1.0 CB C:ASP565 4.7 76.1 1.0 CB C:ASP573 4.7 40.6 1.0 CA C:ASP565 4.7 73.8 1.0 CG C:LEU571 4.8 55.8 1.0 CB C:ASP569 4.9 91.6 1.0 O C:ALA572 4.9 31.2 1.0 CB C:GLU567 4.9 82.3 1.0 CD1 C:LEU571 4.9 57.7 1.0 C C:ASP565 4.9 68.7 1.0 N C:ASP569 5.0 94.8 1.0 C C:ALA572 5.0 31.2 1.0

Calcium binding site 9 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2002 b:36.2 occ:1.00 O D:GLU325 2.4 27.7 1.0 O D:SER116 2.4 26.2 1.0 OD1 D:ASP120 2.4 28.3 1.0 O D:HOH4176 2.4 26.0 1.0 OD1 D:ASP119 2.6 57.8 1.0 O D:HOH4212 2.7 28.9 1.0 CG D:ASP119 3.3 51.5 1.0 OD2 D:ASP119 3.3 56.4 1.0 O D:HOH4025 3.5 29.8 1.0 C D:SER116 3.5 15.7 1.0 CG D:ASP120 3.6 27.4 1.0 C D:GLU325 3.6 21.6 1.0 CA D:MET117 3.9 20.6 1.0 O D:HOH4014 4.0 56.1 1.0 OD2 D:ASP120 4.1 29.4 1.0 N D:MET117 4.2 13.4 1.0 O D:HOH4117 4.2 20.6 1.0 CA D:GLU325 4.4 26.6 1.0 C D:MET117 4.5 25.7 1.0 N D:ASP120 4.5 10.5 1.0 N D:ASP326 4.5 23.5 1.0 CA D:ASP326 4.6 20.0 1.0 O D:HOH4171 4.6 44.2 1.0 OD2 D:ASP242 4.6 33.0 1.0 CA D:SER116 4.7 19.3 1.0 CB D:ASP119 4.8 30.9 1.0 CB D:ASP120 4.8 24.3 1.0 CB D:GLU325 4.8 33.2 1.0 N D:LEU118 4.8 28.7 1.0 N D:ASP119 4.8 28.3 1.0 SD D:MET117 4.8 22.6 1.0 CB D:SER116 4.9 22.2 1.0

Calcium binding site 10 out of 15 in the Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structures of Leukocyte Integrin ALB2: the Ai Domain, the Headpiece, and the Pocket For the Internal Ligand within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2003 b:40.0 occ:1.00 OD1 D:ASN207 2.2 15.0 1.0 OD1 D:ASP209 2.3 41.4 1.0 O D:PRO211 2.3 14.4 1.0 OD2 D:ASP151 2.5 22.7 1.0 O D:ASP209 2.5 32.7 1.0 CG D:ASN207 3.3 19.3 1.0 CG D:ASP209 3.3 31.7 1.0 C D:ASP209 3.4 28.6 1.0 C D:PRO211 3.5 20.4 1.0 CG D:ASP151 3.5 18.6 1.0 O D:PHE157 3.8 15.6 1.0 CG D:GLU212 3.8 20.9 1.0 CB D:ASP151 3.8 18.9 1.0 N D:ASP209 3.9 25.3 1.0 CA D:GLU212 3.9 24.6 1.0 OD2 D:ASP209 4.0 30.7 1.0 CA D:ASP209 4.0 28.7 1.0 NE2 D:HIS246 4.1 22.8 1.0 ND2 D:ASN207 4.1 11.7 1.0 N D:GLU212 4.2 24.8 1.0 CB D:ASN207 4.2 15.9 1.0 CB D:ASP209 4.3 23.7 1.0 C D:ALA210 4.3 25.2 1.0 O D:ALA210 4.4 25.9 1.0 CD2 D:HIS246 4.4 18.5 1.0 CB D:GLU212 4.4 24.9 1.0 N D:ALA210 4.4 23.3 1.0 N D:PRO211 4.5 19.8 1.0 CA D:PRO211 4.6 20.7 1.0 OD1 D:ASP151 4.7 14.6 1.0 C D:PHE157 4.7 17.6 1.0 CA D:PHE157 4.8 14.6 1.0 N D:LEU208 4.8 27.1 1.0 CB D:PHE157 4.8 17.3 1.0 CA D:ALA210 4.8 21.5 1.0 C D:LEU208 5.0 27.5 1.0

M.Sen, T.A.Springer. Leukocyte Integrin Alpha L Beta 2 Headpiece Structures: the Alpha I Domain, the Pocket For the Internal Ligand, and Concerted Movements of Its Loops. Proc.Natl.Acad.Sci.Usa V. 113 2940 2016.
ISSN: ESSN 1091-6490
PubMed: 26936951
DOI: 10.1073/PNAS.1601379113