Calcium in PDB 5e6u: 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: 5e6u was solved by M.Sen, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.44 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	154.980, 154.980, 115.450, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 22.6

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)	2 atoms
Chlorine	(Cl)	1 atom

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 5e6u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 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: 5e6u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 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:57.5 occ:1.00 OE1 A:GLU451 2.2 46.6 1.0 O A:GLU449 2.3 60.5 1.0 OD1 A:ASP447 2.3 56.2 1.0 OD1 A:ASP443 2.3 38.5 1.0 O A:HOH4154 2.3 58.5 1.0 OD1 A:ASP445 2.5 63.2 1.0 CD A:GLU451 3.2 47.0 1.0 CG A:ASP443 3.2 41.8 1.0 CG A:ASP447 3.3 62.5 1.0 CG A:ASP445 3.4 64.4 1.0 C A:GLU449 3.4 47.3 1.0 OE2 A:GLU451 3.6 44.0 1.0 OD2 A:ASP445 3.7 70.7 1.0 OD2 A:ASP447 3.8 72.6 1.0 CA A:ASP443 4.0 35.3 1.0 OD2 A:ASP443 4.0 50.0 1.0 CB A:ASP443 4.0 30.3 1.0 N A:ASP447 4.1 49.9 1.0 N A:GLU449 4.1 43.5 1.0 CA A:GLU449 4.2 42.5 1.0 N A:VAL444 4.2 38.8 1.0 C A:ASP443 4.3 40.1 1.0 N A:GLU451 4.3 42.5 1.0 CG A:GLU451 4.4 47.7 1.0 N A:GLN446 4.4 57.4 1.0 CB A:GLU449 4.4 46.4 1.0 N A:ASP445 4.4 51.6 1.0 CB A:ASP447 4.4 55.1 1.0 N A:THR450 4.5 39.7 1.0 CB A:GLU451 4.5 41.7 1.0 CA A:THR450 4.6 34.3 1.0 CA A:ASP447 4.7 50.1 1.0 CB A:ASP445 4.8 52.4 1.0 N A:GLY448 4.9 36.0 1.0 CA A:ASP445 4.9 54.3 1.0 C A:ASP445 4.9 57.6 1.0 C A:THR450 4.9 42.3 1.0

Calcium binding site 2 out of 4 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:49.3 occ:1.00 O A:LEU511 2.2 56.7 1.0 OD1 A:ASP505 2.3 44.7 1.0 OD1 A:ASN507 2.3 55.3 1.0 O A:HOH4041 2.3 27.7 1.0 OD2 A:ASP513 2.4 42.9 1.0 OD1 A:ASP509 2.5 52.8 1.0 OD1 A:ASP513 2.5 37.9 1.0 CG A:ASP513 2.8 38.5 1.0 C A:LEU511 3.4 50.2 1.0 CG A:ASP505 3.4 53.2 1.0 CG A:ASN507 3.5 59.7 1.0 CG A:ASP509 3.6 52.2 1.0 CA A:ASP505 3.9 52.2 1.0 N A:ILE506 3.9 44.3 1.0 N A:ASN507 4.0 53.9 1.0 CB A:ASP505 4.0 53.7 1.0 OD2 A:ASP509 4.1 62.9 1.0 N A:LEU511 4.1 52.2 1.0 CA A:LEU511 4.2 48.6 1.0 CB A:ASP513 4.2 34.7 1.0 ND2 A:ASN507 4.2 66.1 1.0 C A:VAL512 4.3 38.6 1.0 C A:ASP505 4.3 48.3 1.0 N A:ASP513 4.3 38.1 1.0 N A:VAL512 4.4 48.4 1.0 CB A:LEU511 4.4 45.9 1.0 OD2 A:ASP505 4.4 56.4 1.0 CA A:VAL512 4.6 43.6 1.0 O A:VAL512 4.6 35.4 1.0 CB A:ASN507 4.6 57.7 1.0 N A:ASP509 4.7 49.2 1.0 CA A:ASN507 4.7 56.9 1.0 N A:GLY531 4.7 40.8 1.0 CA A:ASP513 4.8 32.8 1.0 N A:GLY508 4.8 53.1 1.0 CB A:ASP509 4.9 46.9 1.0 C A:ASN507 4.9 57.5 1.0 O A:THR504 4.9 64.8 1.0 CA A:ILE506 4.9 47.4 1.0 N A:GLY510 4.9 42.2 1.0 C A:ILE506 4.9 55.1 1.0

Calcium binding site 3 out of 4 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 B:Ca2002 b:56.6 occ:1.00 OD1 B:ASP120 2.3 42.6 1.0 O B:HOH4203 2.3 47.9 1.0 OD1 B:ASP119 2.4 50.9 1.0 O B:SER116 2.4 30.9 1.0 O B:HOH4032 2.4 47.8 1.0 O B:GLU325 2.4 42.5 1.0 CG B:ASP119 3.2 45.8 1.0 OD2 B:ASP119 3.3 44.2 1.0 CG B:ASP120 3.4 42.7 1.0 C B:SER116 3.6 32.6 1.0 C B:GLU325 3.7 41.6 1.0 O B:HOH4033 3.9 40.9 1.0 OD2 B:ASP120 3.9 28.5 1.0 CA B:MET117 4.1 35.3 1.0 N B:MET117 4.3 38.5 1.0 O B:HOH4052 4.4 44.6 1.0 N B:ASP120 4.4 37.1 1.0 OD2 B:ASP242 4.5 24.8 1.0 CA B:GLU325 4.5 45.3 1.0 N B:ASP326 4.6 42.1 1.0 C B:MET117 4.6 37.8 1.0 CB B:ASP119 4.6 36.5 1.0 CA B:ASP326 4.7 42.3 1.0 CB B:ASP120 4.7 34.0 1.0 CA B:SER116 4.7 32.8 1.0 N B:ASP119 4.7 33.0 1.0 CB B:GLU325 4.8 54.6 1.0 N B:LEU118 4.8 31.9 1.0 CB B:SER116 4.9 27.9 1.0 SD B:MET117 4.9 33.4 1.0

Calcium binding site 4 out of 4 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:Ca2003 b:34.8 occ:1.00 O B:PRO211 2.2 52.1 1.0 OD1 B:ASP209 2.3 38.8 1.0 OD2 B:ASP151 2.3 52.1 1.0 OD1 B:ASN207 2.3 52.4 1.0 O B:ASP209 2.4 34.9 1.0 OE1 B:GLU212 2.4 42.2 1.0 CG B:ASP209 3.3 38.0 1.0 C B:PRO211 3.3 34.7 1.0 CG B:ASP151 3.4 39.2 1.0 C B:ASP209 3.4 31.5 1.0 CG B:ASN207 3.4 39.7 1.0 CD B:GLU212 3.6 38.1 1.0 CA B:GLU212 3.8 30.3 1.0 CB B:ASP151 3.8 37.1 1.0 OD2 B:ASP209 3.9 34.3 1.0 N B:GLU212 4.0 31.0 1.0 N B:ASP209 4.0 31.8 1.0 ND2 B:ASN207 4.0 44.3 1.0 CA B:ASP209 4.1 33.7 1.0 C B:ALA210 4.2 32.0 1.0 NE2 B:HIS246 4.2 31.8 1.0 O B:ALA210 4.2 34.3 1.0 CB B:ASP209 4.3 32.2 1.0 N B:PRO211 4.4 33.3 1.0 OE2 B:GLU212 4.4 36.7 1.0 N B:ALA210 4.4 30.3 1.0 CA B:PRO211 4.5 27.6 1.0 OD1 B:ASP151 4.5 35.4 1.0 CD2 B:HIS246 4.5 28.2 1.0 CG B:GLU212 4.5 30.1 1.0 O B:PHE157 4.5 39.5 1.0 CB B:GLU212 4.5 28.0 1.0 CB B:ASN207 4.6 31.5 1.0 CA B:ALA210 4.8 30.9 1.0 C B:GLU212 4.8 31.0 1.0 O B:VAL150 5.0 40.3 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