Calcium in PDB 5e6r: 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: 5e6r 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)	46.24 / 2.90
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	153.929, 153.929, 116.454, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.9

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)

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 5e6r). 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: 5e6r:
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:0.9 occ:1.00 OD1 A:ASP443 2.2 98.8 1.0 OD1 A:ASP447 2.2 94.3 1.0 OE1 A:GLU451 2.4 1.0 1.0 O A:HOH4001 2.4 89.9 1.0 OD2 A:ASP447 2.5 92.0 1.0 CG A:ASP447 2.5 92.9 1.0 OD1 A:ASP445 2.6 98.5 1.0 O A:GLU449 2.7 71.3 1.0 CG A:ASP443 3.3 92.1 1.0 CD A:GLU451 3.3 1.0 1.0 OE2 A:GLU451 3.6 0.4 1.0 N A:ASP447 3.8 91.1 1.0 CG A:ASP445 3.8 99.2 1.0 C A:GLU449 3.8 72.2 1.0 OD2 A:ASP443 3.8 93.4 1.0 CB A:ASP447 3.8 94.8 1.0 N A:GLU449 4.2 82.4 1.0 N A:GLN446 4.2 90.8 1.0 CB A:GLU449 4.3 88.0 1.0 CA A:ASP447 4.3 92.8 1.0 CA A:GLU449 4.3 81.2 1.0 CB A:ASP443 4.3 85.8 1.0 OD2 A:ASP445 4.4 98.9 1.0 N A:ASP445 4.4 88.2 1.0 CA A:ASP443 4.5 80.3 1.0 N A:VAL444 4.6 90.2 1.0 C A:ASP443 4.7 86.7 1.0 CG A:GLU451 4.7 94.8 1.0 C A:ASP445 4.8 91.9 1.0 C A:GLN446 4.8 88.2 1.0 C A:ASP447 4.9 89.2 1.0 N A:GLY448 4.9 89.4 1.0 CA A:GLN446 4.9 90.0 1.0 CB A:ASP445 4.9 98.8 1.0 CA A:ASP445 4.9 92.7 1.0 N A:THR450 4.9 72.5 1.0 N A:GLU451 5.0 65.9 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:95.2 occ:1.00 O A:LEU511 1.9 0.0 1.0 OD1 A:ASP505 2.2 89.0 1.0 O A:HOH4010 2.3 85.1 1.0 OD1 A:ASN507 2.4 87.0 1.0 OD1 A:ASP513 2.4 100.0 1.0 OD1 A:ASP509 2.5 0.4 1.0 OD2 A:ASP513 2.5 94.9 1.0 CG A:ASP513 2.7 91.9 1.0 C A:LEU511 3.1 97.0 1.0 CG A:ASP505 3.3 91.8 1.0 CG A:ASN507 3.4 89.0 1.0 CG A:ASP509 3.4 98.5 1.0 OD2 A:ASP509 3.7 0.2 1.0 ND2 A:ASN507 3.8 87.4 1.0 CA A:LEU511 3.9 86.2 1.0 N A:LEU511 4.0 85.3 1.0 CB A:ASP505 4.0 95.4 1.0 CA A:ASP505 4.0 97.8 1.0 N A:ASP513 4.0 73.7 1.0 CB A:ASP513 4.1 82.7 1.0 CB A:LEU511 4.1 77.2 1.0 C A:VAL512 4.1 78.0 1.0 N A:ILE506 4.1 94.2 1.0 N A:VAL512 4.1 96.7 1.0 OD2 A:ASP505 4.2 92.6 1.0 N A:ASN507 4.3 96.8 1.0 CA A:VAL512 4.3 83.2 1.0 C A:ASP505 4.5 93.9 1.0 O A:VAL512 4.5 75.4 1.0 CA A:ASP513 4.6 75.0 1.0 N A:GLY531 4.6 78.7 1.0 CB A:ASN507 4.7 93.1 1.0 N A:ASP509 4.7 82.5 1.0 ND2 A:ASN530 4.8 92.1 1.0 CB A:ASP509 4.8 95.0 1.0 O A:GLY531 4.9 79.6 1.0 CA A:ASN507 4.9 94.7 1.0 O A:THR504 5.0 99.0 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:78.7 occ:1.00 OD1 B:ASP120 2.2 0.1 1.0 O B:HOH4033 2.4 81.4 1.0 O B:HOH4049 2.4 74.8 1.0 O B:GLU325 2.4 78.7 1.0 O B:SER116 2.4 69.7 1.0 OD1 B:ASP119 2.5 93.6 1.0 CG B:ASP119 3.2 89.0 1.0 OD2 B:ASP119 3.2 92.3 1.0 CG B:ASP120 3.3 94.1 1.0 C B:SER116 3.6 69.8 1.0 C B:GLU325 3.6 78.2 1.0 OD2 B:ASP120 3.7 92.6 1.0 CA B:MET117 4.1 71.0 1.0 N B:MET117 4.3 68.5 1.0 CA B:GLU325 4.3 78.8 1.0 N B:ASP120 4.3 68.1 1.0 CB B:ASP120 4.6 81.7 1.0 N B:ASP326 4.6 79.0 1.0 CB B:GLU325 4.6 88.3 1.0 CB B:ASP119 4.7 83.3 1.0 CA B:SER116 4.7 70.5 1.0 C B:MET117 4.7 72.8 1.0 OD2 B:ASP242 4.8 80.4 1.0 CA B:ASP326 4.8 79.0 1.0 OE1 B:GLU325 4.9 0.9 1.0 CB B:SER116 4.9 74.5 1.0 N B:ASP119 4.9 69.0 1.0 SD B:MET117 5.0 77.0 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:91.6 occ:1.00 O B:ASP209 2.3 71.1 1.0 O B:PRO211 2.3 68.5 1.0 OD1 B:ASP209 2.3 73.6 1.0 OD1 B:ASN207 2.4 69.5 1.0 OD2 B:ASP151 2.5 73.7 1.0 C B:ASP209 3.3 69.2 1.0 CG B:ASN207 3.5 68.2 1.0 O B:PHE157 3.5 55.3 1.0 CG B:ASP209 3.5 73.0 1.0 C B:PRO211 3.5 65.0 1.0 CG B:ASP151 3.6 65.8 1.0 N B:ASP209 3.8 62.8 1.0 CA B:ASP209 4.0 66.3 1.0 NE2 B:HIS246 4.0 60.8 1.0 CB B:ASP151 4.1 62.1 1.0 C B:ALA210 4.2 64.5 1.0 O B:ALA210 4.2 62.3 1.0 CG B:GLU212 4.2 73.2 1.0 CB B:ASN207 4.2 66.7 1.0 N B:PRO211 4.3 65.5 1.0 CA B:GLU212 4.3 62.1 1.0 C B:PHE157 4.3 58.6 1.0 N B:ALA210 4.3 74.1 1.0 CB B:ASP209 4.4 70.2 1.0 OD2 B:ASP209 4.4 77.9 1.0 N B:GLU212 4.4 60.7 1.0 ND2 B:ASN207 4.4 69.0 1.0 CA B:PHE157 4.4 58.7 1.0 N B:LEU208 4.5 65.5 1.0 CA B:PRO211 4.5 62.7 1.0 CD2 B:HIS246 4.5 60.0 1.0 C B:LEU208 4.6 69.5 1.0 OD1 B:ASP151 4.6 65.5 1.0 CB B:PHE157 4.7 59.9 1.0 CA B:ALA210 4.7 73.1 1.0 CB B:GLU212 4.9 68.6 1.0 CD B:PRO211 4.9 63.3 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