Magnesium 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:

Calcium

(Ca)

15 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg2001 b:22.3 occ:0.99 O A:HOH4030 2.0 28.6 1.0 O A:HOH4046 2.0 27.8 1.0 OG A:SER139 2.0 26.9 1.0 OG A:SER141 2.1 40.3 1.0 OD1 A:ASP239 2.1 31.2 1.0 O A:HOH4090 2.1 32.6 1.0 CG A:ASP239 3.1 31.4 1.0 CB A:SER139 3.1 23.3 1.0 CB A:SER141 3.4 37.9 1.0 OD2 A:ASP239 3.4 36.9 1.0 OG1 A:THR206 3.6 30.9 1.0 OD2 A:ASP137 3.6 25.6 1.0 N A:SER141 4.2 34.0 1.0 O A:HOH4377 4.2 65.7 1.0 OD1 A:ASP137 4.2 36.2 1.0 N A:GLY240 4.2 28.2 1.0 C A:ASP239 4.2 28.7 1.0 CG A:ASP137 4.3 35.4 1.0 CA A:SER141 4.3 33.9 1.0 O A:HOH4328 4.4 26.2 1.0 CA A:SER139 4.4 30.1 1.0 CB A:ASP239 4.4 26.3 1.0 O A:ASP239 4.4 31.0 1.0 CA A:GLY240 4.4 31.3 1.0 C A:SER139 4.6 34.3 1.0 CA A:ASP239 4.7 23.6 1.0 N A:ASP239 4.8 20.4 1.0 CB A:THR206 4.9 30.4 1.0 N A:SER139 4.9 30.8 1.0 N A:MET140 4.9 41.7 1.0

Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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 C:Mg2001 b:22.9 occ:1.00 OG C:SER141 2.0 29.1 1.0 O C:HOH4030 2.1 45.9 1.0 OG C:SER139 2.2 25.7 1.0 OD1 C:ASP239 2.3 41.5 1.0 O C:HOH4246 2.4 22.3 1.0 O C:HOH4262 2.7 47.5 1.0 CB C:SER139 3.1 18.4 1.0 CB C:SER141 3.1 28.2 1.0 CG C:ASP239 3.2 34.1 1.0 OD2 C:ASP239 3.4 33.9 1.0 OG1 C:THR206 3.6 29.0 1.0 O C:HOH4206 4.0 33.7 1.0 OD2 C:ASP137 4.1 27.9 1.0 N C:SER141 4.2 29.2 1.0 CA C:SER141 4.2 30.0 1.0 C C:ASP239 4.4 24.5 1.0 N C:GLY240 4.4 20.1 1.0 O C:HOH4039 4.4 42.3 1.0 OD1 C:ASP137 4.4 31.4 1.0 CA C:SER139 4.4 26.9 1.0 O C:ASP239 4.5 26.6 1.0 O C:HOH4362 4.5 43.4 1.0 CA C:GLY240 4.6 26.2 1.0 CB C:ASP239 4.6 18.2 1.0 CG C:ASP137 4.6 27.9 1.0 C C:SER139 4.8 30.8 1.0 CB C:THR206 4.9 17.5 1.0 CA C:ASP239 4.9 19.7 1.0 O C:HOH4368 5.0 35.5 1.0

Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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 E:Mg2001 b:26.8 occ:1.00 OG E:SER141 1.9 38.6 1.0 O E:HOH4271 2.0 27.5 1.0 O E:HOH4032 2.2 22.1 1.0 O E:HOH4325 2.2 45.0 1.0 OD1 E:ASP239 2.3 31.2 1.0 OG E:SER139 2.3 30.8 1.0 CB E:SER141 3.0 35.8 1.0 CG E:ASP239 3.1 32.0 1.0 OD2 E:ASP239 3.2 37.9 1.0 CB E:SER139 3.3 26.7 1.0 OG1 E:THR206 4.0 35.5 1.0 N E:SER141 4.0 26.4 1.0 CA E:SER141 4.1 28.8 1.0 OD2 E:ASP137 4.1 21.4 1.0 O E:ASP239 4.3 25.5 1.0 C E:ASP239 4.3 19.5 1.0 O E:HOH4262 4.5 33.2 1.0 N E:GLY240 4.5 18.7 1.0 CB E:ASP239 4.5 22.8 1.0 OD1 E:ASP137 4.5 35.9 1.0 CA E:SER139 4.6 28.1 1.0 O E:HOH4376 4.6 37.2 1.0 CA E:GLY240 4.6 22.6 1.0 CG E:ASP137 4.7 28.3 1.0 C E:SER139 4.8 26.5 1.0 C E:SER141 4.9 27.8 1.0 CA E:ASP239 4.9 20.6 1.0 N E:LEU142 5.0 27.1 1.0 N E:MET140 5.0 27.8 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