Magnesium in PDB 5es4: Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation

The structure of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation, PDB code: 5es4 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)	49.51 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	132.030, 163.480, 536.650, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 30.7

The structure of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation also contains other interesting chemical elements:

Calcium

(Ca)

16 atoms

The binding sites of Magnesium atom in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation (pdb code 5es4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation, PDB code: 5es4:

Magnesium binding site 1 out of 1 in the Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Re-Refinement of Integrin ALPHAXBETA2 Ectodomain in the Closed/Bent Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2009 b:1.0 occ:1.00 O A:HOH4012 2.0 0.1 1.0 OG A:SER142 2.1 0.1 1.0 O A:HOH4008 2.1 0.9 1.0 OG A:SER140 2.1 0.7 1.0 OD1 A:ASP240 2.2 0.3 1.0 O A:HOH4011 2.3 0.5 1.0 CG A:ASP240 3.1 0.9 1.0 OD2 A:ASP240 3.3 0.9 1.0 CB A:SER140 3.4 0.3 1.0 CB A:SER142 3.4 0.2 1.0 OD2 A:ASP138 3.9 0.8 1.0 OD1 A:ASP138 4.0 0.1 1.0 OG1 A:THR207 4.0 0.7 1.0 N A:SER142 4.3 0.3 1.0 CG A:ASP138 4.3 0.3 1.0 CA A:SER142 4.4 0.0 1.0 CG1 A:ILE143 4.5 0.6 1.0 CB A:ASP240 4.5 0.1 1.0 CA A:SER140 4.5 0.5 1.0 C A:SER140 4.7 0.9 1.0 CD1 A:ILE143 4.7 0.7 1.0 N A:GLY241 4.7 0.9 1.0 O A:SER140 4.7 0.8 1.0 C A:ASP240 4.8 0.7 1.0 C A:SER142 4.8 0.3 1.0 N A:ILE143 5.0 0.3 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