Magnesium in PDB 4nen: An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2

The structure of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2, PDB code: 4nen was solved by M.Sen, K.Yuki, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.81 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	127.087, 119.851, 182.399, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 26.4

The structure of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	5 atoms

The binding sites of Magnesium atom in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 (pdb code 4nen). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2, PDB code: 4nen:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1116 b:72.0 occ:1.00 OG A:SER142 2.0 78.5 1.0 O A:HOH1218 2.1 69.8 1.0 O A:HOH1205 2.1 82.0 1.0 OG1 A:THR207 2.1 91.6 1.0 OG A:SER140 2.3 59.9 1.0 CL A:CL1117 2.3 85.6 1.0 CB A:SER142 3.0 77.5 1.0 CB A:SER140 3.3 59.7 1.0 CB A:THR207 3.4 87.1 1.0 O A:LYS242 3.7 83.2 1.0 N A:SER142 3.8 84.9 1.0 CG2 A:THR207 4.0 87.4 1.0 CA A:SER142 4.0 77.2 1.0 OD2 A:ASP240 4.0 75.5 1.0 OD1 A:ASP240 4.1 74.6 1.0 OD1 A:ASP138 4.3 76.7 1.0 OD2 A:ASP138 4.3 75.8 1.0 CA A:THR207 4.5 81.5 1.0 CG A:ASP240 4.5 74.3 1.0 CA A:SER140 4.5 62.6 1.0 C A:SER140 4.6 73.0 1.0 N A:THR207 4.7 88.4 1.0 CG A:ASP138 4.7 71.4 1.0 N A:GLY141 4.7 88.2 1.0 N A:ILE143 4.7 73.2 1.0 CB A:LYS242 4.7 90.2 1.0 C A:SER142 4.8 78.4 1.0 C A:LYS242 4.8 83.4 1.0

Magnesium binding site 2 out of 2 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg707 b:59.4 occ:1.00 OG B:SER116 2.0 39.4 1.0 O B:HOH806 2.1 50.6 1.0 O B:HOH807 2.1 57.1 1.0 OE1 A:GLU318 2.1 50.0 1.0 OG B:SER114 2.2 35.4 1.0 OE2 B:GLU212 2.2 56.0 1.0 CB B:SER114 3.3 35.6 1.0 CD A:GLU318 3.3 42.9 1.0 CB B:SER116 3.3 46.6 1.0 CD B:GLU212 3.3 47.2 1.0 OD1 B:ASP242 3.4 49.8 1.0 CG B:GLU212 3.9 37.5 1.0 CG A:GLU318 4.0 42.5 1.0 CB A:GLU318 4.1 42.1 1.0 OD2 B:ASP112 4.1 61.2 1.0 O B:ALA210 4.1 37.0 1.0 OE2 A:GLU318 4.2 50.2 1.0 N B:SER116 4.2 46.7 1.0 CA B:SER116 4.3 51.0 1.0 OE1 B:GLU212 4.4 56.7 1.0 CB B:ASP243 4.4 59.5 1.0 CG B:ASP242 4.4 54.7 1.0 CA B:SER114 4.5 35.4 1.0 OD2 B:ASP242 4.5 54.4 1.0 OD2 B:ASP243 4.6 70.3 1.0 OD1 B:ASP112 4.6 47.7 1.0 C B:SER114 4.7 35.2 1.0 CG B:ASP112 4.7 51.3 1.0 CG B:MET117 4.9 63.5 1.0 C B:SER116 5.0 53.8 1.0 O B:SER114 5.0 40.7 1.0 N B:TYR115 5.0 35.7 1.0 N B:MET117 5.0 44.5 1.0

M.Sen, K.Yuki, T.A.Springer. An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, Alpha X Beta 2. J.Cell Biol. V. 203 629 2013.
ISSN: ISSN 0021-9525
PubMed: 24385486
DOI: 10.1083/JCB.201308083