Magnesium in PDB 5hdb: Integrin ALPHAIIBBETA3 in Complex with Ro-435054

The structure of Integrin ALPHAIIBBETA3 in Complex with Ro-435054, PDB code: 5hdb was solved by F.Y.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	259.346, 144.439, 104.901, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.8

The structure of Integrin ALPHAIIBBETA3 in Complex with Ro-435054 also contains other interesting chemical elements:

Calcium	(Ca)	11 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Magnesium atom in the Integrin ALPHAIIBBETA3 in Complex with Ro-435054 (pdb code 5hdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Integrin ALPHAIIBBETA3 in Complex with Ro-435054, PDB code: 5hdb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Integrin ALPHAIIBBETA3 in Complex with Ro-435054


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Integrin ALPHAIIBBETA3 in Complex with Ro-435054 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:31.4 occ:1.00 O19 B:5YB2011 2.0 34.3 1.0 OG B:SER121 2.1 45.6 1.0 O B:HOH2125 2.1 31.4 1.0 O B:HOH2116 2.1 31.4 1.0 OG B:SER123 2.1 48.0 1.0 OE2 B:GLU220 2.1 44.4 1.0 HB2 B:SER121 2.5 54.5 1.0 CB B:SER121 2.8 45.4 1.0 H B:SER123 3.0 60.1 1.0 HB3 B:SER123 3.2 59.7 1.0 CB B:SER123 3.2 49.7 1.0 CD B:GLU220 3.2 44.0 1.0 C17 B:5YB2011 3.2 48.0 1.0 HB3 B:SER121 3.3 54.5 1.0 HG3 B:GLU220 3.3 63.9 1.0 CG B:GLU220 3.7 53.2 1.0 N B:SER123 3.8 50.1 1.0 H151 B:5YB2011 3.8 77.1 1.0 HB2 B:SER123 3.9 59.7 1.0 O18 B:5YB2011 3.9 41.4 1.0 HD21 B:ASN215 3.9 68.6 1.0 HG2 B:GLU220 3.9 63.9 1.0 OD2 B:ASP119 4.0 44.1 1.0 CA B:SER121 4.1 46.2 1.0 OD1 B:ASP251 4.1 48.1 1.0 CA B:SER123 4.1 50.8 1.0 HB2 B:ALA252 4.2 74.2 1.0 C B:SER121 4.2 47.9 1.0 HB3 B:ALA252 4.2 74.2 1.0 OE1 B:GLU220 4.3 42.7 1.0 C16 B:5YB2011 4.3 63.1 1.0 HG2 B:MET124 4.4 57.4 1.0 OD1 B:ASP119 4.4 47.9 1.0 H B:TYR122 4.4 58.5 1.0 N B:TYR122 4.4 48.7 1.0 C15 B:5YB2011 4.5 64.2 1.0 O B:ALA218 4.5 46.1 1.0 H161 B:5YB2011 4.5 75.8 1.0 H B:MET124 4.5 60.3 1.0 H B:SER121 4.6 54.9 1.0 CG B:ASP119 4.6 44.1 1.0 CB B:ALA252 4.6 61.9 1.0 ND2 B:ASN215 4.7 57.2 1.0 O B:SER121 4.7 48.5 1.0 O B:HOH2247 4.7 37.2 1.0 HA B:SER121 4.7 55.5 1.0 HD22 B:ASN215 4.8 68.6 1.0 C13 B:5YB2011 4.8 64.3 1.0 N B:SER121 4.8 45.8 1.0 HA B:SER123 4.8 61.0 1.0 C B:SER123 4.9 51.1 1.0 N B:MET124 4.9 50.2 1.0 C B:TYR122 5.0 51.1 1.0 HB1 B:ALA252 5.0 74.2 1.0 HA B:ALA218 5.0 54.5 1.0

Magnesium binding site 2 out of 2 in the Integrin ALPHAIIBBETA3 in Complex with Ro-435054


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Integrin ALPHAIIBBETA3 in Complex with Ro-435054 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:47.2 occ:1.00 O19 D:5YB501 2.1 68.6 1.0 OG D:SER121 2.1 78.5 1.0 OE2 D:GLU220 2.1 71.1 1.0 O D:HOH2148 2.1 41.5 1.0 O D:HOH2108 2.1 50.9 1.0 OG D:SER123 2.1 83.4 1.0 HB2 D:SER121 2.9 92.5 1.0 CB D:SER121 3.0 77.1 1.0 O D:HOH2117 3.1 94.2 1.0 CD D:GLU220 3.3 69.5 1.0 H D:SER123 3.3 0.7 1.0 C17 D:5YB501 3.3 69.5 1.0 HB3 D:SER121 3.4 92.5 1.0 CB D:SER123 3.5 86.5 1.0 HG3 D:GLU220 3.6 86.9 1.0 H151 D:5YB501 3.6 78.7 1.0 OD1 D:ASP251 3.9 88.9 1.0 HB3 D:SER123 3.9 0.8 1.0 CG D:GLU220 3.9 72.5 1.0 HB2 D:SER123 4.0 0.8 1.0 HD21 D:ASN215 4.0 0.1 1.0 HB3 D:ALA252 4.0 1.0 1.0 HB2 D:ALA252 4.0 1.0 1.0 O18 D:5YB501 4.1 66.2 1.0 HG2 D:GLU220 4.1 86.9 1.0 N D:SER123 4.1 85.5 1.0 C15 D:5YB501 4.3 65.6 1.0 OD2 D:ASP119 4.3 76.1 1.0 OE1 D:GLU220 4.3 67.1 1.0 CA D:SER121 4.3 78.3 1.0 C16 D:5YB501 4.3 71.5 1.0 O D:ALA218 4.4 69.0 1.0 CA D:SER123 4.4 87.5 1.0 C D:SER121 4.5 81.1 1.0 CB D:ALA252 4.5 90.0 1.0 H D:TYR122 4.5 98.2 1.0 HG2 D:MET124 4.5 0.1 1.0 C13 D:5YB501 4.6 77.3 1.0 OD1 D:ASP119 4.6 76.4 1.0 H161 D:5YB501 4.6 85.8 1.0 N D:TYR122 4.6 81.8 1.0 H D:SER121 4.8 93.5 1.0 ND2 D:ASN215 4.8 90.1 1.0 HA D:ALA218 4.8 85.7 1.0 CG D:ASP251 4.9 85.5 1.0 CG D:ASP119 4.9 76.2 1.0 HB1 D:ALA252 4.9 1.0 1.0 HA D:SER121 4.9 93.9 1.0 O14 D:5YB501 4.9 76.9 1.0 O D:HOH2194 5.0 69.1 1.0 HD22 D:ASN215 5.0 0.1 1.0 O D:SER121 5.0 82.8 1.0

F.Y.Lin, J.Zhu, E.T.Eng, N.E.Hudson, T.A.Springer. Beta-Subunit Binding Is Sufficient For Ligands to Open the Integrin Alpha Iib Beta 3 Headpiece. J.Biol.Chem. V. 291 4537 2016.
ISSN: ESSN 1083-351X
PubMed: 26631735
DOI: 10.1074/JBC.M115.705624