Magnesium in PDB 2vdm: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban, PDB code: 2vdm was solved by T.A.Springer, J.Zhu, T.Xiao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.23 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	148.577, 148.577, 177.239, 90.00, 90.00, 120.00
R / Rfree (%)	16.7 / 20.6

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban also contains other interesting chemical elements:

Calcium

(Ca)

6 atoms

The binding sites of Magnesium atom in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban (pdb code 2vdm). 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 ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban, PDB code: 2vdm:

Magnesium binding site 1 out of 1 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban


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 ALPHAIIBBETA3 Headpiece Bound to Antagonist Tirofiban within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:37.6 occ:1.00 OE1 B:GLU220 2.1 53.1 1.0 OG B:SER121 2.1 42.6 1.0 OG B:SER123 2.1 53.1 1.0 O B:HOH4028 2.1 34.0 1.0 O B:HOH4008 2.2 40.4 1.0 OXT B:AGG1462 2.4 43.4 1.0 CD B:GLU220 3.1 52.2 1.0 CB B:SER121 3.2 44.6 1.0 CB B:SER123 3.2 53.6 1.0 C B:AGG1462 3.4 42.5 1.0 CG B:GLU220 3.5 50.3 1.0 OD1 B:ASP251 3.8 52.9 1.0 N B:SER123 4.0 51.9 1.0 O B:AGG1462 4.1 40.9 1.0 OD1 B:ASP119 4.1 47.9 1.0 O B:ALA218 4.2 50.5 1.0 CA B:SER123 4.2 53.0 1.0 OE2 B:GLU220 4.2 50.8 1.0 OD2 B:ASP119 4.4 50.1 1.0 CA B:AGG1462 4.4 42.0 1.0 O B:HOH4002 4.4 25.2 1.0 CB B:ALA252 4.5 50.4 1.0 CA B:SER121 4.5 46.0 1.0 CB B:AGG1462 4.5 42.7 1.0 C B:SER121 4.6 47.7 1.0 CG B:ASP119 4.7 49.4 1.0 N B:TYR122 4.8 49.7 1.0 ND2 B:ASN215 4.8 43.4 1.0 N B:MET124 4.8 51.7 1.0 C B:SER123 4.9 52.0 1.0 CG B:MET124 4.9 50.7 1.0 CG B:ASP251 4.9 52.3 1.0 O B:SER121 4.9 48.8 1.0 CB B:GLU220 5.0 49.6 1.0

T.A.Springer, J.Zhu, T.Xiao. Structural Basis For Distinctive Recognition of Fibrinogen Gammac Peptide By the Platelet Integrin ALPHAIIBBETA3. J.Cell Biol. V. 182 791 2008.
ISSN: ISSN 0021-9525
PubMed: 18710925
DOI: 10.1083/JCB.200801146