Magnesium in PDB 2vdn: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide, PDB code: 2vdn 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)	47.19 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.593, 149.593, 175.683, 90.00, 90.00, 120.00
R / Rfree (%)	16.3 / 21.3

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist Eptifibatide 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 Eptifibatide (pdb code 2vdn). 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 Eptifibatide, PDB code: 2vdn:

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


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 Eptifibatide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:50.9 occ:1.00 OE1 B:GLU220 1.9 51.6 1.0 O B:HOH4005 2.0 40.4 1.0 OD2 C:ASP4 2.1 49.0 1.0 OG B:SER123 2.1 51.2 1.0 O B:HOH4035 2.1 35.0 1.0 OG B:SER121 2.4 46.8 1.0 CD B:GLU220 3.1 52.4 1.0 CG C:ASP4 3.1 48.0 1.0 CB B:SER123 3.1 52.4 1.0 CB B:SER121 3.3 47.4 1.0 CG B:GLU220 3.6 51.8 1.0 N B:SER123 3.8 53.3 1.0 CB C:ASP4 3.8 46.3 1.0 O B:ALA218 4.0 49.2 1.0 OD1 B:ASP251 4.0 53.9 1.0 OD1 C:ASP4 4.0 47.5 1.0 CA B:SER123 4.1 54.4 1.0 CA C:ASP4 4.1 46.8 1.0 OE2 B:GLU220 4.1 51.8 1.0 O C:HOH4002 4.3 40.7 1.0 N B:TYR122 4.5 52.0 1.0 CA B:SER121 4.6 48.4 1.0 OD2 B:ASP119 4.6 47.4 1.0 OD1 B:ASP119 4.6 47.3 1.0 C B:SER121 4.6 50.1 1.0 C C:ASP4 4.7 46.5 1.0 ND2 B:ASN215 4.7 48.4 1.0 CB B:ALA252 4.7 50.1 1.0 C B:SER123 4.9 56.7 1.0 N B:MET124 4.9 56.7 1.0 C B:ALA218 4.9 50.0 1.0 N C:TRP5 5.0 45.8 1.0 CG B:ASP251 5.0 53.8 1.0 C B:TYR122 5.0 53.2 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