Magnesium in PDB 2vc2: Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758, PDB code: 2vc2 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)	42.72 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.151, 149.151, 176.217, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 21.7

The structure of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 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 L-739758 (pdb code 2vc2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758, PDB code: 2vc2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


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 L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1460 b:2.0 occ:1.00 O A:HOH4023 2.7 2.0 1.0 OD1 A:ASP232 3.0 2.0 1.0 OD2 A:ASP232 3.1 2.0 1.0 O A:HOH4020 3.3 2.0 1.0 CG A:ASP232 3.4 2.0 1.0 CB B:ALA218 4.0 2.2 1.0 CB A:PHE231 4.2 2.0 1.0 CD1 A:PHE231 4.4 2.0 1.0 CG A:PHE231 4.5 2.0 1.0 C7 B:1801477 4.6 2.0 1.0 N A:ASP232 4.7 2.0 1.0 C8 B:1801477 4.7 2.0 1.0 C17 B:1801477 4.7 2.0 1.0 O A:TYR190 4.8 2.4 1.0 CB A:ASP232 4.8 2.0 1.0 N B:ALA218 4.9 2.0 1.0 C6 B:1801477 4.9 2.0 1.0 C9 B:1801477 4.9 2.0 1.0 CA A:PHE231 5.0 2.0 1.0

Magnesium binding site 2 out of 2 in the Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Re-Refinement of Integrin ALPHAIIBBETA3 Headpiece Bound to Antagonist L-739758 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:2.0 occ:1.00 O B:HOH4006 1.9 2.0 1.0 OE1 B:GLU220 1.9 3.6 1.0 O1 B:1801477 2.1 2.0 1.0 OG B:SER123 2.2 2.0 1.0 OG B:SER121 2.4 2.0 1.0 O B:HOH4024 2.5 2.0 1.0 CD B:GLU220 3.0 2.5 1.0 C1 B:1801477 3.2 2.0 1.0 CB B:SER123 3.2 2.0 1.0 CB B:SER121 3.2 2.0 1.0 CG B:GLU220 3.7 2.0 1.0 O B:ALA218 3.8 2.0 1.0 C2 B:1801477 3.9 2.0 1.0 C3 B:1801477 4.0 2.0 1.0 OE2 B:GLU220 4.1 2.4 1.0 N B:SER123 4.1 2.0 1.0 O2 B:1801477 4.1 2.0 1.0 O3 B:1801477 4.1 2.0 1.0 OD1 B:ASP251 4.2 6.5 1.0 CA B:SER123 4.3 2.0 1.0 ND2 B:ASN215 4.4 2.0 1.0 CB B:ALA252 4.5 4.1 1.0 CA B:SER121 4.5 2.0 1.0 C B:SER121 4.7 2.0 1.0 OD2 B:ASP119 4.7 2.0 1.0 OD1 B:ASP119 4.7 2.0 1.0 C B:ALA218 4.7 2.0 1.0 N B:TYR122 4.8 2.0 1.0 CA B:ALA218 4.8 2.0 1.0 O B:ASP217 4.9 2.0 1.0 N1 B:1801477 5.0 2.0 1.0 C4 B:1801477 5.0 2.0 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