Magnesium in PDB 3zdy: Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex

The structure of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex, PDB code: 3zdy was solved by J.H.Zhu, J.Q.Zhu, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 2.45
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	257.760, 145.250, 106.060, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 21.6

The structure of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Magnesium atom in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex (pdb code 3zdy). 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 Alphaiib BETA3 Headpiece and Rgd Peptide Complex, PDB code: 3zdy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:33.8 occ:1.00 O B:HOH3020 2.1 22.2 1.0 OD1 I:ASP495 2.1 68.0 1.0 O B:HOH3021 2.1 36.7 1.0 O B:HOH3079 2.1 23.4 1.0 OE2 B:GLU220 2.1 35.3 1.0 OG B:SER121 2.1 38.1 1.0 HB2 B:SER121 2.6 35.5 1.0 CB B:SER121 2.8 29.6 1.0 CG I:ASP495 3.1 69.6 1.0 HB3 B:SER121 3.1 35.5 1.0 CD B:GLU220 3.2 32.8 1.0 HA I:ASP495 3.3 99.0 1.0 HG3 B:GLU220 3.4 38.7 1.0 HG B:SER123 3.7 66.3 1.0 HD22 B:ASN215 3.8 36.6 1.0 CG B:GLU220 3.8 32.2 1.0 OG B:SER123 3.8 55.3 1.0 HB2 I:ASP495 3.8 94.0 1.0 CB I:ASP495 3.9 78.3 1.0 OD2 I:ASP495 3.9 62.8 1.0 HG2 B:GLU220 3.9 38.7 1.0 H B:SER123 3.9 43.9 1.0 CA I:ASP495 4.0 82.5 1.0 CA B:SER121 4.2 31.3 1.0 H B:TYR122 4.2 32.1 1.0 O B:ALA218 4.2 34.2 1.0 OE1 B:GLU220 4.3 37.7 1.0 HB3 B:ALA252 4.3 26.7 1.0 OD2 B:ASP119 4.4 27.0 1.0 ND2 B:ASN215 4.4 30.5 1.0 OD1 B:ASP119 4.5 26.4 1.0 HD21 B:ASN215 4.5 36.6 1.0 HB1 B:ALA252 4.6 26.7 1.0 C B:SER121 4.6 32.9 1.0 N B:TYR122 4.6 26.8 1.0 HB3 B:SER123 4.6 55.9 1.0 HA B:ALA218 4.6 34.5 1.0 H B:SER121 4.7 32.6 1.0 OD1 B:ASP251 4.7 39.5 1.0 H I:SER496 4.7 97.5 1.0 HB3 I:ASP495 4.8 94.0 1.0 HA B:SER121 4.8 37.6 1.0 O I:HOH3005 4.8 48.8 1.0 CB B:SER123 4.8 46.6 1.0 N B:SER123 4.8 36.6 1.0 CB B:ALA252 4.8 22.3 1.0 C I:ASP495 4.9 84.3 1.0 CG B:ASP119 4.9 29.9 1.0 N B:SER121 5.0 27.2 1.0 HG2 B:MET124 5.0 38.7 1.0

Magnesium binding site 2 out of 2 in the Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Integrin Alphaiib BETA3 Headpiece and Rgd Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:50.2 occ:1.00 HB2 D:SER121 2.1 46.0 1.0 OD1 J:ASP495 2.1 70.5 1.0 O D:HOH3016 2.1 35.0 1.0 O D:HOH3049 2.1 39.5 1.0 O D:HOH3017 2.1 38.1 1.0 OE2 D:GLU220 2.1 46.0 1.0 OG D:SER121 2.2 38.9 1.0 CB D:SER121 2.4 38.3 1.0 HB3 D:SER121 2.6 46.0 1.0 CG J:ASP495 3.2 84.9 1.0 HA J:ASP495 3.2 0.3 1.0 CD D:GLU220 3.3 46.1 1.0 HG3 D:GLU220 3.7 53.7 1.0 HD22 D:ASN215 3.7 52.4 1.0 OD2 J:ASP495 3.8 74.7 1.0 CA D:SER121 3.9 41.1 1.0 CG D:GLU220 4.0 44.8 1.0 HG D:SER123 4.0 58.4 1.0 CA J:ASP495 4.0 97.7 1.0 OG D:SER123 4.1 48.6 1.0 H D:SER123 4.1 60.8 1.0 H D:TYR122 4.1 53.8 1.0 OD2 D:ASP119 4.2 37.0 1.0 O J:HOH3001 4.2 77.3 1.0 CB J:ASP495 4.2 94.2 1.0 HG2 D:GLU220 4.2 53.7 1.0 OE1 D:GLU220 4.3 42.5 1.0 H D:SER121 4.3 44.2 1.0 OD1 D:ASP119 4.4 41.2 1.0 O J:ASP495 4.4 0.6 1.0 C D:SER121 4.4 43.8 1.0 HA D:SER121 4.4 49.4 1.0 ND2 D:ASN215 4.4 43.7 1.0 N D:TYR122 4.5 44.8 1.0 HD21 D:ASN215 4.6 52.4 1.0 HB3 D:ALA252 4.6 46.6 1.0 OD1 D:ASP251 4.6 43.6 1.0 N D:SER121 4.6 36.9 1.0 HB2 J:ASP495 4.7 0.1 1.0 C J:ASP495 4.7 0.2 1.0 HB1 D:ALA252 4.7 46.6 1.0 CG D:ASP119 4.7 40.4 1.0 O D:ALA218 4.7 44.9 1.0 HB3 J:ASP495 4.9 0.1 1.0 HG2 D:MET124 4.9 47.9 1.0 HB3 D:SER123 4.9 53.5 1.0 N D:SER123 5.0 50.7 1.0

J.Zhu, J.Zhu, T.A.Springer. Complete Integrin Headpiece Opening in Eight Steps. J.Cell Biol. V. 201 1053 2013.
ISSN: ISSN 0021-9525
PubMed: 23798730
DOI: 10.1083/JCB.201212037