Magnesium in PDB 3nig: The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening

The structure of The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening, PDB code: 3nig 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)	48.49 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	260.670, 145.170, 104.440, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.2

The structure of The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Magnesium atom in the The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening (pdb code 3nig). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening, PDB code: 3nig:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:38.9 occ:1.00 O B:HOH1037 2.0 23.4 1.0 OE2 B:GLU220 2.2 28.0 1.0 O B:HOH1039 2.3 21.6 1.0 O B:HOH514 2.5 39.3 1.0 OG B:SER121 2.6 24.3 1.0 O B:HOH897 2.8 53.1 1.0 CB B:SER121 3.2 26.4 1.0 CD B:GLU220 3.2 25.2 1.0 CG B:GLU220 3.6 30.9 1.0 O B:HOH510 3.8 52.0 1.0 OG B:SER123 3.9 32.5 1.0 O B:HOH1038 4.0 50.6 1.0 O B:ALA218 4.3 27.6 1.0 OD1 B:ASP251 4.3 23.4 1.0 OE1 B:GLU220 4.3 24.6 1.0 OD2 B:ASP119 4.4 26.6 1.0 CB B:ALA252 4.4 19.8 1.0 O B:HOH473 4.5 15.0 1.0 OD1 B:ASP119 4.5 22.0 1.0 O B:HOH853 4.6 45.4 1.0 CA B:SER121 4.6 22.1 1.0 ND2 B:ASN215 4.8 24.9 1.0 CG B:ASP119 4.9 20.5 1.0 C B:SER121 5.0 30.5 1.0 N B:TYR122 5.0 30.4 1.0

Magnesium binding site 2 out of 2 in the The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Closed Headpiece of Integrin Iib 3 and Its Complex with An Iib 3 - Specific Antagonist That Does Not Induce Opening within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:42.9 occ:1.00 O D:HOH475 2.2 28.3 1.0 O D:HOH505 2.3 36.0 1.0 OE2 D:GLU220 2.3 39.2 1.0 O D:HOH864 2.4 59.4 1.0 O D:HOH1092 2.5 32.2 1.0 OG D:SER121 2.6 38.2 1.0 O D:HOH1179 3.2 64.9 1.0 CD D:GLU220 3.2 40.2 1.0 CB D:SER121 3.5 36.0 1.0 O D:HOH1090 3.5 57.9 1.0 CG D:GLU220 3.6 30.2 1.0 O D:HOH500 4.1 57.6 1.0 O D:ALA218 4.2 27.2 1.0 CB D:ALA252 4.2 25.5 1.0 OG D:SER123 4.2 42.3 1.0 OE1 D:GLU220 4.3 39.5 1.0 OD1 D:ASP251 4.3 33.9 1.0 OD2 D:ASP119 4.4 32.8 1.0 O D:HOH540 4.5 45.6 1.0 O D:HOH480 4.5 22.6 1.0 OD1 D:ASP119 4.6 37.0 1.0 ND2 D:ASN215 4.8 25.5 1.0 O D:HOH998 4.8 61.3 1.0 CA D:SER121 4.9 32.3 1.0 CG D:ASP119 4.9 33.4 1.0

J.Zhu, J.Zhu, A.Negri, D.Provasi, M.Filizola, B.S.Coller, T.A.Springer. Closed Headpiece of Integrin {Alpha}Iib{Beta}3 and Its Complex with An {Alpha}Iib{Beta}3-Specific Antagonist That Does Not Induce Opening. Blood V. 116 5050 2010.
ISSN: ISSN 0006-4971
PubMed: 20679525
DOI: 10.1182/BLOOD-2010-04-281154