Magnesium in PDB 3vi3: Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)

The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form), PDB code: 3vi3 was solved by M.Nagae, T.Nogi, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.00 / 2.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	92.956, 102.805, 125.079, 76.10, 70.19, 71.28
R / Rfree (%)	20.7 / 26.7

The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) (pdb code 3vi3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form), PDB code: 3vi3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2003 b:62.1 occ:1.00 OE1 B:GLU229 1.9 64.2 1.0 OG B:SER132 2.1 65.6 1.0 CB B:SER132 3.0 64.2 1.0 CD B:GLU229 3.2 63.3 1.0 OG B:SER134 3.9 60.9 1.0 CG B:GLU229 4.0 59.9 1.0 OE2 B:GLU229 4.1 66.2 1.0 OD1 B:ASP130 4.1 59.9 1.0 OD2 B:ASP130 4.2 61.0 1.0 O B:SER227 4.4 56.4 1.0 CA B:SER132 4.4 62.3 1.0 OD1 B:ASP259 4.4 65.8 1.0 CB B:ALA260 4.5 50.9 1.0 ND2 B:ASN224 4.5 68.1 1.0 CG B:ASP130 4.6 58.9 1.0 C B:SER132 4.7 64.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of ALPHA5BETA1 Integrin Headpiece (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2003 b:57.2 occ:1.00 OE1 D:GLU229 1.9 55.7 1.0 OG D:SER132 2.1 63.9 1.0 CB D:SER132 3.0 59.3 1.0 CD D:GLU229 3.2 53.4 1.0 OG D:SER134 3.9 69.2 1.0 OE2 D:GLU229 4.0 54.5 1.0 CG D:GLU229 4.1 52.4 1.0 O D:SER227 4.1 48.3 1.0 OD1 D:ASP130 4.1 61.0 1.0 OD1 D:ASP259 4.3 66.3 1.0 CA D:SER132 4.4 55.3 1.0 OD2 D:ASP130 4.4 60.7 1.0 CB D:ALA260 4.5 49.8 1.0 ND2 D:ASN224 4.7 55.0 1.0 CG D:ASP130 4.7 59.2 1.0 C D:SER132 4.8 56.2 1.0

M.Nagae, S.Re, E.Mihara, T.Nogi, Y.Sugita, J.Takagi. Crystal Structure of ALPHA5BETA1 Integrin Ectodomain: Atomic Details of the Fibronectin Receptor J.Cell Biol. V. 197 131 2012.
ISSN: ISSN 0021-9525
PubMed: 22451694
DOI: 10.1083/JCB.201111077