Magnesium in PDB 3vi4: Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide

The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide, PDB code: 3vi4 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 (°)	92.805, 103.869, 125.262, 75.72, 70.16, 70.90
R / Rfree (%)	21.5 / 27.5

The structure of Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide (pdb code 3vi4). 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 in Complex with Rgd Peptide, PDB code: 3vi4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide


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 in Complex with Rgd Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:66.1 occ:1.00 OE1 B:GLU229 1.9 60.1 1.0 OD1 I:ASP5003 1.9 76.9 1.0 OG B:SER134 2.1 69.4 1.0 OG B:SER132 2.1 62.9 1.0 CD B:GLU229 3.1 55.4 1.0 CB B:SER132 3.2 65.9 1.0 CG I:ASP5003 3.2 78.6 1.0 CB B:SER134 3.4 70.0 1.0 CG B:GLU229 3.7 53.8 1.0 OD1 B:ASP130 3.8 65.9 1.0 OD1 B:ASP259 3.9 65.5 1.0 OD2 B:ASP130 3.9 71.0 1.0 OD2 I:ASP5003 4.0 75.4 1.0 CB B:ALA260 4.1 53.9 1.0 OE2 B:GLU229 4.1 58.7 1.0 O B:SER227 4.1 63.4 1.0 CB I:ASP5003 4.1 79.7 1.0 CG B:ASP130 4.3 66.4 1.0 N B:SER134 4.3 75.0 1.0 CA B:SER132 4.4 65.7 1.0 CA B:SER134 4.5 70.9 1.0 CA I:ASP5003 4.6 77.7 1.0 C B:SER132 4.6 67.7 1.0 ND2 B:ASN224 4.9 71.1 1.0 CG B:ASP259 4.9 62.4 1.0 N B:TYR133 5.0 70.5 1.0 O B:SER132 5.0 65.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of ALPHA5BETA1 Integrin Headpiece in Complex with Rgd Peptide


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 in Complex with Rgd Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg502 b:66.8 occ:1.00 OD1 G:ASP5003 1.9 78.3 1.0 OE1 D:GLU229 1.9 56.6 1.0 OG D:SER132 2.1 68.1 1.0 OG D:SER134 2.1 76.8 1.0 CD D:GLU229 3.1 51.8 1.0 CG G:ASP5003 3.1 82.0 1.0 CB D:SER132 3.3 65.2 1.0 CB D:SER134 3.5 74.0 1.0 OD1 D:ASP130 3.6 57.0 1.0 OD1 D:ASP259 3.7 65.2 1.0 CG D:GLU229 3.7 52.4 1.0 OD2 G:ASP5003 3.9 73.5 1.0 OE2 D:GLU229 4.1 53.3 1.0 OD2 D:ASP130 4.2 58.5 1.0 CB G:ASP5003 4.2 85.0 1.0 CB D:ALA260 4.2 54.4 1.0 O D:SER227 4.2 48.7 1.0 CG D:ASP130 4.3 56.5 1.0 N D:SER134 4.4 70.7 1.0 CA D:SER132 4.4 61.7 1.0 CA D:SER134 4.5 71.5 1.0 C D:SER132 4.5 62.8 1.0 O D:SER132 4.6 62.1 1.0 CA G:ASP5003 4.8 90.4 1.0 CG D:ASP259 4.8 64.1 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