Magnesium in PDB 4um9: Crystal Structure of Alpha V Beta 6 with Peptide

The structure of Crystal Structure of Alpha V Beta 6 with Peptide, PDB code: 4um9 was solved by X.Dong, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	185.020, 168.090, 101.800, 90.00, 98.95, 90.00
R / Rfree (%)	22.2 / 26.6

The structure of Crystal Structure of Alpha V Beta 6 with Peptide also contains other interesting chemical elements:

Calcium

(Ca)

12 atoms

The binding sites of Magnesium atom in the Crystal Structure of Alpha V Beta 6 with Peptide (pdb code 4um9). 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 Alpha V Beta 6 with Peptide, PDB code: 4um9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Alpha V Beta 6 with 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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:62.0 occ:1.00 O B:HOH4014 2.1 44.6 1.0 O B:HOH4027 2.1 48.1 1.0 OE2 B:GLU223 2.1 52.5 1.0 O B:HOH4013 2.1 36.5 1.0 OG B:SER125 2.1 85.1 1.0 OD1 E:ASP243 2.2 58.8 1.0 CB B:SER125 2.2 50.5 1.0 CG E:ASP243 3.0 57.3 1.0 CD B:GLU223 3.3 38.2 1.0 OG B:SER127 3.6 72.7 1.0 OD2 E:ASP243 3.6 61.7 1.0 CA B:SER125 3.7 39.3 1.0 CG B:GLU223 3.9 32.6 1.0 CB E:ASP243 4.0 55.6 1.0 OD1 B:ASP123 4.2 67.6 1.0 OD2 B:ASP123 4.2 56.0 1.0 C B:SER125 4.2 42.7 1.0 OE1 B:GLU223 4.3 53.2 1.0 N B:ALA126 4.4 52.0 1.0 O B:HOH4015 4.4 68.3 1.0 CA E:ASP243 4.5 46.9 1.0 O B:THR221 4.5 48.2 1.0 ND2 B:ASN218 4.5 39.5 1.0 CG B:ASP123 4.6 63.9 1.0 N B:SER125 4.6 42.8 1.0 N B:SER127 4.6 84.3 1.0 CB B:SER127 4.7 58.3 1.0 OD1 B:ASP254 4.7 59.8 1.0 O E:ASP243 4.8 69.7 1.0 CB B:ALA255 4.9 28.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Alpha V Beta 6 with 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 Alpha V Beta 6 with Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:81.6 occ:1.00 O D:HOH4005 2.1 91.3 1.0 O D:HOH4011 2.1 66.0 1.0 O D:HOH4004 2.1 49.8 1.0 OG D:SER125 2.1 80.4 1.0 OD1 F:ASP243 2.1 62.5 1.0 OE2 D:GLU223 2.1 56.3 1.0 CB D:SER125 2.4 61.2 1.0 CD D:GLU223 3.2 48.1 1.0 CG F:ASP243 3.4 44.8 1.0 OG D:SER127 3.4 76.2 1.0 OD2 D:ASP123 3.6 79.7 1.0 CG D:GLU223 3.7 47.8 1.0 CA D:SER125 3.9 49.2 1.0 OD2 F:ASP243 4.2 49.9 1.0 OD1 D:ASP254 4.3 76.8 1.0 OE1 D:GLU223 4.3 44.5 1.0 CB F:ASP243 4.3 38.8 1.0 CG D:ASP123 4.4 64.0 1.0 OD1 D:ASP123 4.4 69.8 1.0 CB D:ALA255 4.4 38.0 1.0 C D:SER125 4.5 49.6 1.0 O D:THR221 4.5 57.3 1.0 CB D:SER127 4.6 67.4 1.0 N D:SER125 4.7 52.5 1.0 N D:ALA126 4.7 53.6 1.0 CA F:ASP243 4.7 46.9 1.0 N D:SER127 4.8 76.2 1.0 O F:ASP243 5.0 68.5 1.0

X.Dong, N.E.Hudson, C.Lu, T.A.Springer. Structural Determinants of Integrin Beta-Subunit Specificity For Latent Tgf-Beta Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25383667
DOI: 10.1038/NSMB.2905