Magnesium in PDB 6om2: Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide

The structure of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide, PDB code: 6om2 was solved by J.C.Wang, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.43 / 2.77
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	161.190, 53.850, 176.620, 90.00, 111.47, 90.00
R / Rfree (%)	25.1 / 28.2

The structure of Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide also contains other interesting chemical elements:

Calcium

(Ca)

10 atoms

The binding sites of Magnesium atom in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide (pdb code 6om2). 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 Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide, PDB code: 6om2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand 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 Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2001 b:0.3 occ:1.00 OE2 B:GLU212 2.1 89.0 1.0 OD1 E:ASP217 2.1 1.0 1.0 OG B:SER114 2.1 0.1 1.0 OG B:SER116 2.1 0.1 1.0 O B:HOH3203 2.1 0.8 1.0 O B:HOH3206 2.2 91.2 1.0 HG B:SER116 2.5 0.9 1.0 HB2 B:SER114 2.6 0.9 1.0 HG B:SER114 2.8 0.5 1.0 CB B:SER114 2.8 0.3 1.0 H B:SER116 3.0 0.3 1.0 CD B:GLU212 3.2 87.0 1.0 CG E:ASP217 3.2 0.6 1.0 HB3 B:SER114 3.2 0.9 1.0 CB B:SER116 3.3 1.0 1.0 HG3 B:GLU212 3.4 0.2 1.0 HB3 B:SER116 3.4 0.2 1.0 CG B:GLU212 3.7 87.7 1.0 N B:SER116 3.8 0.4 1.0 HG2 B:GLU212 3.9 0.2 1.0 OD2 B:ASP112 3.9 0.8 1.0 HB2 B:SER116 4.0 0.2 1.0 CB E:ASP217 4.0 0.3 1.0 OD2 E:ASP217 4.1 0.1 1.0 HD21 B:ASN207 4.1 0.5 1.0 CA B:SER116 4.1 0.1 1.0 HG2 B:MET117 4.1 1.0 1.0 CA B:SER114 4.1 0.0 1.0 H B:ALA115 4.2 0.9 1.0 HG3 B:GLN244 4.2 0.7 1.0 OE1 B:GLU212 4.2 84.9 1.0 OD1 B:ASP243 4.2 84.3 1.0 O B:THR210 4.2 94.2 1.0 HB2 B:GLN244 4.3 0.4 1.0 N B:ALA115 4.3 0.3 1.0 C B:SER114 4.3 0.0 1.0 CA E:ASP217 4.4 0.6 1.0 H B:MET117 4.4 0.1 1.0 H B:SER114 4.7 0.1 1.0 HA B:SER114 4.7 0.6 1.0 CG B:ASP112 4.8 0.2 1.0 OD1 B:ASP112 4.8 0.3 1.0 ND2 B:ASN207 4.8 90.4 1.0 N B:MET117 4.8 0.8 1.0 C B:SER116 4.8 0.1 1.0 HA B:THR210 4.9 0.8 1.0 C B:ALA115 4.9 0.4 1.0 CG B:GLN244 4.9 94.8 1.0 HA B:SER116 4.9 0.9 1.0 HD22 B:ASN207 5.0 0.5 1.0 N B:SER114 5.0 0.4 1.0 O E:ASP217 5.0 1.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand 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 Atypical Integrin Alphav BETA8 with Protgf-BETA1 Ligand Peptide within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg3208 b:0.6 occ:1.00 OD1 F:ASP217 2.1 0.9 1.0 HG D:SER114 2.1 0.6 1.0 OE2 D:GLU212 2.1 0.4 1.0 OG D:SER114 2.1 0.5 1.0 OG D:SER116 2.1 0.3 1.0 O D:HOH3303 2.2 0.1 1.0 O D:HOH3309 2.3 85.4 1.0 HG D:SER116 2.5 0.1 1.0 HB2 D:SER114 2.7 0.8 1.0 CB D:SER114 2.9 99.0 1.0 H D:SER116 3.2 0.3 1.0 CD D:GLU212 3.2 0.2 1.0 CG F:ASP217 3.2 0.3 1.0 HB3 D:SER114 3.3 0.8 1.0 HG3 D:GLU212 3.3 0.2 1.0 CB D:SER116 3.4 0.6 1.0 HB3 D:SER116 3.5 0.9 1.0 CG D:GLU212 3.7 0.7 1.0 OD2 D:ASP112 3.8 0.4 1.0 HG2 D:GLU212 3.8 0.2 1.0 N D:SER116 3.9 1.0 1.0 OD1 D:ASP243 4.0 95.3 1.0 HB2 D:SER116 4.0 0.9 1.0 OD2 F:ASP217 4.0 0.2 1.0 CB F:ASP217 4.1 0.7 1.0 HG3 D:GLN244 4.2 0.8 1.0 HB2 D:GLN244 4.2 0.8 1.0 CA D:SER116 4.2 0.2 1.0 CA D:SER114 4.2 97.3 1.0 OE1 D:GLU212 4.3 0.9 1.0 HD21 D:ASN207 4.3 0.6 1.0 O D:THR210 4.3 85.1 1.0 HG2 D:MET117 4.3 0.0 1.0 H D:ALA115 4.3 0.4 1.0 H D:MET117 4.5 0.9 1.0 C D:SER114 4.5 98.8 1.0 N D:ALA115 4.5 0.0 1.0 CA F:ASP217 4.6 0.0 1.0 CG D:ASP112 4.7 0.6 1.0 H D:SER114 4.7 0.7 1.0 OD1 D:ASP112 4.8 0.5 1.0 OD2 D:ASP243 4.8 99.2 1.0 CG D:ASP243 4.8 97.5 1.0 CG D:GLN244 4.8 0.1 1.0 HA D:SER114 4.8 0.8 1.0 N D:MET117 4.9 98.3 1.0 C D:SER116 4.9 0.5 1.0 CB D:GLN244 4.9 99.0 1.0 HG2 D:GLN244 4.9 0.8 1.0 HA D:THR210 5.0 1.0 1.0

J.C.Wang, R.E.Iacob, J.R.Engen, T.A.Springer. Crystal Structure of Atypical Integrin Alphav BETA8 Nat Commun 2019.
ISSN: ESSN 2041-1723