Manganese in PDB 5ffo: Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta

The structure of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta, PDB code: 5ffo was solved by X.Dong, B.Zhao, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.72 / 3.49
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	81.440, 91.440, 131.030, 89.98, 86.25, 89.85
R / Rfree (%)	22.4 / 27.7

The structure of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta also contains other interesting chemical elements:

Calcium

(Ca)

8 atoms

The binding sites of Manganese atom in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta (pdb code 5ffo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta, PDB code: 5ffo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:0.5 occ:1.00 OD2 B:ASP131 2.2 0.0 1.0 OD1 B:ASP130 2.2 0.0 1.0 OD2 B:ASP130 2.2 0.4 1.0 OD2 B:ASP254 2.2 0.8 1.0 O B:HOH2103 2.2 84.9 1.0 O B:SER127 2.3 0.3 1.0 OD1 B:ASP131 2.3 0.9 1.0 CG B:ASP130 2.4 0.7 1.0 CG B:ASP131 2.5 0.6 1.0 CG B:ASP254 3.3 0.8 1.0 C B:SER127 3.5 0.1 1.0 CB B:ASP254 3.8 0.7 1.0 CB B:ASP130 3.9 0.8 1.0 CB B:ASP131 4.0 0.5 1.0 N B:ASP131 4.2 0.6 1.0 CA B:MET128 4.3 0.0 1.0 N B:MET128 4.3 0.7 1.0 OD1 B:ASP254 4.3 0.8 1.0 C B:ASP130 4.5 1.0 1.0 N B:ASP130 4.5 0.4 1.0 CA B:SER127 4.5 0.7 1.0 CA B:ASP130 4.5 0.6 1.0 CB B:SER127 4.6 0.2 1.0 CG2 D:THR220 4.7 0.3 1.0 CA B:ASP131 4.7 0.5 1.0 C B:MET128 4.8 0.6 1.0

Manganese binding site 2 out of 6 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:0.3 occ:1.00 OD1 D:ASP217 2.1 0.3 1.0 OE2 B:GLU223 2.1 0.1 1.0 OG B:SER125 2.2 0.3 1.0 O B:HOH2102 2.2 0.4 1.0 OG B:SER127 2.2 0.4 1.0 O B:HOH2101 2.2 0.7 1.0 CG D:ASP217 2.7 0.8 1.0 CB B:SER125 2.9 0.9 1.0 OD2 D:ASP217 3.1 0.1 1.0 CD B:GLU223 3.2 0.1 1.0 CB B:SER127 3.3 0.2 1.0 N B:SER127 3.5 0.3 1.0 CG B:GLU223 3.7 90.0 1.0 CB D:ASP217 3.8 0.5 1.0 O B:THR221 4.0 92.5 1.0 N B:ALA126 4.0 0.7 1.0 CA B:SER127 4.0 0.7 1.0 OD2 B:ASP123 4.0 0.7 1.0 OD1 B:ASP254 4.0 0.8 1.0 CA B:SER125 4.1 0.6 1.0 C B:SER125 4.1 0.9 1.0 OE1 B:GLU223 4.3 0.9 1.0 CB B:ALA255 4.4 95.6 1.0 CA D:ASP217 4.5 0.2 1.0 C B:ALA126 4.6 0.8 1.0 ND2 B:ASN218 4.6 0.8 1.0 C B:SER127 4.7 0.1 1.0 OD1 B:ASP123 4.8 0.4 1.0 O B:SER125 4.8 0.9 1.0 CA B:ALA126 4.8 0.4 1.0 CG B:ASP123 4.8 0.7 1.0 O D:ASP217 4.9 0.0 1.0 N B:SER125 5.0 0.0 1.0

Manganese binding site 3 out of 6 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:0.6 occ:1.00 O B:ASP220 2.1 94.4 1.0 OE2 B:GLU162 2.1 0.4 1.0 OD1 B:ASN218 2.2 0.9 1.0 OE1 B:GLU223 2.2 0.9 1.0 OD1 B:ASP220 2.2 0.2 1.0 O B:PRO222 2.4 81.0 1.0 CD B:GLU162 3.1 0.0 1.0 CG B:ASN218 3.1 0.9 1.0 CD B:GLU223 3.1 0.1 1.0 CG B:ASP220 3.3 86.5 1.0 C B:ASP220 3.3 96.0 1.0 C B:PRO222 3.4 79.2 1.0 CG B:GLU162 3.7 0.2 1.0 ND2 B:ASN218 3.7 0.8 1.0 OE2 B:GLU223 3.7 0.1 1.0 CA B:GLU223 3.8 88.0 1.0 OE1 B:GLU162 3.9 77.0 1.0 N B:ASP220 4.0 0.3 1.0 CA B:ASP220 4.0 0.4 1.0 OD2 B:ASP220 4.0 81.1 1.0 N B:GLU223 4.0 76.5 1.0 CB B:GLU162 4.2 91.7 1.0 C B:THR221 4.2 91.1 1.0 CG B:GLU223 4.2 90.0 1.0 CB B:ASN218 4.2 0.7 1.0 CB B:ASP220 4.2 91.5 1.0 O B:THR221 4.3 92.5 1.0 N B:PRO222 4.3 0.7 1.0 N B:THR221 4.4 97.3 1.0 CB B:GLU223 4.4 83.2 1.0 CA B:PRO222 4.5 79.4 1.0 NE2 B:HIS258 4.6 0.9 1.0 CA B:THR221 4.7 97.5 1.0 CD2 B:HIS258 4.7 68.2 1.0 CB D:ASP217 4.9 0.5 1.0 OD2 D:ASP217 4.9 0.1 1.0 C B:ILE219 5.0 0.1 1.0 N B:ILE219 5.0 1.0 1.0 C B:GLU223 5.0 73.0 1.0 O B:VAL161 5.0 92.0 1.0

Manganese binding site 4 out of 6 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn2001 b:0.1 occ:1.00 OD1 F:ASP130 2.2 1.0 1.0 OD2 F:ASP254 2.2 0.7 1.0 O F:SER127 2.2 0.4 1.0 OD2 F:ASP130 2.2 0.5 1.0 OD2 F:ASP131 2.2 0.7 1.0 CG F:ASP130 2.5 0.4 1.0 CG F:ASP131 3.1 0.2 1.0 CG F:ASP254 3.3 0.6 1.0 OD1 F:ASP131 3.3 0.4 1.0 C F:SER127 3.4 0.5 1.0 CB F:ASP254 3.9 0.4 1.0 CB F:ASP130 4.0 0.1 1.0 N F:MET128 4.2 1.0 1.0 CA F:MET128 4.3 1.0 1.0 OD1 F:ASP254 4.3 0.7 1.0 CA F:SER127 4.3 0.9 1.0 CB F:ASP131 4.4 0.6 1.0 CB F:SER127 4.4 0.2 1.0 N F:ASP131 4.5 0.1 1.0 N F:ASP130 4.6 0.5 1.0 CA F:ASP130 4.7 0.1 1.0 CG2 H:THR220 4.8 0.1 1.0 C F:ASP130 4.8 0.4 1.0 C F:MET128 4.8 0.1 1.0

Manganese binding site 5 out of 6 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn2002 b:0.7 occ:1.00 OE2 F:GLU223 2.1 0.4 1.0 OG F:SER127 2.2 0.6 1.0 OD1 H:ASP217 2.2 0.9 1.0 OG F:SER125 2.2 0.5 1.0 O F:HOH2101 2.2 0.7 1.0 O F:HOH2102 2.2 1.0 1.0 CG H:ASP217 2.9 0.2 1.0 CB F:SER125 2.9 0.2 1.0 CD F:GLU223 3.2 0.4 1.0 OD2 H:ASP217 3.3 0.1 1.0 CB F:SER127 3.3 0.2 1.0 CG F:GLU223 3.5 0.4 1.0 N F:SER127 3.6 0.6 1.0 OD2 F:ASP123 3.9 0.6 1.0 O F:THR221 3.9 0.2 1.0 CB H:ASP217 4.0 0.6 1.0 OD1 F:ASP254 4.0 0.7 1.0 CA F:SER127 4.1 0.9 1.0 N F:ALA126 4.1 0.0 1.0 CA F:SER125 4.2 0.4 1.0 C F:SER125 4.3 0.2 1.0 OE1 F:GLU223 4.3 0.5 1.0 CB F:ALA255 4.5 0.4 1.0 ND2 F:ASN218 4.6 0.9 1.0 CA H:ASP217 4.7 0.3 1.0 C F:ALA126 4.7 0.9 1.0 C F:SER127 4.8 0.5 1.0 CG F:ASP123 4.8 0.4 1.0 OD1 F:ASP123 4.9 0.8 1.0 O F:SER125 5.0 0.1 1.0 CA F:ALA126 5.0 0.8 1.0

Manganese binding site 6 out of 6 in the Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Integrin Alpha V Beta 6 in Complex with Pro-Tgf-Beta within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn2003 b:0.9 occ:1.00 OD1 F:ASP220 2.2 0.2 1.0 OE2 F:GLU162 2.2 0.3 1.0 O F:ASP220 2.2 0.9 1.0 OD1 F:ASN218 2.2 0.6 1.0 OE1 F:GLU223 2.2 0.5 1.0 O F:PRO222 2.3 0.3 1.0 CG F:ASN218 3.1 0.3 1.0 CD F:GLU162 3.2 0.3 1.0 CG F:ASP220 3.2 0.7 1.0 CD F:GLU223 3.2 0.4 1.0 C F:ASP220 3.3 0.1 1.0 C F:PRO222 3.4 0.9 1.0 CG F:GLU162 3.6 0.0 1.0 ND2 F:ASN218 3.8 0.9 1.0 OE2 F:GLU223 3.8 0.4 1.0 CA F:GLU223 3.9 0.8 1.0 OD2 F:ASP220 3.9 0.8 1.0 N F:ASP220 3.9 0.7 1.0 CA F:ASP220 4.0 0.9 1.0 N F:GLU223 4.1 0.4 1.0 CB F:GLU162 4.2 0.1 1.0 CB F:ASN218 4.2 0.8 1.0 CB F:ASP220 4.2 0.6 1.0 OE1 F:GLU162 4.3 0.8 1.0 C F:THR221 4.3 0.1 1.0 CG F:GLU223 4.3 0.4 1.0 N F:PRO222 4.4 0.3 1.0 O F:THR221 4.4 0.2 1.0 N F:THR221 4.4 0.6 1.0 CB F:GLU223 4.5 0.6 1.0 CA F:PRO222 4.5 0.1 1.0 NE2 F:HIS258 4.6 1.0 1.0 CD2 F:HIS258 4.7 0.1 1.0 CA F:THR221 4.8 0.1 1.0 C F:ILE219 4.9 0.7 1.0 N F:ILE219 4.9 0.4 1.0 C F:GLU223 5.0 0.7 1.0

X.Dong, B.Zhao, R.E.Iacob, J.Zhu, A.C.Koksal, C.Lu, J.R.Engen, T.A.Springer. Force Interacts with Macromolecular Structure in Activation of Tgf-Beta. Nature V. 542 55 2017.
ISSN: ESSN 1476-4687
PubMed: 28117447
DOI: 10.1038/NATURE21035