Manganese in PDB 8tcg: Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF

The structure of Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF (pdb code 8tcg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF, PDB code: 8tcg:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2001 b:82.4 occ:1.00 OD2 B:ASP131 1.8 81.3 1.0 OD2 B:ASP254 1.8 80.9 1.0 OD1 B:ASP130 1.8 82.4 1.0 O B:SER127 1.9 81.7 1.0 CG B:ASP130 2.6 82.5 1.0 OD2 B:ASP130 2.7 82.7 1.0 HA B:MET128 2.9 96.5 1.0 CG B:ASP254 2.9 80.5 1.0 CG B:ASP131 3.0 81.4 1.0 C B:SER127 3.1 81.2 1.0 HG3 C:GLU15 3.3 101.9 1.0 H B:ASP130 3.5 98.4 1.0 OD1 B:ASP131 3.7 81.5 1.0 OD1 B:ASP254 3.7 80.2 1.0 CA B:MET128 3.7 80.5 1.0 H B:ASP131 3.7 98.0 1.0 HB3 B:ASP254 3.7 96.3 1.0 CB B:ASP254 3.8 80.3 1.0 N B:MET128 3.8 80.8 1.0 HB2 B:ASP254 3.9 96.3 1.0 HB2 B:ASP131 3.9 97.5 1.0 HB2 B:SER127 4.0 97.0 1.0 CB B:ASP131 4.0 81.2 1.0 CB B:ASP130 4.0 82.5 1.0 C B:MET128 4.2 81.2 1.0 N B:ASP131 4.2 81.6 1.0 CG C:GLU15 4.2 84.9 1.0 CA B:SER127 4.3 81.2 1.0 N B:ASP130 4.3 82.0 1.0 HG B:SER127 4.3 96.4 1.0 HA B:SER127 4.3 97.5 1.0 CD C:GLU15 4.4 86.5 1.0 OE1 C:GLU15 4.5 87.6 1.0 HB3 B:ASP130 4.5 99.0 1.0 CA B:ASP130 4.6 82.0 1.0 CB B:SER127 4.6 80.8 1.0 N B:ASP129 4.6 81.6 1.0 H B:ASP129 4.6 97.9 1.0 O B:MET128 4.6 81.6 1.0 SD B:MET128 4.6 79.7 1.0 HG2 C:GLU15 4.7 101.9 1.0 C B:ASP130 4.7 81.7 1.0 HB2 B:ASP130 4.7 99.0 1.0 HG21 B:THR314 4.7 96.8 1.0 CA B:ASP131 4.8 81.3 1.0 OE2 C:GLU15 4.8 86.5 1.0 H B:MET128 4.8 97.0 1.0 HB3 B:ASP131 4.9 97.5 1.0 OG B:SER127 4.9 80.3 1.0 CB B:MET128 5.0 80.1 1.0

Manganese binding site 2 out of 3 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2002 b:79.5 occ:1.00 OE2 B:GLU223 1.8 79.2 1.0 OD1 C:ASP12 1.8 80.3 1.0 OG B:SER125 2.0 79.8 1.0 OG B:SER127 2.1 80.3 1.0 HG B:SER125 2.3 95.7 1.0 CD B:GLU223 2.6 78.8 1.0 HB2 B:SER125 2.7 95.0 1.0 HB3 B:SER127 2.8 97.0 1.0 CB B:SER125 2.8 79.2 1.0 H B:SER127 2.9 97.2 1.0 HG B:SER127 2.9 96.4 1.0 CB B:SER127 2.9 80.8 1.0 CG C:ASP12 3.0 80.7 1.0 OE1 B:GLU223 3.3 78.6 1.0 HB3 B:SER125 3.3 95.0 1.0 HG3 B:GLU223 3.4 94.4 1.0 CG B:GLU223 3.6 78.7 1.0 N B:SER127 3.7 81.0 1.0 OD2 C:ASP12 3.7 80.7 1.0 HB2 B:SER127 3.8 97.0 1.0 HA C:ASP12 3.8 97.7 1.0 HD21 B:ASN218 3.8 95.3 1.0 CA B:SER127 3.9 81.2 1.0 HG2 B:GLU223 3.9 94.4 1.0 CB C:ASP12 4.0 80.7 1.0 HB2 C:ASP12 4.0 96.8 1.0 CA B:SER125 4.1 79.1 1.0 H B:ALA126 4.2 96.1 1.0 C B:SER125 4.3 79.7 1.0 O B:THR221 4.3 79.1 1.0 HG2 B:MET128 4.3 95.7 1.0 N B:ALA126 4.3 80.1 1.0 HB3 B:ALA255 4.4 95.5 1.0 HB2 B:ALA255 4.4 95.5 1.0 H B:MET128 4.4 97.0 1.0 CA C:ASP12 4.5 81.4 1.0 OD1 B:ASP254 4.6 80.2 1.0 C B:SER127 4.7 81.2 1.0 ND2 B:ASN218 4.7 79.4 1.0 OD1 B:ASP123 4.7 78.3 1.0 HA B:SER127 4.7 97.5 1.0 H B:SER125 4.8 94.5 1.0 HA B:SER125 4.8 95.0 1.0 N B:MET128 4.8 80.8 1.0 C B:ALA126 4.8 81.2 1.0 CB B:ALA255 4.9 79.5 1.0 OD2 B:ASP123 4.9 78.2 1.0 O B:SER125 4.9 80.5 1.0 O C:ASP12 4.9 82.8 1.0 HB3 C:ASP12 4.9 96.8 1.0 CB B:GLU223 4.9 78.1 1.0 N B:SER125 5.0 78.8 1.0 HA B:THR221 5.0 95.3 1.0

Manganese binding site 3 out of 3 in the Integrin Alpha-V Beta-6 in Complex with Minibinder B6_BP_DSLF


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 Minibinder B6_BP_DSLF within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn2003 b:79.1 occ:1.00 OD1 B:ASP220 1.8 79.0 1.0 OE2 B:GLU162 1.9 78.4 1.0 O B:PRO222 1.9 78.9 1.0 O B:ASP220 2.1 79.8 1.0 OD1 B:ASN218 2.5 79.2 1.0 CG B:ASP220 3.0 79.0 1.0 C B:ASP220 3.0 79.4 1.0 CD B:GLU162 3.1 78.4 1.0 C B:PRO222 3.1 78.8 1.0 HA B:GLU223 3.2 93.6 1.0 CG B:ASN218 3.4 78.9 1.0 OE1 B:GLU223 3.4 78.6 1.0 HD21 B:ASN218 3.5 95.3 1.0 H B:ASP220 3.6 95.5 1.0 CA B:ASP220 3.7 79.4 1.0 OD2 B:ASP220 3.8 78.8 1.0 N B:PRO222 3.8 78.8 1.0 OE1 B:GLU162 3.8 78.0 1.0 ND2 B:ASN218 3.8 79.4 1.0 N B:ASP220 3.8 79.6 1.0 C B:THR221 3.8 79.0 1.0 HG2 B:GLU162 3.8 93.8 1.0 CD B:GLU223 3.8 78.8 1.0 CB B:ASP220 3.9 79.2 1.0 HB2 C:ASP12 3.9 96.8 1.0 N B:THR221 3.9 79.5 1.0 HE2 B:HIS258 3.9 94.1 1.0 HG2 B:PRO222 4.0 94.5 1.0 N B:GLU223 4.0 78.4 1.0 HD2 B:PRO222 4.0 94.7 1.0 CA B:PRO222 4.1 78.9 1.0 OE2 B:GLU223 4.1 79.2 1.0 CG B:GLU162 4.1 78.2 1.0 CA B:GLU223 4.1 78.0 1.0 O B:THR221 4.2 79.1 1.0 CA B:THR221 4.3 79.4 1.0 CD B:PRO222 4.4 78.9 1.0 HB2 B:GLU162 4.4 93.6 1.0 HB2 B:ASP220 4.4 95.0 1.0 HD2 B:HIS258 4.4 93.9 1.0 HB2 B:ASN218 4.4 95.0 1.0 CB B:ASN218 4.6 79.2 1.0 CG B:PRO222 4.6 78.7 1.0 HA B:THR221 4.6 95.3 1.0 NE2 B:HIS258 4.6 78.4 1.0 HD22 B:ASN218 4.7 95.3 1.0 H B:THR221 4.7 95.3 1.0 HB3 B:ASP220 4.7 95.0 1.0 HA B:ASP220 4.7 95.3 1.0 CG B:GLU223 4.8 78.7 1.0 C B:ILE219 4.8 79.9 1.0 CD2 B:HIS258 4.8 78.2 1.0 CB B:PRO222 4.8 78.6 1.0 HG2 B:GLU223 4.9 94.4 1.0 CB B:GLU162 4.9 78.0 1.0 HG3 B:GLU162 4.9 93.8 1.0 HA B:PRO222 4.9 94.6 1.0 CB B:GLU223 4.9 78.1 1.0 H B:GLU223 4.9 94.1 1.0 HB2 B:PRO222 5.0 94.3 1.0 CB C:ASP12 5.0 80.7 1.0 H B:ILE219 5.0 95.7 1.0

A.Roy, L.Shi, A.Chang, X.Dong, A.Fernandez, J.C.Kraft, J.Li, V.Q.Le, R.V.Winegar, G.M.Cherf, D.Slocum, P.D.Poulson, G.E.Casper, M.L.Vallecillo-Zuniga, J.C.Valdoz, M.C.Miranda, H.Bai, Y.Kipnis, A.Olshefsky, T.Priya, L.Carter, R.Ravichandran, C.M.Chow, M.R.Johnson, S.Cheng, M.Smith, C.Overed-Sayer, D.K.Finch, D.Lowe, A.K.Bera, G.Matute-Bello, T.P.Birkland, F.Dimaio, G.Raghu, J.R.Cochran, L.J.Stewart, M.G.Campbell, P.M.Van Ry, T.Springer, D.Baker. De Novo Design of Highly Selective Miniprotein Inhibitors of Integrins Alpha V Beta 6 and Alpha V Beta 8. Nat Commun V. 14 5660 2023.
ISSN: ESSN 2041-1723
PubMed: 37704610
DOI: 10.1038/S41467-023-41272-Z