Manganese in PDB 9ckv: Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin

The structure of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin (pdb code 9ckv). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin, PDB code: 9ckv:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn803 b:135.8 occ:1.00 OE2 B:GLU229 1.7 119.3 1.0 OG B:SER134 1.8 126.0 1.0 OG B:SER132 2.1 121.0 1.0 HG B:SER134 2.3 126.0 1.0 OD1 C:ASP10 2.3 124.7 1.0 HG B:SER132 2.6 121.0 1.0 CD B:GLU229 2.8 119.3 1.0 CB B:SER134 2.9 126.0 1.0 HB3 B:SER134 3.0 126.0 1.0 HG3 B:GLU229 3.1 119.3 1.0 H B:SER134 3.2 126.0 1.0 CB B:SER132 3.2 121.0 1.0 HB2 B:SER132 3.3 121.0 1.0 CG B:GLU229 3.3 119.3 1.0 HG2 B:GLU229 3.3 119.3 1.0 HB2 B:ALA260 3.4 119.9 1.0 CG C:ASP10 3.4 124.7 1.0 HB2 B:SER134 3.5 126.0 1.0 HB3 B:ALA260 3.5 119.9 1.0 HB3 B:SER132 3.6 121.0 1.0 HA C:ASP10 3.7 124.7 1.0 O B:SER227 3.8 119.4 1.0 N B:SER134 3.9 126.0 1.0 CB B:ALA260 3.9 119.9 1.0 OE1 B:GLU229 3.9 119.3 1.0 OD2 B:ASP130 3.9 117.7 1.0 CA B:SER134 4.0 126.0 1.0 HB2 C:ASP10 4.1 124.7 1.0 CB C:ASP10 4.2 124.7 1.0 OD2 C:ASP10 4.2 124.7 1.0 HB1 B:ALA260 4.4 119.9 1.0 CA C:ASP10 4.4 124.7 1.0 CA B:SER132 4.5 121.0 1.0 HB3 B:ASP259 4.5 122.9 1.0 C B:SER132 4.6 121.0 1.0 HA B:SER227 4.6 119.4 1.0 HG2 B:MET135 4.7 122.7 1.0 C B:SER134 4.7 126.0 1.0 HA B:SER134 4.7 126.0 1.0 H B:SER132 4.8 121.0 1.0 H B:TYR133 4.8 128.5 1.0 N B:TYR133 4.8 128.5 1.0 CB B:GLU229 4.8 119.3 1.0 H B:MET135 4.8 122.7 1.0 C B:SER227 4.9 119.4 1.0 CG B:ASP130 4.9 117.7 1.0

Manganese binding site 2 out of 3 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn804 b:151.1 occ:1.00 OD1 B:ASP137 1.8 131.2 1.0 OD2 B:ASP259 1.8 122.9 1.0 OD2 B:ASP137 2.3 131.2 1.0 CG B:ASP137 2.3 131.2 1.0 OD2 B:ASP138 2.3 123.6 1.0 O B:SER134 2.5 126.0 1.0 CG B:ASP259 2.9 122.9 1.0 CG B:ASP138 3.2 123.6 1.0 OD1 B:ASP259 3.6 122.9 1.0 OD1 B:ASP138 3.6 123.6 1.0 C B:SER134 3.7 126.0 1.0 CB B:ASP137 3.8 131.2 1.0 H B:ASP137 3.8 131.2 1.0 HA C:PRO12 3.8 137.8 1.0 HB2 B:ASP259 3.9 122.9 1.0 CB B:ASP259 3.9 122.9 1.0 HB2 B:SER134 4.0 126.0 1.0 HA B:MET135 4.0 122.7 1.0 HB3 B:ASP259 4.1 122.9 1.0 HB3 B:ASP137 4.1 131.2 1.0 HB3 C:PRO12 4.2 137.8 1.0 H B:ASP138 4.2 123.6 1.0 HB2 B:ASP137 4.3 131.2 1.0 H C:SER13 4.4 145.9 1.0 HA B:SER134 4.4 126.0 1.0 N B:ASP137 4.4 131.2 1.0 CB B:ASP138 4.5 123.6 1.0 HB2 B:ASP138 4.5 123.6 1.0 N B:ASP138 4.5 123.6 1.0 CA B:ASP137 4.6 131.2 1.0 CA B:SER134 4.6 126.0 1.0 N B:MET135 4.6 122.7 1.0 CA C:PRO12 4.7 137.8 1.0 CA B:MET135 4.7 122.7 1.0 CB B:SER134 4.7 126.0 1.0 CB C:PRO12 4.8 137.8 1.0 C B:ASP137 4.8 131.2 1.0 HG1 B:THR318 4.9 121.8 1.0 HB2 C:PRO12 4.9 137.8 1.0

Manganese binding site 3 out of 3 in the Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Cryo-Em Structure of ALPHA5BETA1 Integrin in Complex with Neonectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn805 b:136.2 occ:1.00 OD1 B:ASP226 1.8 119.4 1.0 OD1 B:ASN224 1.8 120.1 1.0 O B:PRO228 2.3 117.9 1.0 OE2 B:GLU169 2.4 119.5 1.0 O B:ASP226 2.7 119.4 1.0 OE1 B:GLU229 2.7 119.3 1.0 CG B:ASP226 2.9 119.4 1.0 CG B:ASN224 3.0 120.1 1.0 HG2 B:GLU169 3.1 119.5 1.0 HA B:GLU229 3.2 119.3 1.0 HB2 B:GLU169 3.2 119.5 1.0 CD B:GLU169 3.3 119.5 1.0 H B:ASP226 3.4 119.4 1.0 HD22 B:ASN224 3.5 120.1 1.0 C B:PRO228 3.5 117.9 1.0 CG B:GLU169 3.5 119.5 1.0 C B:ASP226 3.5 119.4 1.0 OD2 B:ASP226 3.6 119.4 1.0 ND2 B:ASN224 3.7 120.1 1.0 CD B:GLU229 3.8 119.3 1.0 HE2 B:HIS263 3.8 116.6 1.0 N B:ASP226 3.8 119.4 1.0 CB B:GLU169 3.9 119.5 1.0 CA B:ASP226 4.0 119.4 1.0 CA B:GLU229 4.0 119.3 1.0 CB B:ASP226 4.0 119.4 1.0 HB3 B:ASN224 4.1 120.1 1.0 CB B:ASN224 4.2 120.1 1.0 N B:GLU229 4.2 119.3 1.0 HB3 B:GLU169 4.2 119.5 1.0 H B:LEU225 4.3 118.8 1.0 OE1 B:GLU169 4.4 119.5 1.0 OE2 B:GLU229 4.4 119.3 1.0 HD2 B:HIS263 4.4 116.6 1.0 HG3 B:GLU169 4.4 119.5 1.0 HB3 B:TYR175 4.5 114.9 1.0 HD21 B:ASN224 4.5 120.1 1.0 NE2 B:HIS263 4.5 116.6 1.0 HB2 B:ASP226 4.6 119.4 1.0 N B:PRO228 4.6 117.9 1.0 C B:SER227 4.6 119.4 1.0 HD2 B:PRO228 4.6 117.9 1.0 CA B:PRO228 4.6 117.9 1.0 N B:SER227 4.6 119.4 1.0 HB2 C:ASP10 4.6 124.7 1.0 HB3 B:ASP226 4.7 119.4 1.0 HB2 B:ASN224 4.7 120.1 1.0 O B:SER227 4.7 119.4 1.0 H B:GLY230 4.7 118.2 1.0 N B:LEU225 4.7 118.8 1.0 CB B:GLU229 4.8 119.3 1.0 CG B:GLU229 4.8 119.3 1.0 HB3 B:GLU229 4.8 119.3 1.0 O B:VAL168 4.8 117.4 1.0 C B:LEU225 4.8 118.8 1.0 CD2 B:HIS263 4.8 116.6 1.0 O B:TYR175 4.9 114.9 1.0 HA B:ASP226 5.0 119.4 1.0 HB2 B:PRO228 5.0 117.9 1.0

X.Wang, J.Guillem-Marti, S.Kumar, D.S.Lee, D.Cabrerizo-Aguado, R.Werther, K.A.Estrada Alamo, Y.T.Zhao, A.Nguyen, I.Kopyeva, B.Huang, J.Li, Y.Hao, X.Li, A.Brizuela-Velasco, A.N.Murray, S.Gerben, A.Roy, C.A.Deforest, T.Springer, H.Ruohola-Baker, J.A.Cooper, M.G.Campbell, J.Maria Manero, M.Ginebra, D.Baker. De Novo Design of Integrin ALPHA5BETA1 Modulating Proteins For Regenerative Medicine To Be Published.