Manganese in PDB 4d69: Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn

The structure of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn, PDB code: 4d69 was solved by D.Madariaga, N.Martinez-Saez, V.J.Somovilla, H.Coelho, J.Valero-Gonzalez, J.Castro-Lopez, J.L.Asensio, J.Jimenez-Barbero, J.H.Busto, A.Avenoza, F.Marcelo, R.Hurtado-Guerrero, F.Corzana, J.M.Peregrina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	202.89 / 2.70
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	114.232, 114.232, 202.893, 90.00, 90.00, 120.00
R / Rfree (%)	23.022 / 27.433

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Manganese atom in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn (pdb code 4d69). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 24 binding sites of Manganese where determined in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn, PDB code: 4d69:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1236 b:61.5 occ:1.00 OE2 A:GLU124 2.0 65.8 1.0 OD1 A:ASP133 2.1 78.9 1.0 OD2 A:ASP126 2.2 69.5 1.0 NE2 A:HIS138 2.6 71.6 1.0 CD A:GLU124 3.0 64.2 1.0 CG A:ASP133 3.2 80.2 1.0 OE1 A:GLU124 3.3 64.6 1.0 CG A:ASP126 3.3 69.6 1.0 CE1 A:HIS138 3.5 73.1 1.0 CD2 A:HIS138 3.6 70.4 1.0 OD2 A:ASP133 3.7 80.4 1.0 OG A:SER148 3.8 64.3 1.0 CB A:ASP126 3.9 68.1 1.0 O A:ILE146 4.1 68.7 1.0 NE1 A:TRP132 4.1 79.7 1.0 CD1 A:TRP132 4.3 80.5 1.0 CB A:ASP133 4.4 81.9 1.0 OD1 A:ASP126 4.4 70.5 1.0 CG A:GLU124 4.4 62.1 1.0 MN A:MN1237 4.4 86.3 1.0 ND1 A:HIS138 4.7 72.8 1.0 CG A:HIS138 4.7 71.1 1.0 CA A:ASP133 4.8 82.3 1.0 CD A:PRO134 4.9 80.9 1.0

Manganese binding site 2 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1237 b:86.3 occ:1.00 OD1 A:ASP126 2.3 70.5 1.0 OD1 A:ASN130 2.4 91.3 1.0 O A:PHE128 2.6 81.5 1.0 OD2 A:ASP126 2.8 69.5 1.0 OD2 A:ASP133 2.8 80.4 1.0 CG A:ASP126 2.9 69.6 1.0 CG A:ASN130 3.6 89.9 1.0 C A:PHE128 3.8 83.2 1.0 CG A:ASP133 3.9 80.2 1.0 O A:ASP88 4.1 69.4 1.0 OD1 A:ASP133 4.2 78.9 1.0 CB A:ASP126 4.3 68.1 1.0 N A:PHE128 4.3 78.9 1.0 N A:ASN130 4.4 88.8 1.0 MN A:MN1236 4.4 61.5 1.0 CA A:PHE128 4.4 82.3 1.0 CB A:ASN130 4.4 89.8 1.0 O A:GLY106 4.5 81.5 1.0 ND2 A:ASN130 4.5 91.0 1.0 OD1 A:ASP88 4.6 76.9 1.0 NE1 A:TRP132 4.6 79.7 1.0 CB A:PHE128 4.6 83.9 1.0 CA A:ASP88 4.6 73.4 1.0 CA A:GLY106 4.6 81.8 1.0 C A:ASP88 4.8 69.4 1.0 N A:ARG129 4.8 85.8 1.0 CA A:ASP126 4.9 67.6 1.0

Manganese binding site 3 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1235 b:55.7 occ:1.00 OE2 B:GLU124 1.9 51.0 1.0 OD2 B:ASP126 2.0 54.9 1.0 O B:HOH2004 2.1 26.8 1.0 OD1 B:ASP133 2.2 63.9 1.0 NE2 B:HIS138 2.5 59.5 1.0 CD B:GLU124 2.9 50.0 1.0 CG B:ASP126 3.1 54.4 1.0 OE1 B:GLU124 3.2 49.9 1.0 CG B:ASP133 3.2 63.5 1.0 CE1 B:HIS138 3.4 60.0 1.0 CD2 B:HIS138 3.4 59.5 1.0 CB B:ASP126 3.7 53.4 1.0 OD2 B:ASP133 3.7 62.7 1.0 OG B:SER148 3.8 55.6 1.0 MN B:MN1236 4.0 60.4 1.0 OD1 B:ASP126 4.2 55.0 1.0 CG B:GLU124 4.3 49.0 1.0 O B:ILE146 4.3 58.6 1.0 CB B:ASP133 4.4 64.6 1.0 NE1 B:TRP132 4.4 63.0 1.0 ND1 B:HIS138 4.5 60.3 1.0 CG B:HIS138 4.6 59.9 1.0 CD1 B:TRP132 4.6 63.6 1.0 CD B:PRO134 4.7 65.3 1.0 CA B:ASP133 4.9 65.2 1.0

Manganese binding site 4 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1236 b:60.4 occ:1.00 O B:HOH2003 2.3 39.4 1.0 OD2 B:ASP133 2.3 62.7 1.0 OD1 B:ASN130 2.4 61.9 1.0 OD1 B:ASP126 2.6 55.0 1.0 OD2 B:ASP126 2.7 54.9 1.0 O B:PHE128 2.7 59.7 1.0 CG B:ASP126 3.0 54.4 1.0 CG B:ASP133 3.4 63.5 1.0 CG B:ASN130 3.5 62.3 1.0 OD1 B:ASP133 3.7 63.9 1.0 C B:PHE128 3.9 60.5 1.0 MN B:MN1235 4.0 55.7 1.0 N B:ASN130 4.2 62.6 1.0 NE1 B:TRP132 4.2 63.0 1.0 CB B:ASN130 4.2 63.0 1.0 O B:GLY106 4.3 55.5 1.0 CB B:ASP126 4.4 53.4 1.0 ND2 B:ASN130 4.5 62.6 1.0 O B:ASP88 4.5 59.3 1.0 CB B:ASP133 4.7 64.6 1.0 N B:PHE128 4.7 58.3 1.0 CA B:PHE128 4.8 59.9 1.0 CZ2 B:TRP132 4.9 63.1 1.0 CE2 B:TRP132 4.9 63.3 1.0 CA B:ASN130 4.9 63.5 1.0 N B:ARG129 4.9 62.1 1.0 CA B:GLY106 4.9 56.9 1.0 OD1 B:ASP88 4.9 65.0 1.0 CE1 B:HIS138 5.0 60.0 1.0 CA B:ARG129 5.0 63.1 1.0

Manganese binding site 5 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1236 b:65.3 occ:1.00 OE2 C:GLU124 2.1 54.4 1.0 OD1 C:ASP133 2.1 64.8 1.0 OD2 C:ASP126 2.3 55.4 1.0 NE2 C:HIS138 2.5 59.5 1.0 CD C:GLU124 3.1 54.5 1.0 CG C:ASP133 3.2 64.5 1.0 OE1 C:GLU124 3.4 54.6 1.0 CG C:ASP126 3.4 55.0 1.0 CD2 C:HIS138 3.4 58.6 1.0 CE1 C:HIS138 3.5 59.9 1.0 OG C:SER148 3.6 54.1 1.0 OD2 C:ASP133 3.7 65.4 1.0 CB C:ASP126 3.9 54.8 1.0 O C:ILE146 4.0 58.8 1.0 CB C:ASP133 4.3 63.7 1.0 NE1 C:TRP132 4.4 64.9 1.0 CG C:GLU124 4.4 53.9 1.0 CD1 C:TRP132 4.4 64.2 1.0 OD1 C:ASP126 4.4 55.1 1.0 MN C:MN1237 4.5 65.5 1.0 CD C:PRO134 4.5 60.6 1.0 ND1 C:HIS138 4.6 59.5 1.0 CG C:HIS138 4.6 58.2 1.0 CA C:ASP133 4.7 63.2 1.0 CB C:SER148 4.9 54.2 1.0

Manganese binding site 6 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn1237 b:65.5 occ:1.00 OD1 C:ASN130 2.2 61.5 1.0 OD2 C:ASP133 2.4 65.4 1.0 O C:PHE128 2.6 60.5 1.0 OD1 C:ASP126 2.7 55.1 1.0 OD2 C:ASP126 3.0 55.4 1.0 CG C:ASP126 3.2 55.0 1.0 CG C:ASN130 3.3 62.0 1.0 CG C:ASP133 3.5 64.5 1.0 C C:PHE128 3.8 61.2 1.0 OD1 C:ASP133 3.9 64.8 1.0 CB C:ASN130 4.0 62.2 1.0 N C:ASN130 4.0 62.4 1.0 O C:GLY106 4.1 72.5 1.0 NE1 C:TRP132 4.3 64.9 1.0 ND2 C:ASN130 4.3 62.6 1.0 MN C:MN1236 4.5 65.3 1.0 O C:ASP88 4.5 67.9 1.0 CA C:PHE128 4.6 60.9 1.0 N C:PHE128 4.6 60.1 1.0 CB C:ASP126 4.6 54.8 1.0 CA C:GLY106 4.6 72.7 1.0 OD1 C:ASP88 4.7 70.1 1.0 CA C:ASN130 4.7 62.8 1.0 CB C:ASP133 4.7 63.7 1.0 N C:ARG129 4.7 62.0 1.0 CZ2 C:TRP132 4.8 66.1 1.0 CB C:PHE128 4.8 61.6 1.0 CE2 C:TRP132 4.8 65.7 1.0 C C:ARG129 4.8 62.8 1.0 CD1 C:PHE128 4.8 62.3 1.0 CA C:ARG129 4.9 62.4 1.0 C C:GLY106 4.9 73.0 1.0 CA C:ASP88 5.0 70.0 1.0

Manganese binding site 7 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1236 b:37.3 occ:1.00 OE2 D:GLU124 1.9 48.0 1.0 OD2 D:ASP126 2.0 49.0 1.0 OD1 D:ASP133 2.2 50.1 1.0 O D:HOH2007 2.2 21.3 1.0 NE2 D:HIS138 2.4 48.9 1.0 CD D:GLU124 3.0 47.6 1.0 CG D:ASP126 3.2 48.9 1.0 CG D:ASP133 3.3 50.7 1.0 OE1 D:GLU124 3.3 47.8 1.0 CD2 D:HIS138 3.4 48.5 1.0 CE1 D:HIS138 3.4 49.4 1.0 CB D:ASP126 3.7 48.3 1.0 OG D:SER148 3.7 48.2 1.0 OD2 D:ASP133 3.8 50.8 1.0 MN D:MN1237 4.2 55.7 1.0 OD1 D:ASP126 4.2 49.3 1.0 CG D:GLU124 4.3 47.0 1.0 O D:ILE146 4.3 49.4 1.0 NE1 D:TRP132 4.4 50.8 1.0 CB D:ASP133 4.5 51.3 1.0 ND1 D:HIS138 4.5 49.3 1.0 CG D:HIS138 4.5 48.7 1.0 CD1 D:TRP132 4.6 51.1 1.0 CD D:PRO134 4.8 50.5 1.0 CA D:ASP133 4.9 51.6 1.0

Manganese binding site 8 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn1237 b:55.7 occ:1.00 OD1 D:ASP126 2.4 49.3 1.0 OD1 D:ASN130 2.4 51.2 1.0 OD2 D:ASP133 2.4 50.8 1.0 O D:PHE128 2.5 51.0 1.0 OD2 D:ASP126 2.6 49.0 1.0 CG D:ASP126 2.8 48.9 1.0 CG D:ASP133 3.5 50.7 1.0 CG D:ASN130 3.5 52.0 1.0 C D:PHE128 3.7 51.5 1.0 OD1 D:ASP133 3.9 50.1 1.0 MN D:MN1236 4.2 37.3 1.0 N D:ASN130 4.2 52.5 1.0 CB D:ASP126 4.3 48.3 1.0 CB D:ASN130 4.3 52.4 1.0 O D:ASP88 4.4 49.2 1.0 N D:PHE128 4.4 50.8 1.0 NE1 D:TRP132 4.4 50.8 1.0 CA D:PHE128 4.5 51.5 1.0 O D:GLY106 4.5 50.0 1.0 ND2 D:ASN130 4.5 52.5 1.0 CB D:PHE128 4.7 51.9 1.0 N D:ARG129 4.7 52.2 1.0 CB D:ASP133 4.7 51.3 1.0 OD1 D:ASP88 4.8 51.4 1.0 CE1 D:HIS138 4.9 49.4 1.0 CA D:ARG129 4.9 52.5 1.0 CA D:ASN130 4.9 53.0 1.0 CA D:ASP88 4.9 50.3 1.0 C D:ARG129 4.9 52.9 1.0 CA D:GLY106 5.0 50.9 1.0 NE2 D:HIS138 5.0 48.9 1.0 CZ2 D:TRP132 5.0 51.5 1.0 CA D:ASP126 5.0 48.2 1.0

Manganese binding site 9 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1236 b:44.0 occ:1.00 OE2 E:GLU124 2.0 48.1 1.0 OD1 E:ASP133 2.1 50.1 1.0 OD2 E:ASP126 2.2 48.6 1.0 NE2 E:HIS138 2.5 49.1 1.0 CD E:GLU124 3.1 47.6 1.0 O E:HOH2003 3.2 42.3 1.0 CG E:ASP133 3.2 50.5 1.0 CG E:ASP126 3.3 48.3 1.0 OE1 E:GLU124 3.4 47.7 1.0 CD2 E:HIS138 3.4 48.9 1.0 CE1 E:HIS138 3.5 49.5 1.0 OG E:SER148 3.7 49.0 1.0 OD2 E:ASP133 3.7 50.3 1.0 CB E:ASP126 3.9 47.8 1.0 O E:ILE146 4.2 49.7 1.0 NE1 E:TRP132 4.3 50.5 1.0 CB E:ASP133 4.3 51.3 1.0 MN E:MN1237 4.3 60.5 1.0 OD1 E:ASP126 4.3 48.5 1.0 CD1 E:TRP132 4.4 51.1 1.0 CG E:GLU124 4.4 47.0 1.0 ND1 E:HIS138 4.6 49.5 1.0 CG E:HIS138 4.6 49.1 1.0 CD E:PRO134 4.6 51.4 1.0 CA E:ASP133 4.7 51.9 1.0

Manganese binding site 10 out of 24 in the Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Soybean Agglutinin From Glycine Max in Complex with the Antigen Tn within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn1237 b:60.5 occ:1.00 OD1 E:ASN130 2.4 50.3 1.0 OD2 E:ASP133 2.4 50.3 1.0 O E:PHE128 2.5 50.0 1.0 OD1 E:ASP126 2.6 48.5 1.0 OD2 E:ASP126 2.8 48.6 1.0 O E:HOH2003 3.0 42.3 1.0 CG E:ASP126 3.0 48.3 1.0 CG E:ASP133 3.4 50.5 1.0 CG E:ASN130 3.5 51.0 1.0 C E:PHE128 3.7 50.3 1.0 OD1 E:ASP133 3.9 50.1 1.0 N E:ASN130 4.1 51.6 1.0 O E:GLY106 4.3 49.1 1.0 CB E:ASN130 4.3 51.7 1.0 MN E:MN1236 4.3 44.0 1.0 NE1 E:TRP132 4.3 50.5 1.0 ND2 E:ASN130 4.4 51.2 1.0 O E:ASP88 4.4 47.8 1.0 N E:PHE128 4.5 49.3 1.0 CB E:ASP126 4.5 47.8 1.0 CA E:PHE128 4.5 50.0 1.0 CB E:PHE128 4.6 50.1 1.0 OD1 E:ASP88 4.7 49.6 1.0 CB E:ASP133 4.7 51.3 1.0 N E:ARG129 4.7 51.1 1.0 CZ2 E:TRP132 4.7 50.8 1.0 CA E:GLY106 4.8 49.6 1.0 CE2 E:TRP132 4.8 51.0 1.0 CA E:ASN130 4.9 52.2 1.0 CA E:ARG129 4.9 51.5 1.0 C E:ARG129 4.9 52.0 1.0 CA E:ASP88 4.9 48.5 1.0

D.Madariaga, N.Martinez-Saez, V.J.Somovilla, H.Coelho, J.Valero-Gonzalez, J.Castro-Lopez, J.L.Asensio, J.Jimenez-Barbero, J.H.Busto, A.Avenoza, F.Marcelo, R.Hurtado-Guerrero, F.Corzana, J.M.Peregrina. Recognition of Tumor-Associated Glycopeptides By A Potential Sensor Lectin: Does the Peptide Context Modulate Carbohydrate Recognition Acs Chem.Biol. 2014.
ISSN: ISSN 1554-8929