Calcium in PDB 9e6h: Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl

The structure of Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl (pdb code 9e6h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl, PDB code: 9e6h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:30.0 occ:1.00 O A:TYR160 2.3 76.1 1.0 OD2 A:ASP169 2.4 54.3 1.0 OD1 A:ASP158 2.4 72.1 1.0 OD2 A:ASP158 2.4 72.1 1.0 OD2 A:ASP166 2.4 49.8 1.0 CG A:ASP158 2.7 79.6 1.0 C A:TYR160 3.4 81.9 1.0 CG A:ASP169 3.5 57.5 1.0 CG A:ASP166 3.5 51.7 1.0 CB A:TYR160 3.7 77.4 1.0 CA A:TYR160 3.9 82.4 1.0 CB A:ASP166 3.9 54.8 1.0 CB A:ASP169 4.1 59.6 1.0 N A:TYR160 4.1 84.7 1.0 CD2 A:TYR160 4.2 68.8 1.0 CB A:ASP158 4.2 86.6 1.0 CG A:TYR160 4.4 75.1 1.0 OD1 A:ASP169 4.4 54.5 1.0 MN A:MN304 4.5 30.0 1.0 N A:PHE161 4.5 72.4 1.0 CE1 A:HIS174 4.6 80.2 1.0 OD1 A:ASP166 4.6 49.0 1.0 CA A:PHE161 4.9 68.9 1.0 NE2 A:HIS174 4.9 81.7 1.0

Calcium binding site 2 out of 4 in the Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:30.0 occ:1.00 O B:TYR160 2.3 76.8 1.0 OD2 B:ASP169 2.4 55.2 1.0 OD1 B:ASP158 2.4 72.2 1.0 OD2 B:ASP158 2.4 72.0 1.0 OD2 B:ASP166 2.4 50.4 1.0 CG B:ASP158 2.7 79.8 1.0 C B:TYR160 3.4 82.0 1.0 CG B:ASP169 3.5 58.1 1.0 CG B:ASP166 3.5 52.0 1.0 CB B:TYR160 3.7 77.4 1.0 CA B:TYR160 3.9 82.2 1.0 CB B:ASP166 3.9 54.9 1.0 CB B:ASP169 4.1 59.9 1.0 N B:TYR160 4.1 84.2 1.0 CD2 B:TYR160 4.2 68.8 1.0 CB B:ASP158 4.2 86.5 1.0 CG B:TYR160 4.4 75.3 1.0 OD1 B:ASP169 4.4 55.3 1.0 MN B:MN304 4.5 30.0 1.0 N B:PHE161 4.5 72.3 1.0 CE1 B:HIS174 4.6 79.8 1.0 OD1 B:ASP166 4.6 49.5 1.0 CA B:PHE161 4.9 68.8 1.0 NE2 B:HIS174 4.9 81.2 1.0

Calcium binding site 3 out of 4 in the Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:30.0 occ:1.00 O C:TYR160 2.3 75.7 1.0 OD2 C:ASP169 2.4 55.1 1.0 OD1 C:ASP158 2.4 72.3 1.0 OD2 C:ASP158 2.4 71.5 1.0 OD2 C:ASP166 2.4 50.0 1.0 CG C:ASP158 2.7 79.3 1.0 C C:TYR160 3.4 81.3 1.0 CG C:ASP169 3.5 58.2 1.0 CG C:ASP166 3.5 51.7 1.0 CB C:TYR160 3.7 76.9 1.0 CA C:TYR160 3.9 81.7 1.0 CB C:ASP166 3.9 54.6 1.0 CB C:ASP169 4.1 60.1 1.0 N C:TYR160 4.1 84.0 1.0 CD2 C:TYR160 4.2 68.2 1.0 CB C:ASP158 4.2 86.4 1.0 CG C:TYR160 4.4 74.6 1.0 OD1 C:ASP169 4.4 55.4 1.0 MN C:MN304 4.5 30.0 1.0 N C:PHE161 4.5 70.8 1.0 CE1 C:HIS174 4.6 79.6 1.0 OD1 C:ASP166 4.6 49.0 1.0 CA C:PHE161 4.9 67.3 1.0 NE2 C:HIS174 4.9 80.8 1.0

Calcium binding site 4 out of 4 in the Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Cryo-Em Structure of Maackia Amurensis Seed Leukoagglutinin (Lectin), Masl within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:30.0 occ:1.00 O D:TYR160 2.3 75.6 1.0 OD2 D:ASP169 2.4 55.5 1.0 OD1 D:ASP158 2.4 71.9 1.0 OD2 D:ASP158 2.4 71.4 1.0 OD2 D:ASP166 2.4 49.7 1.0 CG D:ASP158 2.7 78.9 1.0 C D:TYR160 3.4 81.4 1.0 CG D:ASP169 3.5 58.5 1.0 CG D:ASP166 3.5 51.9 1.0 CB D:TYR160 3.7 76.9 1.0 CA D:TYR160 3.9 81.8 1.0 CB D:ASP166 3.9 54.7 1.0 CB D:ASP169 4.1 60.5 1.0 N D:TYR160 4.1 84.1 1.0 CD2 D:TYR160 4.2 68.7 1.0 CB D:ASP158 4.2 86.4 1.0 CG D:TYR160 4.4 74.7 1.0 OD1 D:ASP169 4.4 55.7 1.0 MN D:MN304 4.5 30.0 1.0 N D:PHE161 4.5 71.3 1.0 CE1 D:HIS174 4.6 79.6 1.0 OD1 D:ASP166 4.6 49.3 1.0 CA D:PHE161 4.9 67.7 1.0 NE2 D:HIS174 4.9 80.9 1.0

A.R.Nayak, G.S.Goldberg, D.Temiakov. Maackia Amurensis Seed Lectin (Masl) Structure and Sequence Comparison with Other Maackia Amurensis Lectins J.Biol.Chem. 2025.
ISSN: ESSN 1083-351X
DOI: 10.1016/J.JBC.2025.108466