Cadmium in PDB 8r8c: Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine

The structure of Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine, PDB code: 8r8c was solved by A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.68 / 1.55
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	36.613, 36.86, 94.813, 90, 99.17, 90
R / Rfree (%)	16.3 / 20.4

The binding sites of Cadmium atom in the Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine (pdb code 8r8c). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine, PDB code: 8r8c:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:28.0 occ:1.00 O A:HOH398 2.1 25.6 1.0 OXT A:ASP132 2.1 22.8 1.0 NE2 A:HIS11 2.1 15.9 1.0 C A:ASP132 3.0 25.7 1.0 CD2 A:HIS11 3.1 18.8 1.0 CE1 A:HIS11 3.1 20.9 1.0 O A:ASP132 3.3 29.0 1.0 O A:HOH438 4.0 35.8 1.0 O A:HOH432 4.1 41.0 1.0 ND1 A:HIS11 4.2 19.9 1.0 CG A:HIS11 4.2 18.0 1.0 CA A:ASP132 4.4 25.4 1.0

Cadmium binding site 2 out of 3 in the Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:25.6 occ:1.00 O A:HOH352 2.0 21.0 1.0 NE2 A:HIS30 2.1 13.8 1.0 OD2 A:ASP75 2.1 15.8 1.0 O A:HOH427 2.1 17.9 1.0 O A:HOH420 2.2 19.9 1.0 CE1 A:HIS30 3.0 15.2 1.0 CG A:ASP75 3.1 17.1 1.0 CD2 A:HIS30 3.1 15.7 1.0 OD1 A:ASP75 3.3 16.2 1.0 O A:HOH368 4.0 27.6 1.0 ND1 A:HIS30 4.1 15.6 1.0 O A:HOH458 4.1 30.0 1.0 NZ A:LYS79 4.1 37.0 1.0 CG A:HIS30 4.2 11.9 1.0 O A:HOH327 4.3 37.5 1.0 O A:HOH459 4.4 31.7 1.0 CB A:ASP75 4.4 15.1 1.0

Cadmium binding site 3 out of 3 in the Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of the N-Terminal Domain of Cma From Cucumis Melo in Complex with N-Acetylgalactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:27.5 occ:1.00 OD1 A:ASN83 2.2 20.4 0.5 O A:HOH301 2.3 18.9 0.5 CG A:ASN83 2.5 19.3 0.5 O A:HOH436 2.5 15.2 1.0 ND2 A:ASN83 2.6 25.1 0.5 CB A:ASN83 3.9 19.4 0.5 CB A:ASN83 4.1 20.5 0.5 N A:ASN83 4.3 19.4 0.5 N A:ASN83 4.3 19.2 0.5 CA A:ASN83 4.4 19.2 0.5 CA A:ASN83 4.4 19.8 0.5 NH1 A:ARG99 4.5 41.3 1.0 CD A:ARG99 4.6 26.4 1.0 OD1 A:ASN83 4.6 28.0 0.5 CB A:PRO82 4.8 19.4 1.0 CG A:ASN83 4.9 21.9 0.5

J.Lundstrom, V.Chazalet, E.Gillon, N.Kerekes, A.Di Maio, Y.Liu, T.Feizi, A.Varrot, D.Bojar. Elucidating the Glycan-Binding Specificity and Structure of Cucumis Melo Agglutinin, A New R-Type Lectin To Be Published.