Cadmium in PDB 8r8a: Structure of the N-Terminal Domain of Cma in Complex with N- Acetyllactosamine

The structure of Structure of the N-Terminal Domain of Cma in Complex with N- Acetyllactosamine, PDB code: 8r8a was solved by J.Lundstrom, A.Varrot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.78 / 1.32
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	36.696, 36.782, 94.786, 90, 99.24, 90
R / Rfree (%)	14.4 / 18.6

The binding sites of Cadmium atom in the Structure of the N-Terminal Domain of Cma in Complex with N- Acetyllactosamine (pdb code 8r8a). 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 in Complex with N- Acetyllactosamine, PDB code: 8r8a:
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 in Complex with N- Acetyllactosamine


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 in Complex with N- Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd201 b:21.5 occ:1.00 O A:HOH434 2.0 19.8 1.0 NE2 A:HIS11 2.1 13.9 1.0 OXT A:ASP132 2.1 19.8 1.0 O A:HOH310 2.1 17.8 1.0 O A:HOH415 2.2 20.3 1.0 C A:ASP132 3.0 16.9 1.0 CE1 A:HIS11 3.1 14.0 1.0 CD2 A:HIS11 3.1 13.5 1.0 O A:ASP132 3.3 16.7 1.0 O A:HOH397 3.7 32.3 1.0 O A:HOH451 4.0 29.8 1.0 O A:HOH435 4.1 28.9 1.0 O A:HOH467 4.2 27.6 1.0 ND1 A:HIS11 4.2 14.5 1.0 CG A:HIS11 4.3 14.1 1.0 CA A:ASP132 4.4 18.6 1.0

Cadmium binding site 2 out of 3 in the Structure of the N-Terminal Domain of Cma in Complex with N- Acetyllactosamine


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 in Complex with N- Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd202 b:19.3 occ:1.00 OD2 A:ASP75 2.1 12.8 1.0 O A:HOH430 2.1 18.9 1.0 NE2 A:HIS30 2.1 12.2 1.0 O A:HOH438 2.1 16.8 1.0 O A:HOH445 2.1 17.2 1.0 O A:HOH362 2.2 20.4 1.0 CG A:ASP75 3.0 11.7 1.0 CE1 A:HIS30 3.0 11.3 1.0 CD2 A:HIS30 3.1 11.3 1.0 OD1 A:ASP75 3.3 13.3 1.0 O A:HOH356 4.0 23.1 1.0 O A:HOH492 4.1 22.5 0.5 ND1 A:HIS30 4.2 11.9 1.0 O A:HOH487 4.2 24.0 1.0 CG A:HIS30 4.3 10.6 1.0 CB A:ASP75 4.4 11.2 1.0 O A:HOH505 4.5 28.1 1.0 CD A:LYS79 4.6 26.7 0.3 O A:LYS79 4.7 21.8 0.7 CE A:MET73 5.0 12.7 1.0

Cadmium binding site 3 out of 3 in the Structure of the N-Terminal Domain of Cma in Complex with N- Acetyllactosamine


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 in Complex with N- Acetyllactosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:24.9 occ:1.00 O A:HOH472 2.1 22.3 0.3 OD2 A:ASP92 2.1 36.7 1.0 OG1 A:THR94 2.3 17.4 1.0 O A:HOH472 2.3 25.1 0.7 O A:HOH349 2.4 29.0 1.0 O A:HOH454 2.6 15.0 1.0 OD1 A:ASP92 2.7 33.3 1.0 CG A:ASP92 2.7 31.7 1.0 CB A:THR94 3.4 13.6 1.0 O A:HOH377 4.2 21.9 1.0 CB A:ASP92 4.2 26.0 1.0 CG2 A:THR94 4.3 14.4 1.0 N A:THR94 4.5 12.9 1.0 CA A:THR94 4.5 12.6 1.0 O A:HOH449 4.7 29.0 1.0 O A:HOH407 4.7 22.6 1.0 ND2 A:ASN120 4.8 18.5 1.0 OG A:SER122 4.8 16.9 0.3 OG A:SER122 4.9 17.7 0.7

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.