Cadmium in PDB 1sm3: Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope

The structure of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope, PDB code: 1sm3 was solved by P.Dokurno, P.A.Bates, H.A.Band, L.M.D.Stewart, J.M.Lally, J.M.Burchell, J.Taylor-Papadimitriou, M.J.E.Sternberg, D.Snary, P.S.Freemont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.200, 83.730, 67.240, 90.00, 93.30, 90.00
R / Rfree (%)	21.3 / 28.3

The structure of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cadmium atom in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope (pdb code 1sm3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope, PDB code: 1sm3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd213 b:56.5 occ:1.00 O L:HOH292 2.2 36.5 1.0 O L:HOH290 2.2 32.7 1.0 O L:HOH232 2.3 34.1 1.0 NE2 L:HIS42 2.8 17.5 1.0 CD2 L:HIS42 3.5 17.6 1.0 CE1 L:HIS42 3.9 19.5 1.0 O H:HOH358 4.8 19.7 1.0 CG L:HIS42 4.8 17.7 1.0 ND1 L:HIS42 4.9 21.6 1.0

Cadmium binding site 2 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd214 b:48.9 occ:0.75 O L:HIS197 2.2 21.5 1.0 O L:HOH249 2.7 23.0 1.0 ND1 L:HIS197 2.8 13.7 1.0 ND1 L:HIS200 3.1 45.6 1.0 C L:HIS197 3.3 19.1 1.0 CG L:HIS197 3.4 9.5 1.0 CE1 L:HIS200 3.5 46.3 1.0 CB L:HIS197 3.5 12.6 1.0 OG L:SER112 3.6 30.0 1.0 CE1 L:HIS197 3.8 10.7 1.0 CG L:HIS200 3.8 42.2 1.0 CB L:GLU198 3.8 25.4 1.0 CA L:HIS197 4.1 13.6 1.0 CG L:GLU198 4.2 26.0 1.0 CB L:HIS200 4.2 34.1 1.0 N L:GLU198 4.2 19.9 1.0 NE2 L:HIS200 4.4 46.2 1.0 CA L:GLU198 4.5 23.3 1.0 O L:GLU198 4.5 25.4 1.0 CD2 L:HIS197 4.6 8.8 1.0 O L:HIS200 4.6 27.6 1.0 CD2 L:HIS200 4.6 44.5 1.0 CA L:SER112 4.6 17.4 1.0 CB L:SER112 4.7 20.9 1.0 NE2 L:HIS197 4.7 13.2 1.0 C L:GLU198 4.7 25.2 1.0 N L:HIS197 4.8 14.4 1.0 CD L:PRO113 4.8 7.8 1.0 N L:HIS200 4.9 29.3 1.0

Cadmium binding site 3 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd215 b:26.8 occ:0.75 O L:HOH237 2.2 15.2 1.0 O L:HOH266 2.2 18.0 1.0 OD1 L:ASN52 2.4 22.6 1.0 O L:HOH282 2.6 26.1 1.0 CG L:ASN52 3.4 24.4 1.0 ND2 L:ASN52 3.7 28.2 1.0 O L:GLY50 4.0 12.5 1.0 O L:HOH311 4.2 43.0 1.0 O L:HOH309 4.4 19.6 1.0 N L:ASN53 4.7 16.3 1.0 CB L:ASN52 4.7 18.4 1.0 C L:ASN52 4.8 15.4 1.0 N L:ASN52 4.8 12.2 1.0 CB L:ASN53 4.9 24.0 1.0 O H:HOH293 4.9 33.6 1.0

Cadmium binding site 4 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd216 b:56.4 occ:0.75 O L:HOH271 2.1 47.0 1.0 O L:HOH242 2.2 29.0 1.0 O L:HOH321 2.3 51.3 1.0 OE1 L:GLU160 2.5 28.3 1.0 CD L:GLU160 3.3 30.1 1.0 OE2 L:GLU160 3.4 30.7 1.0 O L:HOH274 4.2 27.5 1.0 CG L:GLU160 4.8 24.3 1.0

Cadmium binding site 5 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd215 b:34.5 occ:1.00 O L:HOH346 2.5 32.2 1.0 O H:HOH314 2.6 20.9 1.0 NE2 H:HIS164 2.8 19.9 1.0 CD2 H:HIS164 3.6 16.4 1.0 CE1 H:HIS164 3.7 18.9 1.0 O H:HOH374 3.8 26.6 1.0 OD2 L:ASP138 3.8 16.1 1.0 OD1 L:ASP138 4.0 15.9 1.0 CG L:ASP138 4.3 16.6 1.0 OG1 L:THR137 4.7 11.7 1.0 CG H:HIS164 4.7 17.4 1.0 ND1 H:HIS164 4.7 19.8 1.0 O L:HOH322 4.7 15.0 1.0

Cadmium binding site 6 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd216 b:25.1 occ:1.00 O H:HOH285 2.1 17.2 1.0 O H:HOH308 2.1 11.8 1.0 OE1 H:GLU191 2.4 31.1 1.0 OE2 H:GLU191 2.5 26.4 1.0 CL H:CL219 2.6 22.1 1.0 CD H:GLU191 2.8 28.3 1.0 CG H:GLU191 4.3 28.5 1.0 O H:SER190 4.5 25.1 1.0 O H:HOH365 4.7 37.2 1.0

Cadmium binding site 7 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd217 b:17.7 occ:1.00 O H:HOH373 2.0 7.5 1.0 O H:HOH348 2.3 26.2 1.0 CL H:CL220 2.5 26.9 1.0 NE2 H:HIS58 2.6 10.0 1.0 CD2 H:HIS58 3.3 7.3 1.0 CE1 H:HIS58 3.6 8.7 1.0 O H:HOH312 4.1 5.7 1.0 O H:HOH275 4.3 23.0 1.0 CG H:HIS58 4.5 4.6 1.0 ND1 H:HIS58 4.6 5.5 1.0 O L:HOH360 4.8 29.4 1.0 ND2 L:ASN94 4.8 21.5 1.0 CB L:ASN94 4.8 18.1 1.0

Cadmium binding site 8 out of 8 in the Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Tumor Specific Antibody SM3 Complex with Its Peptide Epitope within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd218 b:57.2 occ:1.00 O H:HOH288 2.3 38.2 1.0 O H:HOH318 2.6 35.7 1.0 O H:HOH289 3.0 16.0 1.0 O H:HOH228 4.2 21.3 1.0 OG1 H:THR28 4.5 19.9 1.0 CB P:PRO10 4.6 14.7 1.0

P.Dokurno, P.A.Bates, H.A.Band, L.M.Stewart, J.M.Lally, J.M.Burchell, J.Taylor-Papadimitriou, D.Snary, M.J.Sternberg, P.S.Freemont. Crystal Structure at 1.95 A Resolution of the Breast Tumour-Specific Antibody SM3 Complexed with Its Peptide Epitope Reveals Novel Hypervariable Loop Recognition. J.Mol.Biol. V. 284 713 1998.
ISSN: ISSN 0022-2836
PubMed: 9826510
DOI: 10.1006/JMBI.1998.2209