Cadmium in PDB 1d5i: Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody

The structure of Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody, PDB code: 1d5i was solved by E.C.Mundorff, M.A.Hanson, P.G.Schultz, R.C.Stevens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.170, 64.130, 75.950, 90.00, 99.53, 90.00
R / Rfree (%)	21.6 / 26.3

The binding sites of Cadmium atom in the Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody (pdb code 1d5i). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody, PDB code: 1d5i:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd212 b:39.6 occ:1.00 ND2 L:ASN138 2.2 32.8 1.0 O L:HOH243 2.3 29.8 1.0 O L:HOH242 2.4 26.1 1.0 O L:HOH241 2.4 31.6 1.0 CE1 H:HIS164 2.5 25.2 1.0 O L:HOH304 2.7 50.0 1.0 NE2 H:HIS164 3.0 30.4 1.0 CG L:ASN138 3.1 35.9 1.0 OD1 L:ASN138 3.4 40.8 1.0 ND1 H:HIS164 3.7 30.2 1.0 O L:HOH244 4.0 27.9 1.0 O H:HOH280 4.3 39.9 1.0 CD2 H:HIS164 4.3 29.3 1.0 CB L:ASN138 4.4 31.8 1.0 OD2 L:ASP170 4.6 44.2 1.0 CG H:HIS164 4.6 27.5 1.0 OG L:SER174 4.7 27.2 1.0 ND2 L:ASN137 4.8 30.7 1.0 OD2 L:ASP167 4.8 32.9 1.0 CA H:GLY162 4.9 38.1 1.0 OG1 L:THR172 4.9 28.2 1.0 OD1 L:ASN137 5.0 37.2 1.0 OD1 L:ASP170 5.0 45.5 1.0

Cadmium binding site 2 out of 3 in the Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd213 b:38.1 occ:1.00 O L:HOH312 1.6 20.5 1.0 OE1 L:GLU93 2.4 36.6 1.0 CD L:GLU93 2.9 39.9 1.0 CG L:GLU93 3.1 36.5 1.0 OE2 L:GLU93 3.9 45.0 1.0 O L:HOH233 4.1 30.6 1.0 CB L:GLU93 4.7 33.4 1.0

Cadmium binding site 3 out of 3 in the Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Unliganded Germline Precursor of An Oxy-Cope Catalytic Antibody within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd214 b:27.6 occ:1.00 O L:HOH313 1.6 22.3 1.0 O L:HOH293 2.2 33.0 1.0 OE2 L:GLU81 2.3 25.6 1.0 OE1 L:GLU81 2.5 31.4 1.0 CD L:GLU81 2.7 30.4 1.0 O L:HOH292 4.0 29.6 1.0 CG L:GLU81 4.2 26.7 1.0 OE1 L:GLU79 4.4 31.4 1.0 NH2 L:ARG61 4.5 22.6 1.0 NH1 L:ARG61 4.6 22.9 1.0

E.C.Mundorff, M.A.Hanson, A.Varvak, H.Ulrich, P.G.Schultz, R.C.Stevens. Conformational Effects in Biological Catalysis: An Antibody-Catalyzed Oxy-Cope Rearrangement. Biochemistry V. 39 627 2000.
ISSN: ISSN 0006-2960
PubMed: 10651626
DOI: 10.1021/BI9924314