Cadmium in PDB 1d6v: Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation

The structure of Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation, PDB code: 1d6v 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)	9.92 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.718, 64.446, 73.870, 90.00, 99.09, 90.00
R / Rfree (%)	22.4 / 26.4

The binding sites of Cadmium atom in the Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation (pdb code 1d6v). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation, PDB code: 1d6v:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd501 b:45.3 occ:1.00 OE2 L:GLU79 2.2 34.9 1.0 O L:HOH554 2.6 36.6 1.0 CD L:GLU79 3.0 28.8 1.0 OE1 L:GLU79 3.1 28.2 1.0 O L:HOH581 3.6 41.4 1.0 NH1 L:ARG61 4.0 20.0 1.0 CG L:GLU79 4.4 28.8 1.0 O L:HOH517 4.4 24.1 1.0 O L:HOH562 4.8 41.8 1.0 CZ L:ARG61 5.0 24.6 1.0

Cadmium binding site 2 out of 4 in the Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd502 b:50.1 occ:1.00 O L:HOH556 2.4 36.3 1.0 NE2 H:HIS164 2.4 39.4 1.0 OD1 L:ASN138 2.4 37.8 1.0 CE1 H:HIS164 2.9 41.1 1.0 CG L:ASN138 3.2 37.1 1.0 ND2 L:ASN138 3.3 42.6 1.0 CD2 H:HIS164 3.6 36.3 1.0 O L:HOH571 3.9 34.2 1.0 ND1 H:HIS164 4.2 39.2 1.0 CG H:HIS164 4.5 35.4 1.0 OD1 L:ASN137 4.6 42.9 1.0 CB L:ASN138 4.6 35.1 1.0 O L:HOH534 4.7 57.1 1.0 OD2 L:ASP170 4.7 34.8 1.0 OG L:SER174 4.7 24.4 1.0 OD2 L:ASP167 4.8 39.9 1.0 CA H:GLY162 4.8 39.5 1.0 ND2 L:ASN137 4.9 34.5 1.0

Cadmium binding site 3 out of 4 in the Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd503 b:39.2 occ:1.00 O L:HOH507 2.5 17.7 1.0 O L:HOH568 2.7 23.1 1.0 NZ L:LYS45 3.4 42.1 1.0 NZ L:LYS39 4.2 32.5 1.0 CE L:LYS45 4.5 39.7 1.0 NZ L:LYS42 4.7 41.4 1.0

Cadmium binding site 4 out of 4 in the Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Conformation Effects in Biological Catalysis Introduced By Oxy-Cope Antibody Maturation within 5.0Å range: probe atom residue distance (Å) B Occ L:Cd504 b:34.4 occ:1.00 OE2 L:GLU81 2.3 22.1 1.0 O L:HOH517 2.5 24.1 1.0 O L:HOH566 2.7 91.3 1.0 OE1 L:GLU81 2.8 29.2 1.0 CD L:GLU81 2.9 24.9 1.0 OE1 L:GLU79 4.2 28.2 1.0 CG L:GLU81 4.3 27.0 1.0 NH2 L:ARG61 4.4 30.4 1.0 NH1 L:ARG61 4.6 20.0 1.0 O L:HOH568 4.8 23.1 1.0 CZ L:ARG61 4.9 24.6 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