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Cadmium in PDB 1a4k: Diels Alder Catalytic Antibody with Transition State Analogue

Protein crystallography data

The structure of Diels Alder Catalytic Antibody with Transition State Analogue, PDB code: 1a4k was solved by B.W.Spiller, F.E.Romesburg, 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 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.316, 96.823, 172.730, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 29.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Diels Alder Catalytic Antibody with Transition State Analogue (pdb code 1a4k). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Diels Alder Catalytic Antibody with Transition State Analogue, PDB code: 1a4k:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 1a4k

Go back to Cadmium Binding Sites List in 1a4k
Cadmium binding site 1 out of 4 in the Diels Alder Catalytic Antibody with Transition State Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Diels Alder Catalytic Antibody with Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd5028

b:37.4
occ:1.00
OE1 L:GLU79 2.5 54.0 1.0
OE1 L:GLU81 2.8 60.4 1.0
CD L:GLU79 3.3 55.2 1.0
OE2 L:GLU79 3.3 60.0 1.0
CD L:GLU81 3.8 60.6 1.0
NH2 L:ARG61 4.0 27.5 1.0
OE2 L:GLU81 4.2 46.6 1.0
NE L:ARG61 4.5 30.5 1.0
CG L:GLU79 4.7 46.8 1.0
CZ L:ARG61 4.7 28.6 1.0

Cadmium binding site 2 out of 4 in 1a4k

Go back to Cadmium Binding Sites List in 1a4k
Cadmium binding site 2 out of 4 in the Diels Alder Catalytic Antibody with Transition State Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Diels Alder Catalytic Antibody with Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd5029

b:62.5
occ:1.00
ND2 L:ASN138 2.2 43.9 1.0
O L:HOH5057 2.5 56.1 1.0
CE1 H:HIS164 2.8 68.1 1.0
O L:HOH5049 2.9 24.7 1.0
NE2 H:HIS164 3.1 63.3 1.0
CG L:ASN138 3.2 47.5 1.0
O L:HOH5051 3.2 84.2 1.0
OD1 L:ASN138 3.3 52.5 1.0
ND1 H:HIS164 3.7 65.1 1.0
OD2 L:ASP170 4.1 63.1 1.0
CD2 H:HIS164 4.1 63.2 1.0
O L:HOH5050 4.1 21.7 1.0
O H:HOH3092 4.2 32.5 1.0
CG H:HIS164 4.4 62.0 1.0
CB L:ASN138 4.6 41.0 1.0
ND2 L:ASN137 4.7 47.1 1.0
O H:GLY162 4.8 59.2 1.0
OD1 L:ASN137 4.8 40.3 1.0
OG L:SER174 4.9 38.0 1.0

Cadmium binding site 3 out of 4 in 1a4k

Go back to Cadmium Binding Sites List in 1a4k
Cadmium binding site 3 out of 4 in the Diels Alder Catalytic Antibody with Transition State Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Diels Alder Catalytic Antibody with Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5028

b:41.7
occ:1.00
O A:HOH5051 2.5 25.1 1.0
O A:HOH5055 2.6 22.5 1.0
OE1 A:GLU79 2.6 31.7 1.0
OE2 A:GLU81 2.8 60.4 1.0
CD A:GLU81 3.3 63.2 1.0
OE1 A:GLU81 3.5 64.3 1.0
CD A:GLU79 3.7 36.3 1.0
OE2 A:GLU79 4.3 36.8 1.0
NH2 A:ARG61 4.4 22.0 1.0
CG A:GLU81 4.5 50.3 1.0
NE A:ARG61 4.5 34.1 1.0
CZ A:ARG61 4.9 29.2 1.0
CG A:GLU79 4.9 30.9 1.0
CB A:GLU79 4.9 27.0 1.0

Cadmium binding site 4 out of 4 in 1a4k

Go back to Cadmium Binding Sites List in 1a4k
Cadmium binding site 4 out of 4 in the Diels Alder Catalytic Antibody with Transition State Analogue


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Diels Alder Catalytic Antibody with Transition State Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd5029

b:41.5
occ:1.00
ND2 A:ASN138 2.3 19.3 1.0
CE1 B:HIS164 2.6 39.7 1.0
O A:HOH5061 2.8 48.8 1.0
O A:HOH5071 2.8 44.2 1.0
O A:HOH5059 3.1 78.9 1.0
CG A:ASN138 3.4 28.6 1.0
ND1 B:HIS164 3.5 38.7 1.0
NE2 B:HIS164 3.5 39.7 1.0
OD1 A:ASN138 3.7 43.4 1.0
O B:HOH3102 3.7 50.5 1.0
OD2 A:ASP170 4.0 38.1 1.0
O A:HOH5065 4.2 33.4 1.0
CB A:ASN138 4.6 21.0 1.0
CG B:HIS164 4.6 41.7 1.0
CD2 B:HIS164 4.6 39.9 1.0
CA B:GLY162 4.8 45.8 1.0
ND2 A:ASN137 4.8 26.1 1.0
O B:GLY162 4.8 44.4 1.0
OD1 A:ASN137 4.9 28.4 1.0
OG A:SER174 4.9 21.6 1.0
OG1 A:THR172 4.9 18.1 1.0

Reference:

F.E.Romesberg, B.Spiller, P.G.Schultz, R.C.Stevens. Immunological Origins of Binding and Catalysis in A Diels-Alderase Antibody. Science V. 279 1929 1998.
ISSN: ISSN 0036-8075
PubMed: 9506942
DOI: 10.1126/SCIENCE.279.5358.1929
Page generated: Fri Aug 28 11:37:59 2020
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