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Cadmium in PDB 3bd4: Crystal Structure of Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals

Protein crystallography data

The structure of Crystal Structure of Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals, PDB code: 3bd4 was solved by S.K.Park, J.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 61.852, 61.852, 92.090, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 28.1

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals (pdb code 3bd4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Crystal Structure of Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals, PDB code: 3bd4:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 3bd4

Go back to Cadmium Binding Sites List in 3bd4
Cadmium binding site 1 out of 2 in the Crystal Structure of Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals


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 Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd2

b:0.6
occ:1.00
O A:HOH27 3.1 18.6 1.0
N A:TRP214 3.3 19.0 1.0
O4 A:BTB1 3.5 43.2 1.0
OG A:SER255 3.5 40.8 1.0
N A:LEU197 3.6 24.0 1.0
C6 A:BTB1 3.7 48.8 1.0
O A:LEU197 3.7 22.8 1.0
C A:TYR196 3.7 27.2 1.0
CD1 A:TRP214 3.8 20.2 1.0
C A:LEU197 3.8 21.9 1.0
CA A:TYR196 3.8 29.2 1.0
C4 A:BTB1 4.0 48.0 1.0
CB A:TYR213 4.0 19.3 1.0
O6 A:BTB1 4.0 49.3 1.0
CA A:TRP214 4.1 19.8 1.0
CB A:ALA198 4.1 18.2 1.0
CA A:TYR213 4.1 19.7 1.0
N A:ALA198 4.1 21.0 1.0
C A:TYR213 4.2 18.8 1.0
CA A:LEU197 4.3 23.4 1.0
C5 A:BTB1 4.3 50.4 1.0
CB A:TYR196 4.4 30.6 1.0
O A:TYR196 4.4 27.8 1.0
O A:ASN195 4.4 31.1 1.0
CA A:ALA198 4.5 20.6 1.0
NE1 A:TRP214 4.5 22.5 1.0
CD2 A:TYR196 4.5 34.3 1.0
CB A:SER255 4.6 40.9 1.0
CG A:TRP214 4.7 21.2 1.0
N A:BTB1 4.8 50.9 1.0
CG A:TYR196 4.9 31.2 1.0

Cadmium binding site 2 out of 2 in 3bd4

Go back to Cadmium Binding Sites List in 3bd4
Cadmium binding site 2 out of 2 in the Crystal Structure of Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals


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 Single Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1

b:78.6
occ:1.00
O B:HOH80 2.7 16.7 1.0
O B:HOH81 2.8 35.7 1.0
O B:HOH38 3.2 31.7 1.0
OG B:SER255 3.4 38.3 1.0
CB B:SER255 4.3 34.4 1.0
CD2 B:TYR196 4.4 40.1 1.0
CB B:TYR213 4.5 34.6 1.0
NE1 B:TRP214 4.6 45.7 1.0
CD1 B:TRP214 4.6 42.5 1.0

Reference:

S.Y.Park, W.R.Lee, S.C.Lee, M.H.Kwon, Y.S.Kim, J.S.Kim. Crystal Structure of Single-Domain Vl of An Anti-Dna Binding Antibody 3D8 Scfv and Its Active Site Revealed By Complex Structures of A Small Molecule and Metals Proteins V. 71 2091 2008.
ISSN: ISSN 0887-3585
PubMed: 18338383
DOI: 10.1002/PROT.22011
Page generated: Wed Oct 28 10:00:59 2020
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