Cobalt in PDB 3bd5: 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

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: 3bd5 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)	35.24 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	62.132, 62.132, 93.239, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 27.6

The binding sites of Cobalt 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 3bd5). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt 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: 3bd5:
Jump to Cobalt binding site number: 1; 2;

Cobalt 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 Cobalt with other atoms in the Co 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:Co1 b:49.8 occ:1.00 O A:HOH286 3.2 26.1 1.0 N A:TRP214 3.2 22.7 1.0 C6 A:BTB272 3.2 46.1 1.0 O4 A:BTB272 3.4 39.0 1.0 O6 A:BTB272 3.5 48.5 1.0 N A:LEU197 3.6 24.1 1.0 OG A:SER255 3.6 35.4 1.0 O A:LEU197 3.7 23.8 1.0 C A:LEU197 3.8 23.5 1.0 CD1 A:TRP214 3.8 31.1 1.0 C A:TYR196 3.9 25.1 1.0 C4 A:BTB272 3.9 40.9 1.0 CA A:TYR196 3.9 27.3 1.0 C5 A:BTB272 4.0 46.2 1.0 CA A:TRP214 4.0 26.1 1.0 CB A:TYR213 4.0 22.2 1.0 CB A:ALA198 4.0 22.7 1.0 CA A:TYR213 4.1 24.1 1.0 N A:ALA198 4.1 22.9 1.0 C A:TYR213 4.1 22.8 1.0 CA A:LEU197 4.3 23.6 1.0 O A:ASN195 4.4 28.5 1.0 CA A:ALA198 4.4 22.8 1.0 CB A:TYR196 4.5 29.1 1.0 N A:BTB272 4.6 44.5 1.0 NE1 A:TRP214 4.6 30.6 1.0 O A:TYR196 4.6 22.1 1.0 CD2 A:TYR196 4.6 33.9 1.0 CG A:TRP214 4.7 30.8 1.0 CB A:SER255 4.8 33.3 1.0 CB A:TRP214 5.0 25.2 1.0 C2 A:BTB272 5.0 43.4 1.0

Cobalt 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 Cobalt with other atoms in the Co 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:Co2 b:0.5 occ:1.00 N B:TRP214 3.0 38.7 1.0 O B:HOH277 3.3 30.2 1.0 CB B:TYR213 3.5 43.4 1.0 CA B:TYR213 3.7 40.0 1.0 C B:TYR213 3.8 39.4 1.0 CD1 B:TRP214 3.9 45.5 1.0 CA B:TRP214 3.9 40.2 1.0 N B:LEU197 3.9 31.6 1.0 O B:LEU197 4.0 33.4 1.0 OG B:SER255 4.0 48.8 1.0 C B:LEU197 4.1 31.9 1.0 CB B:ALA198 4.1 29.4 1.0 CA B:TYR196 4.1 38.0 1.0 C B:TYR196 4.2 34.6 1.0 N B:ALA198 4.4 30.7 1.0 CD1 B:TYR196 4.5 47.8 1.0 O B:ASN195 4.5 41.6 1.0 CG B:TYR213 4.5 47.6 1.0 CG B:TRP214 4.5 44.6 1.0 NE1 B:TRP214 4.6 47.1 1.0 CA B:LEU197 4.6 31.3 1.0 CD2 B:TYR213 4.6 49.1 1.0 CA B:ALA198 4.6 28.2 1.0 CB B:TRP214 4.8 40.9 1.0 CB B:TYR196 4.8 40.0 1.0 O B:TYR196 4.9 33.1 1.0

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