Cadmium in PDB 3wzo: Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution

The structure of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution, PDB code: 3wzo was solved by T.Kawato, E.Mizohata, Y.Shimizu, T.Meshizuka, T.Yamamoto, N.Takasu, M.Matsuoka, H.Matsumura, K.Tsumoto, T.Kodama, M.Kanai, H.Doi, T.Inoue, A.Sugiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.241, 85.461, 86.115, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 23.6

The binding sites of Cadmium atom in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution (pdb code 3wzo). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution, PDB code: 3wzo:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


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 the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd203 b:23.1 occ:0.80 OD2 A:ASP101 2.1 19.8 1.0 O A:HOH333 2.3 28.9 1.0 OD1 A:ASP101 2.4 18.1 1.0 O A:HOH334 2.4 21.8 1.0 CG A:ASP101 2.6 19.6 1.0 CB A:ASP101 4.1 16.9 1.0 NZ A:LYS134 4.4 24.1 0.5 NZ A:LYS134 4.5 19.2 0.5 CE A:LYS134 4.5 19.6 0.5 CE A:LYS134 4.9 21.6 0.5 CA A:ASP101 5.0 16.4 1.0

Cadmium binding site 2 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


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 the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd204 b:25.1 occ:0.50 OE1 A:GLU14 2.5 27.4 1.0 OE2 A:GLU14 2.5 25.9 1.0 O A:SER62 2.5 20.6 1.0 O A:HOH337 2.6 23.1 1.0 CD A:GLU14 2.9 22.1 1.0 C A:SER62 3.5 15.6 1.0 CA A:SER62 4.0 13.8 1.0 CB A:SER62 4.1 16.1 1.0 CA A:GLY11 4.4 24.2 1.0 N A:GLY11 4.4 32.0 1.0 CG A:GLU14 4.4 16.7 1.0 CB A:ALA13 4.6 21.8 1.0 N A:ALA63 4.6 16.8 1.0 C A:GLY11 4.8 22.0 1.0 N A:ALA13 4.8 20.5 1.0 CA A:ALA63 4.8 16.4 1.0 O3 A:GOL202 4.9 24.3 1.0 N A:GLU14 4.9 16.1 1.0 CD A:PRO64 5.0 15.8 1.0 CE2 A:TYR60 5.0 9.4 1.0

Cadmium binding site 3 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd205 b:82.8 occ:0.70 O A:HOH356 2.5 48.2 1.0 OE2 A:GLU44 2.5 41.0 1.0 OE1 A:GLU44 2.5 23.6 1.0 CD A:GLU44 2.8 22.6 1.0 CG A:GLU44 4.4 12.6 1.0 NH2 A:ARG53 4.5 33.5 1.0 O A:HOH355 4.7 49.9 1.0 CA A:SER52 4.9 19.5 1.0 CG A:ARG53 5.0 24.9 1.0

Cadmium binding site 4 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd202 b:33.0 occ:0.50 O B:HOH325 2.3 40.9 1.0 O B:SER62 2.5 14.0 1.0 OE1 B:GLU14 2.5 18.0 1.0 O B:HOH331 2.6 23.8 1.0 OE2 B:GLU14 2.6 17.8 1.0 CD B:GLU14 2.9 19.4 1.0 C B:SER62 3.4 12.6 1.0 CA B:SER62 4.0 10.7 1.0 CB B:SER62 4.1 9.3 1.0 CA B:GLY11 4.4 28.5 1.0 CB B:ALA13 4.5 26.7 1.0 CG B:GLU14 4.5 17.1 1.0 O B:HOH353 4.5 49.1 1.0 N B:GLY11 4.5 25.1 1.0 N B:ALA63 4.5 11.2 1.0 CA B:ALA63 4.9 13.8 1.0 C B:GLY11 4.9 26.2 1.0 O B:HOH312 4.9 30.6 1.0 N B:GLU14 4.9 16.0 1.0 N B:ALA13 5.0 23.3 1.0

Cadmium binding site 5 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd203 b:20.6 occ:0.50 O C:HOH331 2.1 44.7 1.0 NE2 C:HIS87 2.4 15.7 1.0 O D:HOH332 2.4 41.8 1.0 CD2 C:HIS87 3.2 14.1 1.0 CE1 C:HIS87 3.4 14.8 1.0 O C:ASN85 4.4 11.3 1.0 CG C:HIS87 4.4 9.1 1.0 ND1 C:HIS87 4.5 11.8 1.0

Cadmium binding site 6 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd203 b:28.2 occ:0.50 NE2 D:HIS87 2.3 12.7 1.0 O D:HOH343 2.4 49.0 1.0 O D:HOH326 2.6 40.1 1.0 O D:HOH353 2.8 51.2 1.0 CD2 D:HIS87 3.2 11.7 1.0 CE1 D:HIS87 3.3 9.5 1.0 O C:HOH351 4.2 51.0 1.0 CG D:HIS87 4.4 9.7 1.0 ND1 D:HIS87 4.4 9.4 1.0 O D:ASN85 4.6 12.9 1.0

Cadmium binding site 7 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd204 b:29.7 occ:0.50 O D:SER62 2.4 17.6 1.0 O D:HOH327 2.5 23.5 1.0 OE1 D:GLU14 2.6 21.8 1.0 OE2 D:GLU14 2.6 16.9 1.0 CD D:GLU14 3.0 16.5 1.0 C D:SER62 3.5 14.5 1.0 CA D:SER62 4.0 11.7 1.0 CB D:SER62 4.1 12.1 1.0 CA D:GLY11 4.4 25.4 1.0 CB D:ALA13 4.4 18.6 1.0 N D:GLY11 4.5 29.6 1.0 CG D:GLU14 4.5 14.2 1.0 N D:ALA63 4.6 12.3 1.0 O3 D:GOL202 4.6 30.0 1.0 C D:GLY11 4.8 24.3 1.0 N D:GLU14 4.8 15.6 1.0 N D:ALA13 4.8 19.7 1.0 CD D:PRO64 5.0 13.3 1.0 CA D:ALA63 5.0 11.3 1.0

Cadmium binding site 8 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd205 b:0.8 occ:0.80 OE2 D:GLU44 2.0 59.9 1.0 OE1 D:GLU44 2.5 46.7 1.0 CD D:GLU44 2.6 38.7 1.0 O D:HOH333 3.4 70.6 1.0 CG D:GLU44 4.1 24.6 1.0 CA D:SER52 4.6 13.7 1.0 NH2 D:ARG53 4.9 32.1 1.0 CG D:ARG53 4.9 25.9 1.0 O D:HOH319 5.0 34.2 1.0 CB D:GLU44 5.0 23.0 1.0

Cadmium binding site 9 out of 9 in the Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of the Core Streptavidin Mutant V21 (Y22S/N23D/S27D/Y83S/R84K/E101D/R103K/E116N) Complexed with Biotin Long Tail (Btntail) at 1.5 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd206 b:22.6 occ:0.60 O D:HOH335 1.3 27.5 1.0 OD1 D:ASP101 2.1 27.9 1.0 O D:HOH344 2.3 32.8 1.0 OD2 D:ASP101 2.6 38.6 1.0 CG D:ASP101 2.7 29.3 1.0 CB D:ASP101 4.2 20.7 1.0 CA D:ASP101 5.0 20.6 1.0

T.Kawato, E.Mizohata, Y.Shimizu, T.Meshizuka, T.Yamamoto, N.Takasu, M.Matsuoka, H.Matsumura, T.Kodama, M.Kanai, H.Doi, T.Inoue, A.Sugiyama. Structure-Based Design of A Streptavidin Mutant Specific For An Artificial Biotin Analogue J.Biochem. 2015.
ISSN: ISSN 0021-924X
PubMed: 25645976
DOI: 10.1093/JB/MVV004