Cadmium in PDB 8wxd: Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis

The structure of Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis, PDB code: 8wxd was solved by S.Yadav, P.Parijat, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.35 / 2.00
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.593, 89.949, 216.408, 90, 90, 90
R / Rfree (%)	20.9 / 25.9

The structure of Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Sodium	(Na)	6 atoms

The binding sites of Cadmium atom in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis (pdb code 8wxd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis, PDB code: 8wxd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd507 b:25.4 occ:0.85 OE2 A:GLU102 2.3 40.2 1.0 NA A:NA504 2.4 23.9 1.0 NE2 A:HIS75 2.4 39.9 1.0 OE1 A:GLU102 2.6 35.4 1.0 CD A:GLU102 2.8 33.9 1.0 CE1 A:HIS75 3.1 38.7 1.0 CD2 A:HIS75 3.7 36.8 1.0 CG A:GLU102 4.2 30.3 1.0 ND1 A:HIS75 4.4 37.5 1.0 CG A:HIS75 4.6 35.7 1.0 CE1 A:PHE76 4.9 25.4 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd508 b:31.4 occ:1.00 CL A:CL510 2.3 32.5 1.0 ND1 A:HIS147 2.5 39.0 1.0 OG A:SER38 2.5 34.6 1.0 NE2 A:HIS41 2.5 37.0 1.0 CE1 A:HIS147 3.3 39.3 1.0 CE1 A:HIS41 3.3 34.0 1.0 CB A:SER38 3.4 37.1 1.0 CG A:HIS147 3.6 36.0 1.0 CD2 A:HIS41 3.6 36.7 1.0 CB A:HIS147 3.9 32.2 1.0 CA A:HIS147 4.0 30.1 1.0 O A:GLY146 4.3 28.9 1.0 O A:GLU39 4.4 39.7 1.0 NE2 A:HIS147 4.4 38.5 1.0 ND1 A:HIS41 4.5 33.2 1.0 CA A:SER38 4.6 39.6 1.0 CD2 A:HIS147 4.6 36.8 1.0 N A:ALA148 4.6 26.7 1.0 N A:SER38 4.6 38.1 1.0 CG A:HIS41 4.7 36.3 1.0 C A:HIS147 4.9 28.2 1.0 N A:HIS147 5.0 30.1 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd509 b:39.0 occ:0.38 ND1 A:HIS47 2.5 30.4 1.0 CG A:HIS47 3.4 28.0 1.0 CE1 A:HIS47 3.5 29.6 1.0 CB A:HIS47 3.5 27.5 1.0 CD A:PRO66 3.8 43.1 1.0 CD A:LYS128 3.8 66.8 1.0 CG A:PRO66 4.0 45.1 1.0 CG A:LYS128 4.2 61.4 1.0 CD2 A:HIS47 4.5 27.1 1.0 NE2 A:HIS47 4.6 27.8 1.0 CB A:LYS128 4.8 55.0 1.0 OH A:TYR132 4.8 33.0 1.0 CE A:LYS128 4.9 72.2 1.0 CA A:GLY111 4.9 50.2 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd504 b:42.6 occ:0.46 ND1 B:HIS47 2.5 40.5 1.0 CE1 B:HIS47 3.3 41.4 1.0 CG B:HIS47 3.3 37.3 1.0 CB B:HIS47 3.6 35.5 1.0 OH B:TYR132 3.8 40.3 1.0 CD B:LYS128 3.8 72.5 1.0 CE B:LYS128 3.9 77.1 1.0 CG B:LYS128 4.1 68.6 1.0 CB B:LYS128 4.3 62.5 1.0 NE2 B:HIS47 4.4 40.1 1.0 CD2 B:HIS47 4.4 37.7 1.0 CE2 B:TYR132 4.5 35.7 1.0 CZ B:TYR132 4.6 36.7 1.0 CD B:PRO66 4.8 45.7 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd505 b:39.6 occ:0.78 ND1 B:HIS75 2.5 41.8 1.0 CE1 B:HIS75 3.1 40.4 1.0 CG B:HIS75 3.7 38.2 1.0 CB B:HIS75 4.1 37.8 1.0 CA B:HIS75 4.2 38.0 1.0 NE2 B:HIS75 4.4 38.2 1.0 O B:HIS75 4.5 36.0 1.0 CD2 B:HIS75 4.6 37.5 1.0 C B:HIS75 4.9 35.1 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis


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 Shaft Pilin Pila From Streptococcus Sanguinis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd506 b:31.1 occ:1.00 O B:HOH617 2.4 13.1 1.0 OG B:SER38 2.4 37.7 1.0 NE2 B:HIS41 2.4 37.2 1.0 ND1 B:HIS147 2.5 31.1 1.0 CE1 B:HIS41 3.2 35.7 1.0 CE1 B:HIS147 3.3 31.8 1.0 CG B:HIS147 3.5 30.3 1.0 CB B:SER38 3.5 38.7 1.0 CD2 B:HIS41 3.6 37.5 1.0 CB B:HIS147 3.8 28.5 1.0 CA B:HIS147 3.9 26.8 1.0 O B:GLY146 4.3 26.9 1.0 O B:GLU39 4.4 40.0 1.0 ND1 B:HIS41 4.4 32.7 1.0 NE2 B:HIS147 4.5 32.9 1.0 N B:ALA148 4.5 23.5 1.0 CD2 B:HIS147 4.6 31.5 1.0 CG B:HIS41 4.6 34.8 1.0 CA B:SER38 4.6 40.2 1.0 C B:HIS147 4.8 24.7 1.0 N B:SER38 4.8 39.5 1.0 N B:HIS147 4.8 27.0 1.0 C B:GLY146 5.0 28.1 1.0

S.Yadav, P.Parijat, V.Krishnan. Crystal Structure of Shaft Pilin Pila From Streptococcus Sanguinis To Be Published.