Cadmium in PDB 5chb: Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal

The structure of Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal, PDB code: 5chb was solved by A.R.D.Voet, H.Noguchi, C.Addy, K.Y.J.Zhang, J.R.H.Tame, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.55
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	61.200, 61.200, 109.558, 90.00, 90.00, 120.00
R / Rfree (%)	15.2 / 18.8

The structure of Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

The binding sites of Cadmium atom in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal (pdb code 5chb). 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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal, PDB code: 5chb:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal


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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd101 b:15.0 occ:1.00 NE2 C:HIS58 2.3 18.1 1.0 NE2 B:HIS58 2.3 16.0 1.0 NE2 A:HIS58 2.4 15.7 1.0 O B:HOH221 2.4 16.3 1.0 O B:HOH219 2.4 15.5 1.0 O B:HOH220 2.4 15.9 1.0 CD2 B:HIS58 3.1 13.4 1.0 CD2 C:HIS58 3.1 16.3 1.0 CD2 A:HIS58 3.2 15.6 1.0 CE1 C:HIS58 3.3 18.6 1.0 CE1 A:HIS58 3.4 17.3 1.0 CE1 B:HIS58 3.4 15.8 1.0 O4 B:SO4107 4.3 26.7 0.7 CG C:HIS58 4.3 17.0 1.0 CG B:HIS58 4.3 15.4 1.0 O3 B:SO4107 4.3 32.3 0.7 CG A:HIS58 4.3 16.2 1.0 O2 B:SO4107 4.3 26.2 0.7 ND1 C:HIS58 4.3 17.0 1.0 ND1 B:HIS58 4.4 17.3 1.0 ND1 A:HIS58 4.4 17.4 1.0 O B:HIS58 4.5 17.8 1.0 O C:HIS58 4.6 16.4 1.0 S B:SO4107 4.6 37.9 0.7 O A:HIS58 4.6 17.9 1.0 CB B:SER16 4.8 14.8 1.0 CB A:SER16 4.8 14.9 1.0 CB C:SER16 4.9 15.9 1.0

Cadmium binding site 2 out of 6 in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal


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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd101 b:13.1 occ:1.00 NE2 B:HIS73 2.4 14.8 1.0 CL B:CL105 2.6 15.2 1.0 CL C:CL105 2.6 13.8 1.0 CL B:CL106 2.7 14.7 1.0 CL B:CL104 2.8 14.1 1.0 CD2 B:HIS73 3.1 14.4 1.0 CE1 B:HIS73 3.4 15.3 1.0 CD C:CD101 4.0 13.3 1.0 CD B:CD102 4.1 14.0 0.5 CD B:CD103 4.1 15.5 0.5 CG B:HIS73 4.3 14.3 1.0 ND1 B:HIS73 4.4 13.7 1.0 CE1 C:HIS31 4.6 16.1 1.0 NE2 C:HIS31 4.7 15.0 1.0 ND1 B:HIS58 4.8 17.3 1.0 CE1 B:HIS58 4.9 15.8 1.0 CL C:CL104 4.9 13.8 1.0

Cadmium binding site 3 out of 6 in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal


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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd102 b:14.0 occ:0.50 NE2 B:HIS31 2.3 15.9 1.0 CL B:CL105 2.6 15.2 1.0 CL B:CL104 2.8 14.1 1.0 CE1 B:HIS31 3.2 16.8 1.0 CD2 B:HIS31 3.4 18.3 1.0 CD B:CD103 4.0 15.5 0.5 CD B:CD101 4.1 13.1 1.0 ND1 B:HIS31 4.4 17.1 1.0 CG B:HIS31 4.5 16.6 1.0 CL B:CL106 4.8 14.7 1.0

Cadmium binding site 4 out of 6 in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal


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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd103 b:15.5 occ:0.50 CL B:CL106 2.7 14.7 1.0 CL B:CL104 2.7 14.1 1.0 CL C:CL104 2.7 13.8 1.0 CD B:CD102 4.0 14.0 0.5 CD C:CD101 4.0 13.3 1.0 CD B:CD101 4.1 13.1 1.0 CD C:CD102 4.1 12.9 0.5 CL B:CL105 4.7 15.2 1.0 CL C:CL103 4.7 15.3 1.0 CL C:CL105 4.7 13.8 1.0

Cadmium binding site 5 out of 6 in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal


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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd101 b:13.3 occ:1.00 NE2 C:HIS31 2.3 15.0 1.0 CL C:CL105 2.6 13.8 1.0 CL C:CL103 2.6 15.3 1.0 CL C:CL104 2.7 13.8 1.0 CL B:CL106 2.8 14.7 1.0 CE1 C:HIS31 3.2 16.1 1.0 CD2 C:HIS31 3.3 17.3 1.0 CD B:CD103 4.0 15.5 0.5 CD C:CD102 4.0 12.9 0.5 CD B:CD101 4.0 13.1 1.0 ND1 C:HIS31 4.4 15.8 1.0 CG C:HIS31 4.4 16.2 1.0 CL B:CL104 4.8 14.1 1.0 NE2 B:HIS73 5.0 14.8 1.0

Cadmium binding site 6 out of 6 in the Crystal Structure of NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal


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 NVPIZZA2-S16H58 Coordinating A CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd102 b:12.9 occ:0.50 NE2 C:HIS73 2.4 14.8 1.0 CL C:CL103 2.6 15.3 1.0 CL C:CL104 2.7 13.8 1.0 CD2 C:HIS73 3.2 14.9 1.0 CE1 C:HIS73 3.4 14.8 1.0 CD C:CD101 4.0 13.3 1.0 CD B:CD103 4.1 15.5 0.5 CG C:HIS73 4.4 15.4 1.0 ND1 C:HIS73 4.4 14.8 1.0 CE1 A:HIS31 4.6 14.2 1.0 NE2 A:HIS31 4.8 15.4 1.0 ND1 C:HIS58 4.9 17.0 1.0 CL B:CL106 4.9 14.7 1.0 CE1 C:HIS58 5.0 18.6 1.0

A.R.D.Voet, H.Noguchi, C.Addy, K.Y.J.Zhang, J.R.H.Tame. Biomineralization of A Cadmium Chloride Nanocrystal By A Designed Symmetrical Protein Angew.Chem.Int.Ed.Engl. V. 54 9857 2015.
ISSN: ESSN 1521-3773
PubMed: 26136355
DOI: 10.1002/ANIE.201503575