Cadmium in PDB 6rel: Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal

The structure of Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal, PDB code: 6rel was solved by H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.41 / 1.08
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.642, 71.642, 166.889, 90.00, 90.00, 90.00
R / Rfree (%)	12.2 / 13.8

The structure of Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal also contains other interesting chemical elements:

Chlorine

(Cl)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal (pdb code 6rel). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal, PDB code: 6rel:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in the Crystal Structure of PIZZA6-Sh with 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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:5.1 occ:1.00 NE2 B:HIS31 2.3 6.8 1.0 NE2 A:HIS199 2.3 5.9 1.0 CL B:CL309 2.6 5.6 1.0 CL A:CL314 2.6 5.5 1.0 CL A:CL313 2.7 5.4 1.0 CL B:CL308 2.7 5.7 1.0 CE1 B:HIS31 3.2 7.7 1.0 CE1 A:HIS199 3.2 6.9 1.0 CD2 A:HIS199 3.3 6.0 1.0 CD2 B:HIS31 3.3 7.0 1.0 CD B:CD301 4.0 5.0 1.0 CD A:CD306 4.0 5.0 1.0 CD A:CD302 4.0 5.0 1.0 ND1 A:HIS199 4.3 7.0 1.0 ND1 B:HIS31 4.4 7.8 1.0 CG A:HIS199 4.4 7.0 1.0 CG B:HIS31 4.5 6.8 1.0 CL B:CL307 4.8 5.5 1.0 CL A:CL312 4.8 5.5 1.0

Cadmium binding site 2 out of 11 in the Crystal Structure of PIZZA6-Sh with 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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:5.0 occ:1.00 NE2 B:HIS241 2.4 7.1 1.0 NE2 A:HIS241 2.4 6.5 1.0 CL A:CL314 2.6 5.5 1.0 CL B:CL304 2.6 5.5 1.0 CL A:CL312 2.8 5.5 1.0 CL B:CL308 2.8 5.7 1.0 CD2 B:HIS241 3.2 6.1 1.0 CD2 A:HIS241 3.2 6.5 1.0 CE1 A:HIS241 3.4 6.0 1.0 CE1 B:HIS241 3.4 6.8 1.0 CD A:CD301 4.0 5.1 1.0 CD A:CD303 4.0 5.1 1.0 CD B:CD301 4.1 5.0 1.0 CG B:HIS241 4.4 6.9 1.0 CG A:HIS241 4.4 5.9 1.0 ND1 A:HIS241 4.4 5.8 1.0 ND1 B:HIS241 4.4 7.1 1.0 CE1 B:HIS31 4.6 7.7 1.0 CE1 A:HIS31 4.7 8.7 1.0 ND1 B:HIS226 4.7 7.0 1.0 NE2 B:HIS31 4.7 6.8 1.0 ND1 A:HIS226 4.8 6.7 1.0 NE2 A:HIS31 4.8 8.8 1.0 CE1 B:HIS226 4.8 7.2 1.0 CE1 A:HIS226 4.8 7.5 1.0 CL A:CL313 4.9 5.4 1.0 CL B:CL305 4.9 5.7 1.0

Cadmium binding site 3 out of 11 in the Crystal Structure of PIZZA6-Sh with 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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:5.1 occ:1.00 NE2 A:HIS31 2.4 8.8 1.0 NE2 B:HIS199 2.4 8.9 1.0 CL B:CL304 2.6 5.5 1.0 CL A:CL311 2.6 5.5 1.0 CL A:CL312 2.7 5.5 1.0 CL B:CL305 2.8 5.7 1.0 CE1 A:HIS31 3.2 8.7 1.0 CE1 B:HIS199 3.3 10.1 1.0 CD2 A:HIS31 3.4 8.8 1.0 CD2 B:HIS199 3.4 8.5 1.0 CD B:CD301 4.0 5.0 1.0 CD A:CD304 4.0 5.0 1.0 CD A:CD302 4.0 5.0 1.0 ND1 A:HIS31 4.3 8.5 1.0 ND1 B:HIS199 4.4 8.0 1.0 CG A:HIS31 4.5 7.5 1.0 CG B:HIS199 4.5 7.6 1.0 CL A:CL310 4.7 5.6 1.0 CL B:CL308 4.8 5.7 1.0

Cadmium binding site 4 out of 11 in the Crystal Structure of PIZZA6-Sh with 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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd304 b:5.0 occ:1.00 NE2 A:HIS73 2.4 6.3 1.0 NE2 B:HIS157 2.4 6.3 1.0 CL A:CL311 2.6 5.5 1.0 CL B:CL306 2.6 5.5 1.0 CL B:CL305 2.8 5.7 1.0 CL A:CL310 2.8 5.6 1.0 CD2 A:HIS73 3.2 6.5 1.0 CD2 B:HIS157 3.2 6.6 1.0 CE1 B:HIS157 3.4 6.4 1.0 CE1 A:HIS73 3.4 6.5 1.0 CD A:CD303 4.0 5.1 1.0 CD A:CD305 4.0 5.0 1.0 CD B:CD301 4.1 5.0 1.0 CG A:HIS73 4.4 6.7 1.0 CG B:HIS157 4.4 6.0 1.0 ND1 B:HIS157 4.4 6.3 1.0 ND1 A:HIS73 4.4 6.6 1.0 CE1 A:HIS115 4.6 7.6 1.0 NE2 A:HIS115 4.7 6.2 1.0 CE1 B:HIS199 4.7 10.1 1.0 ND1 B:HIS142 4.8 6.8 1.0 NE2 B:HIS199 4.8 8.9 1.0 ND1 A:HIS58 4.8 7.0 1.0 CE1 A:HIS58 4.8 6.9 1.0 CE1 B:HIS142 4.8 6.7 1.0 CL A:CL312 4.9 5.5 1.0 CL B:CL307 4.9 5.5 1.0

Cadmium binding site 5 out of 11 in the Crystal Structure of PIZZA6-Sh with 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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd305 b:5.0 occ:1.00 NE2 B:HIS115 2.3 6.5 1.0 NE2 A:HIS115 2.3 6.2 1.0 CL B:CL306 2.6 5.5 1.0 CL A:CL309 2.6 5.5 1.0 CL B:CL307 2.7 5.5 1.0 CL A:CL310 2.8 5.6 1.0 CE1 A:HIS115 3.2 7.6 1.0 CE1 B:HIS115 3.2 6.5 1.0 CD2 B:HIS115 3.3 7.3 1.0 CD2 A:HIS115 3.3 6.5 1.0 CD B:CD301 4.0 5.0 1.0 CD A:CD304 4.0 5.0 1.0 CD A:CD306 4.0 5.0 1.0 ND1 B:HIS115 4.3 7.3 1.0 ND1 A:HIS115 4.3 7.4 1.0 CG B:HIS115 4.4 6.6 1.0 CG A:HIS115 4.4 6.5 1.0 CL B:CL305 4.7 5.7 1.0 CL A:CL313 4.8 5.4 1.0 CE1 B:HIS142 5.0 6.7 1.0

Cadmium binding site 6 out of 11 in the Crystal Structure of PIZZA6-Sh with 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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd306 b:5.0 occ:1.00 NE2 B:HIS73 2.4 6.6 1.0 NE2 A:HIS157 2.4 6.3 1.0 CL B:CL309 2.6 5.6 1.0 CL A:CL309 2.6 5.5 1.0 CL B:CL307 2.8 5.5 1.0 CL A:CL313 2.8 5.4 1.0 CD2 A:HIS157 3.2 6.0 1.0 CD2 B:HIS73 3.2 6.7 1.0 CE1 B:HIS73 3.4 6.5 1.0 CE1 A:HIS157 3.4 6.1 1.0 CD A:CD301 4.0 5.1 1.0 CD A:CD305 4.0 5.0 1.0 CD B:CD301 4.1 5.0 1.0 CG A:HIS157 4.4 5.8 1.0 CG B:HIS73 4.4 6.4 1.0 ND1 B:HIS73 4.4 6.2 1.0 ND1 A:HIS157 4.5 6.4 1.0 CE1 B:HIS115 4.6 6.5 1.0 CE1 A:HIS199 4.7 6.9 1.0 NE2 B:HIS115 4.7 6.5 1.0 NE2 A:HIS199 4.7 5.9 1.0 ND1 B:HIS58 4.8 6.3 1.0 ND1 A:HIS142 4.8 6.7 1.0 CE1 B:HIS58 4.8 6.8 1.0 CE1 A:HIS142 4.9 7.0 1.0 CL B:CL308 4.9 5.7 1.0 CL A:CL310 4.9 5.6 1.0

Cadmium binding site 7 out of 11 in the Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal


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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd307 b:5.8 occ:1.00 NE2 A:HIS142 2.3 6.7 1.0 NE2 A:HIS226 2.3 6.5 1.0 NE2 A:HIS58 2.3 6.8 1.0 O A:HOH489 2.4 7.3 1.0 O A:HOH466 2.4 7.7 1.0 O A:HOH493 2.4 6.9 1.0 CD2 A:HIS226 3.1 6.4 1.0 CD2 A:HIS58 3.2 6.3 1.0 CD2 A:HIS142 3.2 5.9 1.0 CE1 A:HIS142 3.2 7.0 1.0 CE1 A:HIS226 3.3 7.5 1.0 CE1 A:HIS58 3.3 6.9 1.0 O A:HOH661 4.2 4.3 1.0 CG A:HIS142 4.3 6.6 1.0 ND1 A:HIS142 4.3 6.7 1.0 CG A:HIS226 4.3 6.0 1.0 CG A:HIS58 4.3 6.1 1.0 ND1 A:HIS226 4.4 6.7 1.0 ND1 A:HIS58 4.4 7.0 1.0 O A:HIS58 4.6 7.1 1.0 O A:HIS142 4.6 7.4 1.0 O A:HIS226 4.6 6.9 1.0 CB A:SER16 4.8 6.9 1.0 CB A:SER184 4.8 6.5 1.0 CB A:SER100 4.8 6.8 1.0

Cadmium binding site 8 out of 11 in the Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal


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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd308 b:4.8 occ:0.38 O A:HOH416 2.5 15.7 1.0 O A:HOH402 2.6 16.1 1.0 O A:HOH405 2.6 16.6 1.0 O A:HOH626 2.6 5.8 1.0 O A:HOH622 2.6 6.3 1.0 O A:HOH623 2.6 6.0 1.0 O A:HOH574 2.7 18.7 1.0 O A:HOH518 2.8 17.0 1.0 O A:HOH457 2.8 16.8 1.0 O A:HOH661 3.3 4.3 1.0 O A:VAL186 4.3 6.7 1.0 O A:VAL60 4.3 6.9 1.0 O A:VAL102 4.4 6.6 1.0 O A:VAL228 4.4 6.9 1.0 O A:VAL18 4.4 6.7 1.0 O A:VAL144 4.4 6.1 1.0

Cadmium binding site 9 out of 11 in the Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal


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 PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd301 b:5.0 occ:1.00 CL B:CL308 2.7 5.7 1.0 CL B:CL305 2.7 5.7 1.0 CL A:CL313 2.7 5.4 1.0 CL B:CL307 2.7 5.5 1.0 CL A:CL310 2.7 5.6 1.0 CL A:CL312 2.7 5.5 1.0 CD A:CD305 4.0 5.0 1.0 CD A:CD301 4.0 5.1 1.0 CD A:CD303 4.0 5.1 1.0 CD A:CD302 4.1 5.0 1.0 CD A:CD306 4.1 5.0 1.0 CD A:CD304 4.1 5.0 1.0 CL B:CL304 4.7 5.5 1.0 CL A:CL309 4.7 5.5 1.0 CL A:CL314 4.7 5.5 1.0 CL B:CL309 4.7 5.6 1.0 CL B:CL306 4.7 5.5 1.0 CL A:CL311 4.7 5.5 1.0

Cadmium binding site 10 out of 11 in the Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of PIZZA6-Sh with CDCL2 Nanocrystal within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd302 b:6.0 occ:1.00 NE2 B:HIS226 2.3 7.0 1.0 NE2 B:HIS58 2.3 6.6 1.0 NE2 B:HIS142 2.3 6.6 1.0 O B:HOH481 2.4 7.3 1.0 O B:HOH465 2.4 7.6 1.0 O B:HOH470 2.4 8.1 1.0 CD2 B:HIS226 3.1 6.0 1.0 CD2 B:HIS142 3.1 5.9 1.0 CD2 B:HIS58 3.2 6.1 1.0 CE1 B:HIS226 3.3 7.2 1.0 CE1 B:HIS58 3.3 6.8 1.0 CE1 B:HIS142 3.3 6.7 1.0 O B:HOH669 4.2 4.8 1.0 CG B:HIS226 4.3 6.2 1.0 CG B:HIS142 4.3 6.0 1.0 CG B:HIS58 4.3 5.9 1.0 ND1 B:HIS226 4.3 7.0 1.0 ND1 B:HIS58 4.4 6.3 1.0 ND1 B:HIS142 4.4 6.8 1.0 O B:HIS226 4.6 7.5 1.0 O B:HIS58 4.6 7.5 1.0 O B:HIS142 4.6 6.9 1.0 CB B:SER16 4.8 6.9 1.0 CB B:SER100 4.8 6.9 1.0 CB B:SER184 4.8 6.8 1.0

H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet. Artificial Beta-Propeller Protein-Based Hydrolases To Be Published.