Zinc in PDB 5wll: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1

The structure of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1, PDB code: 5wll was solved by S.-Q.Zhang, L.Liu, W.F.Degrado, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.01 / 1.90
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.782, 80.782, 64.923, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 23.8

The binding sites of Zinc atom in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 (pdb code 5wll). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1, PDB code: 5wll:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:28.8 occ:0.80 O B:HOH203 2.1 17.7 0.5 ND1 A:HIS15 2.1 16.9 1.0 OD2 B:ASP12 2.2 15.7 1.0 OD1 A:ASP12 2.5 23.7 1.0 CG B:ASP12 3.0 14.5 1.0 CE1 A:HIS15 3.0 18.1 1.0 OD1 B:ASP12 3.1 14.6 1.0 CG A:HIS15 3.2 15.9 1.0 ZN A:ZN103 3.4 28.0 0.8 CB A:HIS15 3.6 15.1 1.0 CG A:ASP12 3.7 21.8 1.0 NE2 A:HIS15 4.1 17.7 1.0 CA A:ASP12 4.2 17.7 1.0 O A:HOH209 4.2 21.8 0.5 CD2 A:HIS15 4.3 16.4 1.0 CB B:ASP12 4.3 13.8 1.0 CB A:ASP12 4.4 19.6 1.0 OD2 A:ASP12 4.7 24.4 1.0 N A:ASP12 4.8 17.1 1.0 O A:ASP11 5.0 16.5 1.0

Zinc binding site 2 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:16.1 occ:0.83 OD1 A:ASP21 1.9 17.5 1.0 O A:HOH213 1.9 15.7 1.0 OE1 A:GLU20 2.0 16.2 1.0 CG A:ASP21 2.8 17.2 1.0 CD A:GLU20 3.0 16.1 1.0 OD2 A:ASP21 3.1 17.6 1.0 OE2 A:GLU20 3.3 16.4 1.0 O A:HOH208 3.7 22.1 1.0 O A:ALA17 3.8 13.9 1.0 CB A:ASP21 4.1 16.9 1.0 N A:ASP21 4.1 15.7 1.0 CA A:ASP21 4.3 16.4 1.0 CG A:GLU20 4.3 16.1 1.0 CB A:GLU20 4.6 15.3 1.0 O A:HOH219 4.6 38.2 1.0 C A:GLU20 4.7 15.5 1.0 C A:ALA17 4.8 14.1 1.0

Zinc binding site 3 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:28.0 occ:0.80 ND1 B:HIS15 2.2 15.1 1.0 OD1 B:ASP12 2.3 14.6 1.0 O A:HOH209 2.3 21.8 0.5 OD1 A:ASP12 2.7 23.7 1.0 CG A:ASP12 3.1 21.8 1.0 CE1 B:HIS15 3.1 15.9 1.0 CG B:ASP12 3.1 14.5 1.0 OD2 A:ASP12 3.2 24.4 1.0 CG B:HIS15 3.2 14.2 1.0 ZN A:ZN101 3.4 28.8 0.8 CB B:HIS15 3.6 13.7 1.0 OD2 B:ASP12 3.7 15.7 1.0 CA B:ASP12 3.9 12.9 1.0 CB B:ASP12 4.1 13.8 1.0 O B:HOH203 4.1 17.7 0.5 CB A:ASP12 4.2 19.6 1.0 NE2 B:HIS15 4.2 15.6 1.0 CD2 B:HIS15 4.3 14.8 1.0 N B:ASP12 4.5 13.1 1.0 O B:ASP11 4.7 13.7 1.0 C B:ASP11 4.9 13.8 1.0 O B:ASP12 5.0 12.3 1.0

Zinc binding site 4 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:35.6 occ:0.80 O D:HOH201 2.1 19.8 0.5 ND1 C:HIS15 2.1 24.3 1.0 OD1 C:ASP12 2.3 28.1 1.0 OD2 D:ASP12 2.5 25.6 0.7 CG D:ASP12 2.9 24.1 0.7 OD1 D:ASP12 2.9 24.4 0.7 CE1 C:HIS15 3.0 24.6 1.0 CG C:HIS15 3.2 23.8 1.0 ZN C:ZN102 3.3 36.3 0.8 CG C:ASP12 3.3 27.4 1.0 CB C:HIS15 3.6 24.0 1.0 O C:HOH204 3.7 22.6 0.5 OD2 C:ASP12 4.1 29.4 1.0 CA C:ASP12 4.2 26.5 1.0 CB D:ASP12 4.2 24.0 1.0 NE2 C:HIS15 4.2 24.6 1.0 CB C:ASP12 4.2 27.0 1.0 CD2 C:HIS15 4.3 24.2 1.0 N C:ASP12 4.8 26.1 1.0

Zinc binding site 5 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:36.3 occ:0.84 O C:HOH204 2.0 22.6 0.5 ND1 D:HIS15 2.1 21.4 1.0 OD1 D:ASP12 2.4 24.4 0.7 OD2 C:ASP12 2.5 29.4 1.0 OD1 C:ASP12 2.9 28.1 1.0 CG C:ASP12 2.9 27.4 1.0 CE1 D:HIS15 3.0 22.1 1.0 CG D:HIS15 3.1 20.8 1.0 ZN C:ZN101 3.3 35.6 0.8 CG D:ASP12 3.3 24.1 0.7 CB D:HIS15 3.5 20.6 1.0 CA D:ASP12 4.0 23.1 1.0 O D:HOH201 4.1 19.8 0.5 OD2 D:ASP12 4.1 25.6 0.7 CB D:ASP12 4.1 24.0 1.0 NE2 D:HIS15 4.2 22.6 1.0 CB C:ASP12 4.2 27.0 1.0 CD2 D:HIS15 4.2 21.7 1.0 N D:ASP12 4.7 22.8 1.0 O D:ASP11 4.9 23.7 1.0 O D:ASP12 5.0 24.0 1.0

S.Q.Zhang, M.Chino, L.Liu, Y.Tang, X.Hu, W.F.Degrado, A.Lombardi. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized By Hydrogen-Bonded Networks in Helical Bundles. J. Am. Chem. Soc. V. 140 1294 2018.
ISSN: ESSN 1520-5126
PubMed: 29249157
DOI: 10.1021/JACS.7B08261