Zinc in PDB 5wlm: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2

The structure of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2, PDB code: 5wlm 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)	48.24 / 1.95
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.156, 81.156, 66.331, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 18.7

The binding sites of Zinc atom in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2 (pdb code 5wlm). 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-4DH2, PDB code: 5wlm:
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-4DH2


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-4DH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:33.0 occ:1.00 OD2 B:ASP12 2.0 27.9 1.0 ND1 A:HIS15 2.1 28.9 1.0 O B:HOH204 2.3 31.1 0.5 OD1 A:ASP12 2.7 28.9 1.0 CG B:ASP12 2.8 26.5 1.0 CE1 A:HIS15 3.0 30.1 1.0 OD1 B:ASP12 3.0 27.4 1.0 CG A:HIS15 3.2 28.0 1.0 CG A:ASP12 3.3 27.8 1.0 ZN A:ZN104 3.4 34.6 1.0 CB A:HIS15 3.5 27.7 1.0 OD2 A:ASP12 3.7 29.2 1.0 CA A:ASP12 4.1 25.2 1.0 NE2 A:HIS15 4.2 30.0 1.0 CB A:ASP12 4.2 26.4 1.0 CB B:ASP12 4.2 25.2 1.0 CD2 A:HIS15 4.2 28.4 1.0 O A:HOH207 4.6 31.0 0.5 N A:ASP12 4.8 24.8 1.0 O A:ASP12 5.0 24.9 1.0 O A:ASP11 5.0 25.0 1.0

Zinc binding site 2 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2


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-4DH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:40.0 occ:0.70 O A:HOH206 2.2 35.2 1.0 OD2 A:ASP21 2.2 37.1 1.0 CG A:ASP21 3.0 36.3 1.0 OD1 A:ASP21 3.1 37.4 1.0 O A:HOH201 4.2 37.0 1.0 O A:HOH203 4.2 38.2 1.0 CB A:ASP21 4.4 35.6 1.0 NZ A:LYS24 4.5 43.0 0.7 O A:HOH209 4.7 39.0 1.0

Zinc binding site 3 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2


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-4DH2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:34.6 occ:1.00 OD2 A:ASP12 2.0 29.2 1.0 O A:HOH207 2.1 31.0 0.5 ND1 B:HIS15 2.2 25.8 1.0 CG A:ASP12 2.8 27.8 1.0 OD1 A:ASP12 3.0 28.9 1.0 CE1 B:HIS15 3.1 27.0 1.0 CG B:HIS15 3.2 24.6 1.0 OD1 B:ASP12 3.3 27.4 1.0 ZN A:ZN102 3.4 33.0 1.0 CB B:HIS15 3.5 24.4 1.0 CG B:ASP12 3.6 26.5 1.0 OD2 B:ASP12 3.7 27.9 1.0 CB A:ASP12 4.3 26.4 1.0 NE2 B:HIS15 4.3 26.5 1.0 CD2 B:HIS15 4.3 25.1 1.0 CA B:ASP12 4.4 23.9 1.0 CB B:ASP12 4.5 25.2 1.0 O B:HOH204 4.6 31.1 0.5

Zinc binding site 4 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2


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-4DH2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:45.4 occ:0.80 OD2 D:ASP12 1.9 44.0 1.0 ND1 C:HIS15 2.2 42.4 1.0 O D:HOH204 2.3 39.9 0.5 CG D:ASP12 2.8 42.7 1.0 OD1 C:ASP12 2.9 44.4 1.0 OD1 D:ASP12 3.1 42.6 1.0 CE1 C:HIS15 3.1 42.7 1.0 CG C:HIS15 3.2 42.4 1.0 CG C:ASP12 3.4 44.8 1.0 ZN C:ZN103 3.4 49.7 1.0 CB C:HIS15 3.6 42.6 1.0 OD2 C:ASP12 3.7 46.1 1.0 CA C:ASP12 4.2 44.5 1.0 CB D:ASP12 4.2 42.8 1.0 NE2 C:HIS15 4.3 42.9 1.0 CB C:ASP12 4.3 45.3 1.0 CD2 C:HIS15 4.3 42.7 1.0 O C:HOH203 4.8 46.0 0.5 N C:ASP12 4.8 44.2 1.0

Zinc binding site 5 out of 5 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4DH2


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-4DH2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:49.7 occ:1.00 OD2 C:ASP12 2.0 46.1 1.0 ND1 D:HIS15 2.1 40.4 1.0 O C:HOH203 2.2 46.0 0.5 OD1 D:ASP12 2.8 42.6 1.0 CG C:ASP12 2.9 44.8 1.0 CE1 D:HIS15 2.9 40.6 1.0 OD1 C:ASP12 3.0 44.4 1.0 CG D:HIS15 3.2 40.2 1.0 CG D:ASP12 3.4 42.7 1.0 ZN C:ZN102 3.4 45.4 0.8 CB D:HIS15 3.6 40.5 1.0 OD2 D:ASP12 3.7 44.0 1.0 NE2 D:HIS15 4.1 40.9 1.0 CD2 D:HIS15 4.2 40.3 1.0 CB C:ASP12 4.3 45.3 1.0 CA D:ASP12 4.3 42.2 1.0 CB D:ASP12 4.4 42.8 1.0 O D:HOH204 4.7 39.9 0.5 N D:ASP12 5.0 41.9 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