Zinc in PDB 5wlj: De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1

The structure of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1, PDB code: 5wlj 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)	70.00 / 1.60
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	80.828, 80.828, 64.388, 90.00, 90.00, 120.00
R / Rfree (%)	14.7 / 16.7

Pages:

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

Binding sites:

The binding sites of Zinc atom in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1 (pdb code 5wlj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1, PDB code: 5wlj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


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-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:15.1 occ:0.76 NE2 A:HIS15 2.0 16.1 1.0 OD1 A:ASP11 2.0 16.5 0.7 O A:HOH212 2.1 19.7 1.0 OD2 A:ASP11 2.6 16.0 0.7 CG A:ASP11 2.6 16.0 0.7 CD2 A:HIS15 2.8 14.7 1.0 CE1 A:HIS15 3.1 16.1 1.0 CG A:HIS15 4.0 14.1 1.0 O A:HOH205 4.0 43.4 1.0 ND1 A:HIS15 4.1 14.9 1.0 CB A:ASP11 4.1 15.1 0.7 CB A:ASP11 4.1 15.5 0.3 O A:ASP11 4.1 13.4 1.0 OE1 A:GLU18 4.3 18.6 1.0 CG A:ASP11 4.4 17.6 0.3 CA A:ASP11 4.6 14.7 0.3 CA A:ASP11 4.7 14.5 0.7 C A:ASP11 4.7 13.4 1.0 OD1 A:ASP11 4.7 18.8 0.3 NH1 A:ARG14 4.8 26.9 0.7 OD2 A:ASP11 4.9 18.0 0.3 NE A:ARG14 4.9 24.8 0.7 ZN A:ZN102 5.0 25.6 0.4

Zinc binding site 2 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


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-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:25.6 occ:0.38 OD2 A:ASP11 1.8 18.0 0.3 O A:HOH229 2.3 20.6 1.0 O A:HOH224 2.3 25.3 1.0 OD2 A:ASP11 2.7 16.0 0.7 CG A:ASP11 2.8 17.6 0.3 O A:HOH205 3.1 43.4 1.0 CG A:ASP11 3.3 16.0 0.7 CB A:ASP11 3.3 15.5 0.3 CB A:ASP11 3.4 15.1 0.7 OD1 A:ASP11 3.9 18.8 0.3 OD1 A:ASP11 4.3 16.5 0.7 CA A:ILE8 4.6 14.5 1.0 O A:LYS7 4.7 15.4 1.0 CA A:ASP11 4.8 14.7 0.3 CA A:ASP11 4.9 14.5 0.7 ZN A:ZN101 5.0 15.1 0.8 O A:ILE8 5.0 13.5 1.0

Zinc binding site 3 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


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-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:18.2 occ:1.00 OD1 A:ASP21 1.9 20.6 1.0 OE1 A:GLU20 1.9 16.7 1.0 O A:HOH213 2.0 16.5 1.0 CG A:ASP21 2.9 19.9 1.0 CD A:GLU20 2.9 16.3 1.0 OE2 A:GLU20 3.2 16.4 1.0 OD2 A:ASP21 3.3 21.1 1.0 O A:HOH206 3.6 31.0 1.0 O A:ALA17 3.8 14.0 1.0 N A:ASP21 4.1 14.9 1.0 CB A:ASP21 4.1 18.2 1.0 O A:HOH223 4.2 53.3 1.0 CG A:GLU20 4.3 15.2 1.0 CA A:ASP21 4.3 16.2 1.0 CB A:GLU20 4.6 14.1 1.0 O A:HOH230 4.6 59.2 1.0 C A:GLU20 4.7 14.2 1.0 C A:ALA17 4.8 13.4 1.0

Zinc binding site 4 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


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-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:14.3 occ:0.46 ZN A:ZN104 0.0 14.3 0.5 OE1 A:GLU12 1.8 20.4 1.0 ND1 B:HIS15 1.9 15.6 1.0 ZN A:ZN104 2.1 15.1 0.2 OE2 B:GLU12 2.2 17.3 1.0 CE1 B:HIS15 2.7 16.9 1.0 CD A:GLU12 2.9 18.5 1.0 CG B:HIS15 3.1 14.3 1.0 CD B:GLU12 3.2 17.8 1.0 OE2 A:GLU12 3.3 19.6 1.0 OE1 B:GLU12 3.5 20.9 1.0 CB B:HIS15 3.6 13.5 1.0 NE2 B:HIS15 3.9 15.6 1.0 ZN A:ZN104 4.0 10.9 0.1 CD2 B:HIS15 4.1 14.3 1.0 CG A:GLU12 4.2 17.3 1.0 CA B:GLU12 4.2 12.9 1.0 CG B:GLU12 4.4 16.1 1.0 O B:ASP11 4.7 13.0 1.0 CB B:GLU12 4.8 14.4 1.0 N B:GLU12 4.8 12.1 1.0 CB A:GLU12 4.9 16.1 1.0

Zinc binding site 5 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


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-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:15.1 occ:0.19 ZN A:ZN104 0.0 15.1 0.2 ZN A:ZN104 2.0 10.9 0.1 ZN A:ZN104 2.1 14.3 0.5 OE2 B:GLU12 2.2 17.3 1.0 OE1 B:GLU12 2.3 20.9 1.0 OE2 A:GLU12 2.4 19.6 1.0 CD B:GLU12 2.6 17.8 1.0 OE1 A:GLU12 2.6 20.4 1.0 CD A:GLU12 2.8 18.5 1.0 ND1 A:HIS15 3.9 14.9 1.0 CG B:GLU12 4.1 16.1 1.0 ND1 B:HIS15 4.1 15.6 1.0 CG A:GLU12 4.3 17.3 1.0 CE1 A:HIS15 4.6 16.1 1.0 CE1 B:HIS15 4.7 16.9 1.0 CB B:GLU12 4.9 14.4 1.0 CB A:GLU12 5.0 16.1 1.0

Zinc binding site 6 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:10.9 occ:0.15 ZN A:ZN104 0.0 10.9 0.1 OE1 B:GLU12 1.6 20.9 1.0 ND1 A:HIS15 1.9 14.9 1.0 ZN A:ZN104 2.0 15.1 0.2 OE2 A:GLU12 2.4 19.6 1.0 CE1 A:HIS15 2.7 16.1 1.0 CD B:GLU12 2.7 17.8 1.0 CG A:HIS15 3.1 14.1 1.0 OE2 B:GLU12 3.2 17.3 1.0 CD A:GLU12 3.4 18.5 1.0 CB A:HIS15 3.7 13.1 1.0 OE1 A:GLU12 3.8 20.4 1.0 NE2 A:HIS15 3.9 16.1 1.0 CG B:GLU12 3.9 16.1 1.0 ZN A:ZN104 4.0 14.3 0.5 CD2 A:HIS15 4.1 14.7 1.0 CA A:GLU12 4.2 14.3 1.0 CG A:GLU12 4.5 17.3 1.0 CB A:GLU12 4.7 16.1 1.0 CB B:GLU12 4.8 14.4 1.0 O A:ASP11 4.8 13.4 1.0 N A:GLU12 4.9 13.7 1.0

Zinc binding site 7 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:30.7 occ:0.33 OD1 C:ASP11 2.0 30.7 0.3 NE2 C:HIS15 2.1 27.5 1.0 O C:HOH209 2.5 39.5 1.0 CG C:ASP11 2.6 29.2 0.3 OD2 C:ASP11 2.7 30.2 0.3 NH1 C:ARG14 2.7 38.8 0.7 CD2 C:HIS15 2.8 26.7 1.0 CE1 C:HIS15 3.1 27.5 1.0 CZ C:ARG14 3.6 38.2 0.7 NE C:ARG14 3.9 38.4 0.7 CG C:HIS15 4.0 25.0 1.0 CB C:ASP11 4.0 27.6 0.3 CB C:ASP11 4.0 28.3 0.7 O C:ASP11 4.1 25.4 1.0 ND1 C:HIS15 4.1 25.8 1.0 CG C:ASP11 4.2 31.7 0.7 CA C:ASP11 4.5 27.5 0.7 CA C:ASP11 4.5 27.4 0.3 OD1 C:ASP11 4.5 35.1 0.7 C C:ASP11 4.6 25.7 1.0 NH2 C:ARG14 4.7 38.8 0.7 OD2 C:ASP11 4.7 33.5 0.7 OE1 C:GLU18 4.7 33.5 1.0 ZN C:ZN102 5.0 33.7 0.3

Zinc binding site 8 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:33.7 occ:0.34 OD2 C:ASP11 1.6 33.5 0.7 O C:HOH216 2.4 42.0 1.0 OD2 C:ASP11 2.5 30.2 0.3 CG C:ASP11 2.7 31.7 0.7 CG C:ASP11 3.1 29.2 0.3 CB C:ASP11 3.2 28.3 0.7 CB C:ASP11 3.2 27.6 0.3 OD1 C:ASP11 3.7 35.1 0.7 OD1 C:ASP11 4.1 30.7 0.3 O C:LYS7 4.7 27.1 1.0 CA C:ILE8 4.7 24.6 1.0 CA C:ASP11 4.7 27.5 0.7 CA C:ASP11 4.8 27.4 0.3 ZN C:ZN101 5.0 30.7 0.3

Zinc binding site 9 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:27.4 occ:0.23 ZN C:ZN103 0.0 27.4 0.2 OE1 C:GLU12 1.8 29.3 1.0 ND1 D:HIS15 2.0 24.4 1.0 ZN C:ZN103 2.0 21.6 0.3 OE2 D:GLU12 2.3 27.0 1.0 CE1 D:HIS15 2.6 25.9 1.0 CD C:GLU12 2.8 27.3 1.0 OE2 C:GLU12 3.1 28.6 1.0 CD D:GLU12 3.2 26.4 1.0 CG D:HIS15 3.2 23.9 1.0 OE1 D:GLU12 3.6 28.4 1.0 ZN C:ZN103 3.8 24.1 0.2 CB D:HIS15 3.8 23.5 1.0 NE2 D:HIS15 3.9 26.3 1.0 CG C:GLU12 4.1 26.1 1.0 CD2 D:HIS15 4.2 25.2 1.0 CA D:GLU12 4.3 24.6 1.0 CG D:GLU12 4.4 25.3 1.0 CB D:GLU12 4.8 25.4 1.0 N D:GLU12 4.9 24.4 1.0 O D:ASP11 4.9 25.2 1.0 CB C:GLU12 5.0 25.8 1.0

Zinc binding site 10 out of 11 in the De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of De Novo Design of Polynuclear Transition Metal Clusters in Helix Bundles-4EH1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn103 b:21.6 occ:0.29 ZN C:ZN103 0.0 21.6 0.3 ZN C:ZN103 2.0 24.1 0.2 ZN C:ZN103 2.0 27.4 0.2 OE2 D:GLU12 2.2 27.0 1.0 OE2 C:GLU12 2.2 28.6 1.0 OE1 D:GLU12 2.6 28.4 1.0 OE1 C:GLU12 2.6 29.3 1.0 CD D:GLU12 2.7 26.4 1.0 CD C:GLU12 2.7 27.3 1.0 ND1 C:HIS15 4.0 25.8 1.0 ND1 D:HIS15 4.0 24.4 1.0 CG D:GLU12 4.2 25.3 1.0 CG C:GLU12 4.2 26.1 1.0 CE1 D:HIS15 4.6 25.9 1.0 CE1 C:HIS15 4.6 27.5 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