Zinc in PDB 5u9t: The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment

The structure of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment, PDB code: 5u9t was solved by L.Ruckthong, A.F.A.Peacock, J.A.Stuckey, V.L.Pecoraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.53 / 1.92
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	76.119, 28.977, 43.917, 90.00, 119.83, 90.00
R / Rfree (%)	19.7 / 22.8

The structure of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment (pdb code 5u9t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment, PDB code: 5u9t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:29.5 occ:0.90 NE2 A:HIS28 1.9 28.0 1.0 CE1 A:HIS28 2.8 28.5 1.0 CD2 A:HIS28 3.0 29.1 1.0 OE2 A:GLU27 3.9 51.1 1.0 ND1 A:HIS28 4.0 29.6 1.0 CG A:HIS28 4.0 28.4 1.0 CD A:GLU27 4.7 52.6 1.0 O A:HOH202 4.7 37.4 1.0 OE2 A:GLU24 4.7 32.0 1.0 ZN A:ZN102 4.9 26.2 0.9

Zinc binding site 2 out of 6 in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:26.2 occ:0.90 OE2 A:GLU24 1.9 32.0 1.0 OE1 A:GLU24 2.5 20.7 1.0 CD A:GLU24 2.5 32.9 1.0 OE1 A:GLU27 3.6 47.9 1.0 CG A:GLU24 4.0 27.6 1.0 OE2 A:GLU27 4.1 51.1 1.0 NZ C:LYS22 4.1 33.5 1.0 O A:HOH202 4.2 37.4 1.0 CD A:GLU27 4.3 52.6 1.0 CE1 A:HIS28 4.4 28.5 1.0 ZN A:ZN101 4.9 29.5 0.9

Zinc binding site 3 out of 6 in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn103 b:23.9 occ:0.54 O A:ACT111 1.9 57.4 1.0 OE1 A:GLU6 2.1 36.6 1.0 OE1 C:GLU1 2.1 39.2 1.0 OE2 A:GLU6 2.3 40.4 1.0 CD A:GLU6 2.5 36.8 1.0 CD C:GLU1 2.7 66.7 1.0 OE2 C:GLU1 3.0 74.4 1.0 C A:ACT111 3.1 59.7 1.0 NE1 A:TRP2 3.7 36.3 1.0 CG C:GLU1 3.9 51.3 1.0 CG A:GLU6 3.9 35.0 1.0 CD1 A:TRP2 3.9 36.8 1.0 CH3 A:ACT111 4.0 59.7 1.0 OXT A:ACT111 4.0 60.1 1.0 C5 A:15P110 4.1 37.8 1.0 C6 A:15P110 4.6 39.3 1.0 CB A:GLU6 4.8 27.6 1.0 CE2 A:TRP2 5.0 38.5 1.0

Zinc binding site 4 out of 6 in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:41.2 occ:0.70 SG B:DCY16 2.1 40.5 0.8 SG C:DCY16 2.1 29.4 0.7 SG A:DCY16 2.2 38.0 0.7 SG A:DCY16 2.4 35.5 0.3 CL A:CL112 2.4 58.5 1.0 SG C:DCY16 2.6 22.1 0.3 CB B:DCY16 2.8 32.4 0.8 CB C:DCY16 3.1 28.2 0.7 CB C:DCY16 3.3 24.8 0.3 CB A:DCY16 3.3 33.7 0.7 CB A:DCY16 3.4 32.1 0.3 CA B:DCY16 3.8 29.2 0.8 N B:DCY16 4.2 29.0 1.0 O B:LEU12 4.4 30.7 1.0 CA C:DCY16 4.5 26.1 0.7 CA C:DCY16 4.5 25.2 0.3 CD2 A:LEU19 4.5 29.1 1.0 CA A:DCY16 4.7 30.7 0.7 CA A:DCY16 4.7 30.3 0.3 CD1 B:LEU19 4.9 31.7 1.0 C B:LYS15 4.9 30.8 1.0

Zinc binding site 5 out of 6 in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:75.0 occ:0.63 OE2 C:GLU6 2.1 60.1 1.0 O B:HOH202 2.2 32.7 1.0 OE1 B:GLU1 2.3 58.7 1.0 CD C:GLU6 2.9 64.6 1.0 OE1 C:GLU6 3.0 65.5 1.0 CD B:GLU1 3.5 69.8 1.0 NE1 C:TRP2 3.6 36.9 0.9 CD1 B:LEU5 3.7 41.6 1.0 CE2 C:TRP2 3.7 37.5 0.9 O B:HOH206 3.8 53.0 1.0 CG C:GLU6 4.3 37.8 1.0 OE2 B:GLU1 4.3 69.0 1.0 CG B:GLU1 4.4 47.0 1.0 CB B:GLU1 4.4 31.8 1.0 O B:GLU1 4.7 30.9 1.0 NZ B:LYS8 4.7 79.6 1.0 CA B:GLU1 4.8 29.7 1.0 CD1 C:TRP2 4.9 36.6 0.9

Zinc binding site 6 out of 6 in the The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Tris-Thiolate Zn(II)S3CL Binding Site Engineered By D-Cysteine Ligands in De Novo Three-Stranded Coiled Coil Environment within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:29.9 occ:0.54 OE1 C:GLU27 2.0 42.1 1.0 OE1 C:GLU24 2.3 39.8 1.0 OE2 C:GLU24 2.3 44.5 1.0 CD C:GLU24 2.6 51.7 1.0 CD C:GLU27 3.0 48.7 1.0 OE2 C:GLU27 3.3 37.2 1.0 CG C:GLU24 4.1 34.6 1.0 NZ B:LYS22 4.2 67.8 1.0 CG C:GLU27 4.3 29.1 1.0 CE B:LYS22 4.3 57.1 1.0 CE1 C:HIS28 4.4 27.1 1.0 CB C:GLU27 4.6 26.6 1.0 CA C:GLU24 4.8 22.8 1.0 CB C:GLU24 4.8 24.5 1.0 O C:HOH209 4.9 48.3 1.0 CD B:LYS22 5.0 46.2 1.0

L.Ruckthong, A.F.A.Peacock, C.E.Pascoe, L.Hemmingsen, J.A.Stuckey, V.L.Pecoraro. D-Cysteine Ligands Control Metal Geometries Within De Novo Designed Three-Stranded Coiled Coils. Chemistry V. 23 8232 2017.
ISSN: ISSN 1521-3765
PubMed: 28384393
DOI: 10.1002/CHEM.201700660