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

Protein crystallography data

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

Other elements in 5u9t:

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

Zinc Binding Sites:

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 5u9t

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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 5u9t

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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 5u9t

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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 5u9t

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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 5u9t

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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 5u9t

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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

Reference:

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
Page generated: Wed Dec 16 11:00:51 2020

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