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Chlorine in PDB 6ldg: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5

Protein crystallography data

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5, PDB code: 6ldg was solved by W.J.Song, J.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.38 / 1.98
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 53.723, 53.723, 250.757, 90, 90, 120
R / Rfree (%) 16.8 / 22.1

Other elements in 6ldg:

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5 also contains other interesting chemical elements:

Zinc (Zn) 7 atoms
Magnesium (Mg) 2 atoms
Iron (Fe) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5 (pdb code 6ldg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5, PDB code: 6ldg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6ldg

Go back to Chlorine Binding Sites List in 6ldg
Chlorine binding site 1 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:21.3
occ:1.00
ZN C:ZN202 2.2 22.3 1.0
O C:HOH354 2.8 30.7 1.0
O C:HOH371 3.2 28.3 1.0
NE2 A:HIS93 3.3 25.0 1.0
O C:HOH350 3.6 22.9 1.0
ND1 C:HIS100 3.7 26.3 1.0
CB C:HIS100 3.7 20.1 1.0
CE1 A:HIS93 3.8 24.4 1.0
CG2 C:THR97 3.8 13.8 1.0
O C:HOH328 3.8 34.3 1.0
CA C:THR97 4.0 12.9 1.0
CG C:HIS100 4.2 23.3 1.0
CG2 C:ILE67 4.2 10.7 1.0
O C:THR97 4.3 12.7 1.0
CB C:THR97 4.3 13.3 1.0
CB C:ILE67 4.4 10.9 1.0
OG1 C:THR97 4.4 12.6 1.0
CG1 C:ILE67 4.4 12.1 1.0
CD2 A:HIS93 4.6 22.1 1.0
C C:THR97 4.7 12.6 1.0
CA C:GLY64 4.7 10.3 1.0
CE1 C:HIS100 4.9 28.1 1.0

Chlorine binding site 2 out of 2 in 6ldg

Go back to Chlorine Binding Sites List in 6ldg
Chlorine binding site 2 out of 2 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I AB5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:22.7
occ:1.00
ZN A:ZN204 2.2 19.5 1.0
O A:HOH354 2.9 27.6 1.0
O A:HOH335 3.4 27.7 1.0
NE2 C:HIS93 3.5 33.8 1.0
ND1 A:HIS100 3.6 26.8 1.0
O A:HOH329 3.6 19.4 1.0
O A:HOH370 3.7 20.6 1.0
CG2 A:THR97 3.9 10.3 1.0
O A:HOH379 3.9 24.3 1.0
CB A:HIS100 4.0 21.3 1.0
CG2 A:ILE67 4.0 12.1 1.0
CA A:THR97 4.1 10.9 1.0
CD2 C:HIS93 4.1 27.6 1.0
CG1 A:ILE67 4.2 13.3 1.0
CB A:ILE67 4.2 12.2 1.0
CG A:HIS100 4.2 25.5 1.0
CB A:THR97 4.3 10.3 1.0
OG1 A:THR97 4.3 10.3 1.0
O A:THR97 4.4 9.2 1.0
CE1 C:HIS93 4.6 33.3 1.0
CE1 A:HIS100 4.6 29.9 1.0
CA A:GLY64 4.7 11.0 1.0
O C:HOH355 4.7 32.9 1.0
C A:THR97 4.8 10.5 1.0

Reference:

J.Yu, J.Yang, C.Seok, W.J.Song. Symmetry-Related Residues As Promising Hotspots For the Evolution of De Novo Oligomeric Enzymes Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC06823C
Page generated: Sat Apr 3 14:03:31 2021

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