Chlorine in PDB 6ldf: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5, PDB code: 6ldf 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)	28.62 / 2.35
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.748, 53.748, 253.813, 90, 90, 120
R / Rfree (%)	17.3 / 24.5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5 also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Iron	(Fe)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5 (pdb code 6ldf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5, PDB code: 6ldf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl209 b:88.3 occ:1.00 ND1 A:HIS59 3.1 83.6 1.0 CB A:HIS59 3.5 59.9 1.0 NH2 A:ARG62 3.5 68.4 1.0 CG A:HIS59 3.7 72.1 1.0 O A:HOH335 3.9 43.7 1.0 CA A:HIS59 3.9 51.2 1.0 OD2 A:ASP54 4.1 105.6 1.0 OG1 C:THR31 4.2 51.1 1.0 CA A:ASP54 4.3 85.5 1.0 CE1 A:HIS59 4.3 82.5 1.0 CG2 C:THR31 4.4 52.0 1.0 N A:HIS59 4.4 53.6 1.0 CB A:ASP54 4.5 91.0 1.0 CZ A:ARG62 4.7 60.8 1.0 C A:ASP54 4.7 73.1 1.0 O A:ASP54 4.7 77.7 1.0 CG A:ASP54 4.7 103.0 1.0 O A:SER55 4.7 74.4 1.0 O A:HOH308 4.9 50.8 1.0 CB C:THR31 4.9 49.5 1.0 O A:PRO53 5.0 79.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl210 b:63.8 occ:0.50 OE1 A:GLU81 3.0 74.9 1.0 O A:HIS77 3.2 37.7 1.0 CG A:GLU81 3.2 71.3 1.0 CB A:GLU81 3.4 66.1 1.0 CD A:GLU81 3.4 73.1 1.0 C A:HIS77 4.0 34.4 1.0 CA A:GLU81 4.1 63.2 1.0 CB A:HIS77 4.1 30.9 1.0 CA A:HIS77 4.3 32.8 1.0 N A:GLU81 4.4 57.3 1.0 OE2 A:GLU81 4.5 67.4 1.0 ND1 A:HIS77 4.5 30.6 1.0 CG A:HIS77 4.7 28.9 1.0 C A:ASN80 4.8 55.4 1.0 N A:LEU78 4.9 34.3 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl203 b:75.2 occ:1.00 O C:HOH338 3.0 58.8 1.0 ND1 C:HIS73 3.5 33.5 1.0 O A:TRP66 3.7 31.4 1.0 CA C:GLY70 3.8 35.3 1.0 N C:GLY70 4.2 37.1 1.0 CB C:HIS73 4.3 36.6 1.0 CG C:HIS73 4.3 33.9 1.0 CG2 C:ILE69 4.4 39.0 1.0 C A:TRP66 4.4 31.5 1.0 CB A:TRP66 4.4 39.2 1.0 CE1 C:HIS73 4.4 34.8 1.0 CA A:GLY70 4.4 34.5 1.0 N A:GLY70 4.5 33.9 1.0 C C:ILE69 4.5 32.4 1.0 O C:ILE69 4.5 37.0 1.0 CA A:TRP66 4.6 32.2 1.0 CG A:TRP66 4.6 43.6 1.0 CD1 A:TRP66 4.7 50.4 1.0 O C:HOH319 4.9 41.2 1.0 C C:GLY70 5.0 32.4 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl204 b:107.4 occ:1.00 ZN A:ZN207 2.8 79.7 1.0 O A:HOH340 2.9 70.0 1.0 ND1 C:HIS77 3.3 33.7 1.0 N C:HIS77 3.4 34.5 1.0 NE2 A:HIS59 3.4 85.5 1.0 C C:LEU76 3.5 41.0 1.0 CE1 A:HIS59 3.5 82.5 1.0 CG C:LEU76 3.5 46.2 1.0 O C:LEU76 3.6 43.4 1.0 CA C:HIS77 3.6 35.6 1.0 OD1 C:ASN80 3.6 65.8 1.0 CE1 C:HIS77 3.7 31.6 1.0 CB C:LEU76 3.8 41.9 1.0 CG C:HIS77 3.8 32.0 1.0 CD2 C:LEU76 3.9 49.8 1.0 CA C:LEU76 4.2 42.9 1.0 CB C:HIS77 4.3 35.2 1.0 NE2 C:HIS77 4.4 33.6 1.0 CG C:ASN80 4.4 56.2 1.0 CD2 C:HIS77 4.4 33.2 1.0 CB C:ASN80 4.5 49.6 1.0 O C:HIS73 4.6 40.8 1.0 CD2 A:HIS59 4.7 76.1 1.0 CZ3 A:TRP66 4.7 52.5 1.0 ND1 A:HIS59 4.7 83.6 1.0 CD1 C:LEU76 4.8 46.6 1.0 O A:HOH308 4.9 50.8 1.0 C C:HIS77 5.0 38.8 1.0

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