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

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

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:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms
Iron	(Fe)	2 atoms

The binding sites of Zinc 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 Zinc atom.
In total 7 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 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 Zinc with other atoms in the Zn 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:Zn202 b:10.8 occ:1.00 OD1 C:ASP74 1.9 12.4 1.0 NE2 A:HIS63 2.0 10.3 1.0 CG C:ASP74 2.9 11.7 1.0 CD2 A:HIS63 2.9 10.8 1.0 CE1 A:HIS63 3.1 10.6 1.0 OD2 C:ASP74 3.1 12.3 1.0 O C:HOH346 4.0 16.4 1.0 CG A:HIS63 4.1 10.5 1.0 ND1 A:HIS63 4.1 10.5 1.0 CB C:ASP74 4.2 11.2 1.0 CD1 A:ILE67 4.5 14.2 1.0 CA C:ASP74 4.8 10.6 1.0 O C:ASP74 5.0 11.2 1.0

Zinc binding site 2 out of 7 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 Zinc with other atoms in the Zn 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:Zn203 b:10.8 occ:1.00 OD1 A:ASP74 2.0 11.8 1.0 NE2 C:HIS63 2.0 10.4 1.0 CG A:ASP74 2.9 11.5 1.0 CD2 C:HIS63 2.9 10.6 1.0 CE1 C:HIS63 3.1 11.3 1.0 OD2 A:ASP74 3.1 12.0 1.0 O A:HOH337 4.0 12.8 1.0 CG C:HIS63 4.1 11.0 1.0 ND1 C:HIS63 4.1 10.1 1.0 CB A:ASP74 4.3 10.8 1.0 CD1 C:ILE67 4.3 13.1 1.0 CA A:ASP74 4.8 10.7 1.0 O A:ASP74 4.9 10.9 1.0 O A:HOH376 5.0 30.9 1.0

Zinc binding site 3 out of 7 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 Zinc with other atoms in the Zn binding site number 3 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:Zn204 b:19.5 occ:1.00 NE2 C:HIS93 1.9 33.8 1.0 ND1 A:HIS100 2.2 26.8 1.0 CL A:CL208 2.2 22.7 1.0 O A:HOH370 2.4 20.6 1.0 CE1 C:HIS93 2.9 33.3 1.0 CD2 C:HIS93 2.9 27.6 1.0 CE1 A:HIS100 3.1 29.9 1.0 CG A:HIS100 3.1 25.5 1.0 CB A:HIS100 3.5 21.3 1.0 O A:HOH329 3.9 19.4 1.0 ND1 C:HIS93 4.0 29.3 1.0 CG C:HIS93 4.0 29.3 1.0 O A:HOH335 4.1 27.7 1.0 NE2 A:HIS100 4.2 26.6 1.0 CD2 A:HIS100 4.2 28.8 1.0 O C:HOH384 4.4 35.9 1.0 O C:HOH355 4.4 32.9 1.0 O A:HOH354 4.6 27.6 1.0 O C:HOH356 4.8 42.0 1.0 O A:HOH379 4.8 24.3 1.0 CA C:ALA90 4.9 26.3 1.0 CA A:HIS100 5.0 17.6 1.0

Zinc binding site 4 out of 7 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 Zinc with other atoms in the Zn binding site number 4 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:Zn205 b:34.1 occ:1.00 ND1 A:HIS77 3.9 11.7 1.0 CE1 A:HIS77 4.0 11.3 1.0 O A:HOH362 4.1 27.2 1.0 OD1 A:ASN80 4.5 31.7 1.0 CG A:ASN80 4.6 31.9 1.0 CB A:ASN80 4.6 28.9 1.0

Zinc binding site 5 out of 7 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 Zinc with other atoms in the Zn binding site number 5 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:Zn206 b:18.9 occ:0.50 OE1 A:GLU8 1.9 17.6 1.0 OD2 A:ASP12 2.1 16.0 1.0 OD1 A:ASP12 2.7 15.5 1.0 CG A:ASP12 2.7 14.7 1.0 CD A:GLU8 2.8 20.7 1.0 CG A:GLU8 3.2 18.2 1.0 OE2 A:GLU8 3.9 23.7 1.0 O A:HOH315 4.0 25.2 1.0 CB A:ASP12 4.2 14.5 1.0 O A:HOH333 4.5 36.1 1.0 O A:GLU8 4.6 13.2 1.0 CB A:GLU8 4.7 16.9 1.0

Zinc binding site 6 out of 7 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 Zinc with other atoms in the Zn binding site number 6 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 C:Zn202 b:22.3 occ:1.00 O C:HOH371 1.7 28.3 1.0 ND1 C:HIS100 2.0 26.3 1.0 NE2 A:HIS93 2.0 25.0 1.0 CL A:CL207 2.2 21.3 1.0 CD2 A:HIS93 2.9 22.1 1.0 CE1 C:HIS100 2.9 28.1 1.0 CG C:HIS100 3.0 23.3 1.0 CE1 A:HIS93 3.1 24.4 1.0 CB C:HIS100 3.4 20.1 1.0 NE2 C:HIS100 4.1 27.4 1.0 CG A:HIS93 4.1 24.6 1.0 CD2 C:HIS100 4.1 25.9 1.0 ND1 A:HIS93 4.2 25.4 1.0 O C:HOH350 4.7 22.9 1.0 O A:HOH318 4.8 29.2 1.0 O C:HOH354 4.8 30.7 1.0 O C:ILE96 4.8 12.4 1.0 CA C:THR97 4.9 12.9 1.0 O A:GLU89 4.9 24.3 1.0 CA C:HIS100 5.0 17.4 1.0 O C:HOH328 5.0 34.3 1.0 CG2 C:ILE96 5.0 21.9 1.0

Zinc binding site 7 out of 7 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 Zinc with other atoms in the Zn binding site number 7 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 C:Zn203 b:24.5 occ:0.50 NE2 A:HIS59 1.9 39.7 1.0 O A:HOH357 1.9 22.5 1.0 O A:HOH345 2.1 25.5 1.0 OE1 C:GLU81 2.5 39.4 1.0 CD2 A:HIS59 2.9 38.0 1.0 CE1 A:HIS59 2.9 41.9 1.0 CD C:GLU81 3.2 38.6 1.0 OE2 C:GLU81 3.2 41.1 1.0 NZ C:LYS83 3.3 44.8 1.0 ND1 A:HIS59 4.0 37.4 1.0 CG A:HIS59 4.0 32.0 1.0 O C:HOH347 4.2 38.9 1.0 OD1 A:ASP60 4.4 34.0 1.0 CG C:GLU81 4.6 36.7 1.0 CE C:LYS83 4.7 40.2 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