Zinc in PDB 6lde: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5, PDB code: 6lde 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)	46.55 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.757, 53.757, 250.721, 90, 90, 120
R / Rfree (%)	17.9 / 24

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5 also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5 (pdb code 6lde). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V AB5, PDB code: 6lde:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:14.2 occ:1.00 NE2 A:HIS77 2.0 12.9 1.0 NE2 A:HIS73 2.0 13.6 1.0 NE2 C:HIS63 2.0 13.2 1.0 CD2 C:HIS63 3.0 13.8 1.0 CD2 A:HIS77 3.0 12.9 1.0 CD2 A:HIS73 3.0 12.7 1.0 CE1 A:HIS77 3.0 13.8 1.0 CE1 A:HIS73 3.1 13.7 1.0 CE1 C:HIS63 3.1 14.4 1.0 ND1 A:HIS77 4.1 13.9 1.0 CG A:HIS77 4.1 13.9 1.0 CG C:HIS63 4.1 13.4 1.0 CG A:HIS73 4.2 12.9 1.0 ND1 C:HIS63 4.2 14.3 1.0 ND1 A:HIS73 4.2 13.9 1.0 CD1 C:ILE67 4.5 17.6 1.0 O A:HOH390 4.6 47.6 1.0 O A:HOH339 4.7 27.1 1.0 CE3 C:TRP66 4.9 20.6 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:14.4 occ:1.00 NE2 C:HIS77 2.0 17.1 1.0 NE2 C:HIS73 2.0 14.2 1.0 NE2 A:HIS63 2.0 12.5 1.0 CE1 C:HIS73 2.9 14.7 1.0 CD2 A:HIS63 3.0 12.7 1.0 CD2 C:HIS77 3.0 15.0 1.0 CE1 C:HIS77 3.0 17.8 1.0 CD2 C:HIS73 3.0 14.0 1.0 CE1 A:HIS63 3.1 14.0 1.0 ND1 C:HIS73 4.1 14.6 1.0 CG A:HIS63 4.1 13.2 1.0 ND1 C:HIS77 4.1 16.5 1.0 CG C:HIS77 4.1 17.5 1.0 CG C:HIS73 4.1 13.6 1.0 ND1 A:HIS63 4.2 13.1 1.0 CD1 A:ILE67 4.4 15.4 1.0 O C:HOH389 4.6 26.9 1.0 O C:HOH366 4.7 21.3 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:21.8 occ:1.00 NE2 C:HIS93 2.0 17.8 1.0 O C:HOH309 2.0 27.7 1.0 CL C:CL206 2.2 26.0 1.0 OE2 C:GLU89 2.9 52.4 1.0 CD2 C:HIS93 2.9 18.3 1.0 CE1 C:HIS93 3.0 18.5 1.0 CD C:GLU89 3.9 53.4 1.0 CG C:GLU89 4.1 49.3 1.0 ND1 C:HIS93 4.1 18.9 1.0 CG C:HIS93 4.1 18.6 1.0 O C:HOH359 4.4 27.5 1.0 O C:HOH392 4.6 45.5 1.0 O C:GLU89 4.9 26.8 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:22.4 occ:1.00 ND1 C:HIS100 2.0 17.3 0.5 O C:HOH393 2.4 23.9 1.0 ND1 C:HIS100 2.5 21.3 0.5 CE1 C:HIS100 2.8 17.4 0.5 CG C:HIS100 3.0 17.4 0.5 CG C:HIS100 3.3 20.5 0.5 CB C:HIS100 3.5 17.5 0.5 CB C:HIS100 3.5 18.9 0.5 CE1 C:HIS100 3.5 21.5 0.5 NE2 C:HIS100 4.0 18.1 0.5 CD2 C:HIS100 4.1 18.3 0.5 O C:HOH370 4.1 26.0 1.0 CD2 C:HIS100 4.5 20.7 0.5 NE2 C:HIS100 4.6 21.4 0.5 O C:HOH379 4.6 27.7 1.0 O C:HOH399 4.9 29.8 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn204 b:20.6 occ:0.50 OE2 C:GLU8 1.9 18.2 1.0 OD2 C:ASP12 2.1 17.0 1.0 CG C:ASP12 2.7 16.0 1.0 OD1 C:ASP12 2.7 15.1 1.0 CD C:GLU8 2.8 20.6 1.0 CG C:GLU8 3.1 18.6 1.0 OE1 C:GLU8 4.0 24.0 1.0 O C:HOH328 4.1 22.4 1.0 O C:HOH372 4.2 34.3 1.0 CB C:ASP12 4.2 16.5 1.0 CB C:GLU8 4.6 18.9 1.0 O C:GLU8 4.6 14.8 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96V 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, C96V AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn205 b:14.6 occ:0.50 N C:ALA1 1.8 25.2 1.0 OD2 C:ASP39 2.1 18.8 1.0 O C:ALA1 2.4 23.4 1.0 CA C:ALA1 2.8 22.6 1.0 CG C:ASP39 2.8 19.0 1.0 C C:ALA1 2.9 23.0 1.0 OD1 C:ASP39 2.9 18.9 1.0 CB C:ALA1 3.5 21.6 1.0 N C:ASP2 4.2 23.8 1.0 O C:HOH350 4.3 25.4 1.0 ND2 C:ASN6 4.3 19.8 1.0 CB C:ASP39 4.3 17.3 1.0 O C:HOH390 4.6 23.5 1.0 O C:HOH305 4.7 42.1 1.0 O C:ASP39 4.8 18.2 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