Zinc 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:

Chlorine	(Cl)	4 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, C96K AB5 (pdb code 6ldf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96K AB5


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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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:32.0 occ:1.00 NE2 A:HIS73 2.0 33.4 1.0 NE2 A:HIS77 2.0 32.2 1.0 NE2 C:HIS63 2.0 31.5 1.0 CE1 A:HIS73 2.9 33.5 1.0 CE1 A:HIS77 2.9 30.8 1.0 CD2 C:HIS63 3.0 33.3 1.0 CE1 C:HIS63 3.0 36.1 1.0 CD2 A:HIS73 3.0 34.7 1.0 CD2 A:HIS77 3.0 30.4 1.0 ND1 A:HIS73 4.0 35.6 1.0 ND1 A:HIS77 4.0 30.6 1.0 ND1 C:HIS63 4.1 40.8 1.0 CG C:HIS63 4.1 35.3 1.0 CG A:HIS73 4.1 31.3 1.0 CG A:HIS77 4.1 28.9 1.0 CD1 C:ILE67 4.3 45.2 1.0 O A:HOH334 4.7 45.5 1.0 O A:HOH305 5.0 18.7 0.5

Zinc binding site 2 out of 8 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 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:58.6 occ:1.00 NE2 A:HIS93 1.9 81.1 1.0 O A:HOH341 2.4 35.1 1.0 CD2 A:HIS93 2.8 79.3 1.0 CE1 A:HIS93 3.0 74.4 1.0 O A:HOH306 3.3 57.0 1.0 CG A:HIS93 4.0 76.7 1.0 ND1 A:HIS93 4.0 81.7 1.0

Zinc binding site 3 out of 8 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 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:63.7 occ:1.00 ND1 A:HIS100 2.4 55.1 1.0 CG A:HIS100 3.2 53.9 1.0 CE1 A:HIS100 3.3 44.0 1.0 CB A:HIS100 3.5 43.8 1.0 NZ A:LYS96 3.7 56.2 0.5 O A:HOH325 4.0 57.6 1.0 NE2 A:HIS100 4.3 43.6 1.0 CD2 A:HIS100 4.3 50.5 1.0 CD A:LYS96 4.3 49.9 0.5 CE A:LYS96 4.4 56.2 0.5

Zinc binding site 4 out of 8 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 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:44.0 occ:0.50 OE2 A:GLU8 2.0 47.7 1.0 OD2 A:ASP12 2.2 40.3 1.0 OD1 A:ASP12 2.7 39.0 1.0 CG A:ASP12 2.7 40.2 1.0 CD A:GLU8 3.0 51.1 1.0 CG A:GLU8 3.2 48.6 1.0 OE1 A:GLU8 4.2 51.6 1.0 CB A:ASP12 4.2 39.8 1.0 O A:HOH314 4.3 47.8 1.0 O A:GLU8 4.5 39.2 1.0 CB A:GLU8 4.6 43.5 1.0

Zinc binding site 5 out of 8 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 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:64.2 occ:1.00 OE2 A:GLU81 2.0 67.4 1.0 O A:HOH331 2.3 33.5 1.0 CD A:GLU81 2.6 73.1 1.0 OE1 A:GLU81 2.7 74.9 1.0 CG A:GLU81 4.1 71.3 1.0 NZ A:LYS83 4.1 71.9 1.0 CD A:LYS83 4.6 53.4 1.0 CE A:LYS83 5.0 61.8 1.0

Zinc binding site 6 out of 8 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 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn207 b:79.7 occ:1.00 NE2 A:HIS59 2.1 85.5 1.0 CL C:CL204 2.8 107.4 1.0 CD2 A:HIS59 3.0 76.1 1.0 CE1 A:HIS59 3.2 82.5 1.0 O A:HOH340 3.4 70.0 1.0 ND1 C:HIS77 3.9 33.7 1.0 CE1 C:HIS77 3.9 31.6 1.0 CG A:HIS59 4.2 72.1 1.0 ND1 A:HIS59 4.3 83.6 1.0 OD1 C:ASN80 4.4 65.8 1.0 CG C:ASN80 4.7 56.2 1.0 CB C:ASN80 4.8 49.6 1.0 O A:HOH308 5.0 50.8 1.0

Zinc binding site 7 out of 8 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 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, C96K AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn208 b:54.8 occ:0.50 N A:ALA1 1.6 40.7 1.0 OD2 A:ASP39 2.3 54.8 1.0 O A:ALA1 2.5 42.8 1.0 OD1 A:ASP39 2.7 54.6 1.0 CA A:ALA1 2.8 39.8 1.0 CG A:ASP39 2.8 51.5 1.0 C A:ALA1 3.0 45.0 1.0 CB A:ALA1 3.9 40.5 1.0 O A:HOH304 4.1 52.8 1.0 N A:ASP2 4.3 47.3 1.0 CB A:ASP39 4.3 48.3 1.0 ND2 A:ASN6 4.6 30.7 1.0 O A:ASP39 4.7 45.0 1.0

Zinc binding site 8 out of 8 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 Zinc with other atoms in the Zn binding site number 8 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:Zn202 b:33.6 occ:1.00 NE2 C:HIS77 2.0 33.6 1.0 NE2 C:HIS73 2.0 32.1 1.0 NE2 A:HIS63 2.0 35.0 1.0 CD2 A:HIS63 2.9 35.2 1.0 CE1 C:HIS73 3.0 34.8 1.0 CE1 C:HIS77 3.0 31.6 1.0 CD2 C:HIS77 3.0 33.2 1.0 CD2 C:HIS73 3.0 33.8 1.0 CE1 A:HIS63 3.1 35.4 1.0 ND1 C:HIS73 4.1 33.5 1.0 ND1 C:HIS77 4.1 33.7 1.0 CG A:HIS63 4.1 32.0 1.0 ND1 A:HIS63 4.1 34.9 1.0 CG C:HIS77 4.1 32.0 1.0 CG C:HIS73 4.1 33.9 1.0 CD1 A:ILE67 4.4 42.3 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