Magnesium 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:

Zinc	(Zn)	7 atoms
Chlorine	(Cl)	2 atoms
Iron	(Fe)	2 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg209 b:7.9 occ:1.00 N A:ALA1 1.7 26.7 1.0 OD2 A:ASP39 2.1 20.9 1.0 O A:ALA1 2.4 23.2 1.0 CA A:ALA1 2.8 23.9 1.0 CG A:ASP39 2.9 19.8 1.0 C A:ALA1 2.9 24.8 1.0 OD1 A:ASP39 3.0 18.8 1.0 CB A:ALA1 3.5 23.1 1.0 N A:ASP2 4.3 23.2 1.0 CB A:ASP39 4.3 16.6 1.0 ND2 A:ASN6 4.3 14.2 1.0 O A:HOH330 4.4 27.4 1.0 O A:HOH301 4.6 35.4 1.0 O A:HOH365 4.7 30.0 1.0 O A:ASP39 4.8 15.9 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 C:Mg204 b:31.2 occ:1.00 OE1 C:GLU4 1.9 35.7 1.0 CD C:GLU4 2.6 30.5 1.0 OE2 C:GLU4 2.7 33.3 1.0 O C:HOH334 3.0 29.4 1.0 CG C:GLU4 4.1 25.4 1.0 O C:HOH308 4.2 28.0 1.0 O C:HOH320 4.4 41.0 1.0 O1D C:HEC201 4.6 20.9 1.0 O2D C:HEC201 4.9 20.2 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