Magnesium in PDB 6ai5: Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3

The structure of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5 was solved by W.J.Song, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.60 / 1.81
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.562, 76.871, 96.425, 90.00, 105.84, 90.00
R / Rfree (%)	17.5 / 20.9

The structure of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 also contains other interesting chemical elements:

Zinc	(Zn)	8 atoms
Iron	(Fe)	4 atoms
Chlorine	(Cl)	5 atoms

The binding sites of Magnesium atom in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 (pdb code 6ai5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3, PDB code: 6ai5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:33.5 occ:1.00 OE2 A:GLU8 2.2 40.1 1.0 OD2 A:ASP12 2.4 26.9 1.0 OD1 A:ASP12 3.0 24.9 1.0 CG A:ASP12 3.0 24.8 1.0 CD A:GLU8 3.1 33.6 1.0 CG A:GLU8 3.2 29.7 1.0 O A:HOH335 3.6 48.0 1.0 O A:HOH301 4.0 36.1 1.0 OE1 A:GLU8 4.3 33.7 1.0 CB A:ASP12 4.5 23.5 1.0 CB A:GLU8 4.7 25.1 1.0 O A:GLU8 4.9 19.0 1.0

Magnesium binding site 2 out of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg203 b:45.5 occ:1.00 O C:HOH342 2.8 39.2 1.0 O C:HOH318 2.8 32.8 1.0 ND2 C:ASN13 2.9 18.9 1.0 O C:HOH436 3.3 30.1 1.0 CD C:LYS32 3.7 24.8 1.0 CG2 C:THR9 3.9 17.5 1.0 O C:HOH302 3.9 26.5 1.0 CG C:ASN13 3.9 18.1 1.0 OD1 C:ASN13 4.1 18.0 1.0 CG C:LYS32 4.5 21.3 1.0 CB C:LYS32 4.5 20.3 1.0 CE C:LYS32 4.6 25.2 1.0 NZ C:LYS32 4.6 27.8 1.0 OG1 C:THR9 4.6 16.5 1.0 CB C:THR9 4.6 16.0 1.0 CA C:THR9 4.7 15.9 1.0 O C:THR9 4.8 14.8 1.0

Magnesium binding site 3 out of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg205 b:22.0 occ:1.00 OD2 E:ASP2 2.0 25.3 1.0 O E:HOH302 2.9 40.5 1.0 CG E:ASP2 2.9 23.2 1.0 OD1 E:ASP2 3.2 23.5 1.0 OD1 E:ASP5 3.6 21.6 1.0 CG E:ASP5 4.2 21.6 1.0 CB E:ASP2 4.3 22.7 1.0 OD2 E:ASP5 4.4 26.5 1.0 CB E:GLU4 4.7 26.5 1.0 O E:HOH356 4.8 26.5 1.0 OE1 E:GLU4 4.8 37.9 1.0 N E:ASP5 5.0 20.1 1.0

Magnesium binding site 4 out of 4 in the Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg203 b:35.2 occ:1.00 O C:HOH397 2.5 46.3 1.0 O A:HOH343 2.6 33.9 1.0 OE2 G:GLU81 2.7 26.1 1.0 CE1 C:HIS77 3.2 14.9 1.0 CD G:GLU81 3.5 25.6 1.0 OE1 G:GLU81 3.5 25.2 1.0 ND1 C:HIS77 3.6 14.9 1.0 O C:HOH381 3.7 27.7 1.0 ND2 C:ASN80 3.7 22.9 1.0 CD2 G:LEU78 3.8 19.9 1.0 NZ G:LYS83 4.0 32.8 1.0 CE G:LYS83 4.0 32.1 1.0 CD2 A:HIS63 4.0 15.7 1.0 O A:HOH347 4.2 38.1 1.0 CD G:LYS83 4.3 29.8 1.0 NE2 C:HIS77 4.4 14.7 1.0 CG A:HIS63 4.5 15.9 1.0 OD1 A:ASP60 4.5 30.5 1.0 NE2 A:HIS63 4.6 16.3 1.0 CB A:HIS63 4.9 16.2 1.0 CG C:HIS77 4.9 15.6 1.0 CG G:GLU81 4.9 25.1 1.0 CG C:ASN80 4.9 22.2 1.0

W.J.Song, F.A.Tezcan. Disulfide-Free, Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/A104AB3 To Be Published.