Magnesium in PDB 9dfw: X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam

The structure of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam, PDB code: 9dfw was solved by J.C.Lachowicz, J.B.Bonanno, T.L.Grove, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 1.68
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	85.131, 85.131, 110.471, 90, 90, 120
R / Rfree (%)	15.5 / 18.8

The structure of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam also contains other interesting chemical elements:

Iron

(Fe)

12 atoms

The binding sites of Magnesium atom in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam (pdb code 9dfw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam, PDB code: 9dfw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:30.4 occ:1.00 O A:HOH624 2.6 48.1 1.0 O A:ILE120 2.7 27.1 1.0 O A:GLY117 2.8 30.9 1.0 O A:ASP160 2.8 29.9 1.0 O A:HOH625 3.5 38.2 1.0 C A:ILE120 3.7 23.4 1.0 C A:ASP160 3.8 29.0 1.0 C A:GLY117 3.9 30.3 1.0 O A:ARG118 4.0 31.1 1.0 CG1 A:ILE161 4.1 28.5 1.0 C A:ARG118 4.1 31.2 1.0 O A:TYR159 4.2 33.8 1.0 N A:ILE120 4.3 27.3 1.0 CA A:ARG118 4.3 32.0 1.0 CA A:ILE161 4.3 26.4 1.0 N A:ILE161 4.5 28.9 1.0 N A:ASP121 4.5 23.8 1.0 CA A:ILE120 4.5 26.1 1.0 CA A:ASP121 4.6 23.4 1.0 N A:ARG118 4.6 31.8 1.0 OD2 A:ASP160 4.6 52.5 1.0 O A:HOH513 4.7 48.2 1.0 N A:ASN119 4.8 28.2 1.0 CB A:ILE161 4.8 27.1 1.0 CB A:ASP160 4.9 40.0 1.0 CA A:ASP160 4.9 33.3 1.0 OD1 A:ASP121 4.9 36.2 1.0 CG A:ASP160 4.9 45.6 1.0

Magnesium binding site 2 out of 3 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:43.7 occ:1.00 O A:HOH685 2.0 45.0 1.0 O A:HOH504 2.0 46.5 1.0 OG A:SER229 2.3 27.8 1.0 O A:HOH703 2.4 37.4 1.0 O A:GLU226 2.5 23.1 1.0 CB A:SER229 3.4 29.0 1.0 C A:GLU226 3.6 24.2 1.0 N A:SER229 4.3 25.9 1.0 OE1 A:GLU226 4.3 45.7 1.0 O A:HOH576 4.4 42.2 1.0 O A:HOH568 4.4 27.8 1.0 CA A:GLU226 4.4 26.1 1.0 CA A:SER229 4.4 26.9 1.0 N A:ARG227 4.6 24.2 1.0 C A:ARG227 4.7 21.1 1.0 CA A:ARG227 4.7 22.0 1.0 CB A:GLU226 4.7 31.7 1.0 O A:ARG227 4.8 25.1 1.0 O B:HOH539 4.9 37.2 1.0 O A:HOH538 4.9 32.0 1.0

Magnesium binding site 3 out of 3 in the X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of An Engineered Viperin-Like Enzyme From T. Virens with Bound Ctp and Sam within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg405 b:26.6 occ:1.00 O C:ILE120 2.7 25.1 1.0 O C:GLY117 2.8 25.9 1.0 O C:ASP160 2.8 31.2 1.0 O C:HOH634 3.5 42.9 1.0 C C:ILE120 3.8 25.9 1.0 C C:ASP160 3.8 32.9 1.0 C C:GLY117 3.9 24.3 1.0 CG1 C:ILE161 4.0 30.5 1.0 O C:ARG118 4.0 30.1 1.0 C C:ARG118 4.1 30.5 1.0 O C:TYR159 4.1 35.7 1.0 CA C:ARG118 4.2 30.7 1.0 N C:ILE120 4.3 24.9 1.0 CA C:ILE161 4.3 29.4 1.0 O C:HOH556 4.4 44.0 1.0 N C:ILE161 4.4 32.4 1.0 OD2 C:ASP160 4.4 58.1 1.0 N C:ARG118 4.5 29.0 1.0 CB C:ASP160 4.5 40.5 1.0 N C:ASP121 4.6 24.0 1.0 CA C:ASP121 4.6 22.9 1.0 CA C:ILE120 4.6 24.5 1.0 CG C:ASP160 4.7 49.3 1.0 CB C:ILE161 4.7 31.1 1.0 N C:ASN119 4.7 27.1 1.0 CA C:ASP160 4.8 37.5 1.0 O C:HOH528 4.8 43.0 1.0 CA C:GLY117 4.9 25.2 1.0 OD1 C:ASP121 4.9 34.0 1.0

J.C.Lachowicz, S.Grudman, J.B.Bonanno, A.Fiser, T.L.Grove. Structural Insights From Active Site Variants and B-8 Loop Interactions in Viperin-Like Enzymes To Be Published.