Magnesium in PDB 7b80: Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)

All present enzymatic activity of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2):
3.6.4.10;

The structure of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2), PDB code: 7b80 was solved by L.A.Perera, D.Ron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.40 / 1.87
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	95, 103.89, 104.79, 90, 90, 90
R / Rfree (%)	20.1 / 22.8

The structure of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) also contains other interesting chemical elements:

Potassium

(K)

3 atoms

The binding sites of Magnesium atom in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) (pdb code 7b80). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2), PDB code: 7b80:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:27.1 occ:1.00 O B:HOH807 2.1 26.4 1.0 O B:HOH925 2.1 28.2 1.0 O B:HOH778 2.1 25.2 1.0 O B:HOH796 2.1 25.6 1.0 O B:HOH758 2.1 27.2 1.0 O3 B:PO4603 2.1 28.2 1.0 P B:PO4603 3.3 31.4 1.0 O4 B:PO4603 3.6 30.5 1.0 O B:HOH810 3.7 34.9 1.0 K B:K604 3.7 26.4 1.0 OD1 B:ASP224 3.9 28.7 1.0 OE1 B:GLU201 4.0 27.0 1.0 O2 B:PO4603 4.1 31.1 1.0 OD2 B:ASP34 4.2 29.1 1.0 O B:HOH763 4.3 32.4 1.0 OD1 B:ASP34 4.3 27.7 1.0 OD2 B:ASP224 4.3 29.2 1.0 CA B:GLY226 4.4 28.9 1.0 O1 B:PO4603 4.5 29.7 1.0 CG B:ASP224 4.5 28.0 1.0 CD B:GLU201 4.5 26.6 1.0 O B:HOH948 4.6 40.0 1.0 CG2 B:VAL394 4.6 26.8 1.0 CG B:ASP34 4.7 28.1 1.0 O B:HOH973 4.8 13.8 1.0

Magnesium binding site 2 out of 2 in the Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Deampylation Complex of Monomeric Ficd and Ampylated Bip (State 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:26.3 occ:1.00 O1P B:AMP601 2.1 39.5 1.0 O B:HOH808 2.1 28.2 1.0 O A:HOH671 2.1 26.7 1.0 O A:HOH647 2.1 25.7 1.0 OD1 A:ASP367 2.1 32.8 1.0 O B:HOH875 2.1 26.7 1.0 CG A:ASP367 3.1 32.3 1.0 P B:AMP601 3.4 38.4 1.0 OD2 A:ASP367 3.5 33.3 1.0 O2P B:AMP601 3.8 39.6 1.0 OE1 A:GLU234 4.1 35.4 1.0 N B:THR518 4.2 40.7 1.0 N A:GLY368 4.2 29.0 1.0 NH2 A:ARG371 4.2 29.7 1.0 O A:HOH669 4.4 38.9 1.0 O5' B:AMP601 4.4 37.0 1.0 CB B:THR518 4.4 41.3 1.0 CB A:ASP367 4.4 32.1 1.0 OG1 B:THR518 4.4 39.1 1.0 O B:THR518 4.5 43.6 1.0 CD A:GLU234 4.6 35.0 1.0 CA A:ASP367 4.7 30.9 1.0 C5' B:AMP601 4.7 34.9 1.0 CB A:GLU234 4.8 36.7 1.0 CA B:THR518 4.8 41.3 1.0 O A:HOH850 4.8 55.5 1.0 CG A:GLU234 4.9 35.7 1.0 CA B:GLY517 5.0 40.6 1.0

L.A.Perera, D.Ron. Structures of A Deampylation Complex Rationalise the Switch Between Antagonistic Catalytic Activities of Ficd Nat Commun 2021.
ISSN: ESSN 2041-1723