Magnesium in PDB 1amu: Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine

All present enzymatic activity of Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine:
5.1.1.11;

The structure of Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine, PDB code: 1amu was solved by E.Conti, T.Stachelhaus, M.A.Marahiel, P.Brick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.680, 154.770, 65.300, 90.00, 93.91, 90.00
R / Rfree (%)	21.3 / 24.6

The binding sites of Magnesium atom in the Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine (pdb code 1amu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine, PDB code: 1amu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg564 b:28.0 occ:0.50 O1P A:AMP567 2.3 23.4 0.5 OE1 A:GLU327 2.5 19.7 1.0 O A:HOH789 3.0 44.4 1.0 O A:HOH841 3.3 18.6 1.0 P A:AMP567 3.3 25.9 0.5 CD A:GLU327 3.4 21.4 1.0 O2P A:AMP567 3.4 23.4 0.5 OE2 A:GLU327 3.5 22.7 1.0 CB A:PRO325 3.6 14.5 1.0 O5' A:AMP567 3.8 30.7 1.0 N A:THR326 3.8 18.8 1.0 C5' A:AMP567 3.8 26.6 1.0 OG1 A:THR190 3.8 56.4 1.0 CA A:PRO325 4.0 17.0 1.0 OH A:TYR409 4.2 21.2 1.0 OG1 A:THR326 4.4 21.2 1.0 C A:PRO325 4.4 18.3 1.0 CB A:THR326 4.6 18.7 1.0 O3P A:AMP567 4.6 22.6 0.5 CG2 A:THR190 4.7 54.7 1.0 CB A:THR190 4.7 56.0 1.0 O3' A:AMP567 4.7 20.4 1.0 CA A:THR326 4.7 19.8 1.0 N A:GLU327 4.8 17.5 1.0 C4' A:AMP567 4.8 24.6 1.0 CG A:GLU327 4.9 19.8 1.0

Magnesium binding site 2 out of 2 in the Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phenylalanine Activating Domain of Gramicidin Synthetase 1 in A Complex with Amp and Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg564 b:31.1 occ:0.50 O1P B:AMP567 2.2 21.2 0.5 OE1 B:GLU327 2.7 23.7 1.0 O B:HOH594 3.0 25.6 1.0 P B:AMP567 3.2 23.7 0.5 CB B:PRO325 3.3 15.3 1.0 C5' B:AMP567 3.4 25.5 1.0 O5' B:AMP567 3.5 30.5 1.0 N B:THR326 3.5 18.9 1.0 O2P B:AMP567 3.6 23.3 0.5 O B:HOH739 3.6 40.4 1.0 CA B:PRO325 3.6 17.4 1.0 CD B:GLU327 3.6 24.2 1.0 OE2 B:GLU327 3.8 23.4 1.0 C B:PRO325 4.0 18.8 1.0 OH B:TYR409 4.3 23.3 1.0 OG1 B:THR190 4.3 53.0 1.0 O3' B:AMP567 4.3 20.8 1.0 C4' B:AMP567 4.4 20.5 1.0 OG1 B:THR326 4.5 18.4 1.0 CB B:THR326 4.5 18.5 1.0 O3P B:AMP567 4.6 22.2 0.5 CA B:THR326 4.6 17.6 1.0 CG B:PRO325 4.7 17.5 1.0 N B:GLU327 4.7 18.5 1.0 C3' B:AMP567 4.8 21.1 1.0 OXT B:PHE566 4.9 24.5 1.0 N B:PRO325 5.0 18.2 1.0

E.Conti, T.Stachelhaus, M.A.Marahiel, P.Brick. Structural Basis For the Activation of Phenylalanine in the Non-Ribosomal Biosynthesis of Gramicidin S. Embo J. V. 16 4174 1997.
ISSN: ISSN 0261-4189
PubMed: 9250661
DOI: 10.1093/EMBOJ/16.14.4174