Atomistry » Magnesium » PDB 101d-1an0 » 1amu
Atomistry »
  Magnesium »
    PDB 101d-1an0 »
      1amu »

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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 1amu

Go back to Magnesium Binding Sites List in 1amu
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 1amu

Go back to Magnesium Binding Sites List in 1amu
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

Reference:

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
Page generated: Tue Aug 13 02:06:37 2024

Last articles

Mg in 8GHU
Mg in 8G7N
Mg in 8GIY
Mg in 8GHF
Mg in 8GIP
Mg in 8GIM
Mg in 8GIN
Mg in 8GFT
Mg in 8GI6
Mg in 8GCQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy