Magnesium in PDB 4ylg: Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp

The structure of Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp, PDB code: 4ylg was solved by Seattle Structural Genomics Center For Infectious Disease, Seattlestructural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	123.540, 40.660, 78.950, 90.00, 97.45, 90.00
R / Rfree (%)	22.3 / 27.2

The binding sites of Magnesium atom in the Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp (pdb code 4ylg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp, PDB code: 4ylg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:20.9 occ:1.00 O1B A:GDP201 1.9 15.2 1.0 O A:HOH383 2.1 43.4 1.0 OG1 A:THR27 2.1 13.9 1.0 O A:HOH384 2.2 19.1 1.0 O A:HOH349 2.2 26.4 1.0 O A:HOH406 2.6 33.4 1.0 PB A:GDP201 3.0 11.7 1.0 O3B A:GDP201 3.0 14.4 1.0 CB A:THR27 3.3 17.4 1.0 O2A A:GDP201 3.8 12.6 1.0 OE2 A:GLU50 3.9 31.3 1.0 N A:THR27 3.9 9.1 1.0 OE1 A:GLU50 4.0 25.5 1.0 O2B A:GDP201 4.1 11.1 1.0 O3A A:GDP201 4.1 11.8 1.0 CA A:THR27 4.2 10.7 1.0 CD A:GLU50 4.3 28.5 1.0 CG2 A:THR27 4.3 10.0 1.0 PA A:GDP201 4.4 12.1 1.0 O A:HOH382 4.5 31.0 1.0 OD1 A:ASP63 4.7 25.8 1.0 O1A A:GDP201 4.8 17.2 1.0 O A:HOH397 5.0 30.5 1.0

Magnesium binding site 2 out of 2 in the Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of An Adp Ribosylation Factor From Entamoeba Histolytica Hm- 1:Imss Bound to Mg-Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:13.0 occ:1.00 O B:HOH415 2.0 19.1 1.0 O1B B:GDP201 2.0 11.8 1.0 OG1 B:THR27 2.2 16.9 1.0 O B:HOH399 2.2 21.0 1.0 O B:HOH429 2.3 42.4 1.0 O B:HOH361 2.6 34.1 1.0 PB B:GDP201 3.1 11.5 1.0 O3B B:GDP201 3.2 17.7 1.0 CB B:THR27 3.4 11.2 1.0 OE2 B:GLU50 3.9 32.6 1.0 OE1 B:GLU50 4.0 28.9 1.0 N B:THR27 4.0 13.0 1.0 O2A B:GDP201 4.2 17.5 1.0 O2B B:GDP201 4.2 11.9 1.0 O3A B:GDP201 4.2 12.0 1.0 CA B:THR27 4.3 9.3 1.0 CD B:GLU50 4.3 27.6 1.0 O B:HOH373 4.4 31.4 1.0 CG2 B:THR27 4.5 9.9 1.0 OD1 B:ASP63 4.5 19.9 1.0 O A:HOH429 4.5 34.9 1.0 PA B:GDP201 4.6 13.6 1.0 O B:HOH387 4.7 24.9 1.0 O1A B:GDP201 4.8 13.1 1.0 O B:HOH374 4.9 21.2 1.0

D.A.Serbzhinskiy, M.C.Clifton, B.Sankaran, B.L.Staker, T.E.Edwards, P.J.Myler. Structure of An Adp-Ribosylation Factor, ARF1, From Entamoeba Histolytica Bound to Mg(2+)-Gdp. Acta Crystallogr.,Sect.F V. 71 594 2015.
ISSN: ESSN 2053-230X
PubMed: 25945714
DOI: 10.1107/S2053230X15004677