Magnesium in PDB 5vcu: Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp

The structure of Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp, PDB code: 5vcu was solved by Seattle Structural 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)	35.87 / 1.85
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	48.380, 48.380, 624.560, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp (pdb code 5vcu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp, PDB code: 5vcu:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:23.0 occ:1.00 O3B A:GDP301 2.1 22.9 1.0 O A:HOH441 2.1 22.3 1.0 OG1 A:THR17 2.1 24.2 1.0 O A:THR35 2.1 28.2 1.0 O A:HOH432 2.1 25.9 1.0 O A:HOH414 2.1 20.8 1.0 CB A:THR17 3.2 23.9 1.0 C A:THR35 3.3 31.4 1.0 PB A:GDP301 3.3 22.1 1.0 O2B A:GDP301 3.5 20.9 1.0 N A:THR17 3.9 22.1 1.0 OD2 A:ASP57 4.0 22.4 1.0 O A:PRO34 4.0 32.0 1.0 CA A:THR35 4.0 33.4 1.0 O2A A:GDP301 4.1 23.2 1.0 CA A:THR17 4.1 24.6 1.0 N A:VAL36 4.3 33.8 1.0 CG2 A:THR17 4.3 26.1 1.0 O A:HOH578 4.3 26.2 1.0 OD1 A:ASP57 4.3 23.8 1.0 O1B A:GDP301 4.3 23.3 1.0 O3A A:GDP301 4.4 21.0 1.0 O A:HOH493 4.4 22.1 1.0 CA A:VAL36 4.5 30.5 1.0 PA A:GDP301 4.5 22.9 1.0 CG A:ASP57 4.5 24.5 1.0 O A:THR58 4.6 23.6 1.0 O1A A:GDP301 4.6 21.9 1.0 O A:HOH472 4.9 26.9 1.0 C A:PRO34 4.9 35.0 1.0 NZ A:LYS16 5.0 23.6 1.0 N A:THR35 5.0 36.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:29.4 occ:1.00 O B:HOH463 2.0 31.8 1.0 O B:HOH439 2.0 28.3 1.0 O3B B:GDP301 2.0 28.6 1.0 OG1 B:THR17 2.0 32.3 1.0 O B:HOH430 2.2 30.4 1.0 O B:HOH495 2.3 31.0 1.0 CB B:THR17 3.1 33.3 1.0 PB B:GDP301 3.3 31.5 1.0 O1B B:GDP301 3.6 37.0 1.0 N B:THR17 3.9 24.8 1.0 OD1 B:ASP57 3.9 34.3 1.0 O B:HOH545 4.1 61.6 1.0 CA B:THR17 4.1 26.9 1.0 O1A B:GDP301 4.1 41.2 1.0 CG2 B:THR17 4.2 30.9 1.0 CE1 B:PHE37 4.2 78.5 1.0 O2B B:GDP301 4.3 30.1 1.0 OD2 B:ASP57 4.3 34.5 1.0 CD1 B:PHE37 4.3 68.5 1.0 O B:HOH480 4.4 29.0 1.0 O3A B:GDP301 4.4 31.9 1.0 CG B:ASP57 4.5 33.0 1.0 O B:PRO34 4.6 63.9 1.0 PA B:GDP301 4.6 31.1 1.0 O2A B:GDP301 4.7 29.8 1.0 O B:THR58 4.7 32.1 1.0 O B:VAL36 4.9 71.3 1.0 CB B:LYS16 4.9 24.7 1.0 NZ B:LYS16 4.9 25.1 1.0 O B:HOH437 5.0 47.8 1.0 C B:LYS16 5.0 26.0 1.0

S.J.Mayclin, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of Ras-Related C3 Botulinum Toxin Substrate 1 Isoform X2 From Naegleria Fowleri in Complex with Gdp To Be Published.