Magnesium in PDB 4djt: Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+

The structure of Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+, PDB code: 4djt 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)	50.00 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.570, 89.250, 54.980, 90.00, 108.06, 90.00
R / Rfree (%)	17.5 / 21.6

The structure of Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+ also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+ (pdb code 4djt). 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 A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+, PDB code: 4djt:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+


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 A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:12.2 occ:1.00 O A:HOH476 2.0 11.4 1.0 OG1 A:THR21 2.1 12.2 1.0 O A:HOH475 2.1 12.2 1.0 O A:HOH473 2.1 12.0 1.0 O1B A:GDP301 2.1 11.7 1.0 O A:HOH474 2.2 13.1 1.0 CB A:THR21 3.2 12.6 1.0 PB A:GDP301 3.3 13.6 1.0 O3B A:GDP301 3.5 13.1 1.0 N A:THR21 4.0 12.2 1.0 OD1 A:ASP191 4.1 16.3 1.0 OD2 A:ASP63 4.1 12.7 1.0 O A:HOH523 4.2 35.9 1.0 OD1 A:ASP63 4.2 12.6 1.0 CA A:THR21 4.2 12.6 1.0 OG1 A:THR64 4.2 14.6 1.0 CG2 A:THR21 4.2 12.1 1.0 O A:THR64 4.2 12.9 1.0 O2A A:GDP301 4.2 15.4 1.0 OD2 A:ASP191 4.3 18.7 1.0 OE2 A:GLU68 4.3 16.4 1.0 O2B A:GDP301 4.4 12.8 1.0 O3A A:GDP301 4.4 13.9 1.0 CG A:ASP191 4.5 17.1 1.0 CG A:ASP63 4.6 12.6 1.0 PA A:GDP301 4.7 15.7 1.0 N A:GLY66 4.7 17.0 1.0 O A:HOH419 4.8 19.4 1.0 CE A:LYS20 4.8 14.6 1.0 CA A:GLY66 4.8 17.8 1.0 CB A:LYS20 4.9 13.5 1.0 NZ A:LYS20 4.9 14.6 1.0 O1A A:GDP301 4.9 14.5 1.0 C A:THR64 4.9 13.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+


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 A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg302 b:17.9 occ:1.00 O B:HOH491 1.8 17.1 1.0 O B:HOH493 2.0 20.4 1.0 OG1 B:THR21 2.0 15.9 1.0 O3B B:GDP301 2.1 18.2 1.0 O B:HOH490 2.2 17.9 1.0 O B:HOH492 2.2 19.1 1.0 CB B:THR21 3.1 16.1 1.0 PB B:GDP301 3.3 18.4 1.0 O1B B:GDP301 3.5 16.6 1.0 N B:THR21 4.0 15.8 1.0 OD1 B:ASP191 4.1 22.7 1.0 CA B:THR21 4.1 15.6 1.0 CG2 B:THR21 4.2 16.5 1.0 O1A B:GDP301 4.2 17.9 1.0 OD2 B:ASP63 4.2 17.7 1.0 OG1 B:THR64 4.2 18.3 1.0 O B:HOH453 4.2 25.6 1.0 OD1 B:ASP63 4.2 17.8 1.0 OD2 B:ASP191 4.3 23.5 1.0 O2B B:GDP301 4.3 15.4 1.0 O B:THR64 4.3 16.4 1.0 O3A B:GDP301 4.3 17.2 1.0 OE2 B:GLU68 4.3 20.3 1.0 CG B:ASP191 4.5 22.5 1.0 PA B:GDP301 4.6 19.2 1.0 CG B:ASP63 4.6 16.9 1.0 O2A B:GDP301 4.8 21.4 1.0 CB B:LYS20 4.8 16.0 1.0 CE B:LYS20 4.9 16.5 1.0 NZ B:LYS20 4.9 16.4 1.0 N B:GLY66 4.9 20.9 1.0

T.E.Edwards, J.Abendroth, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Nuclear Gtp-Binding Protein From Encephalitozoon Cuniculi Bound to Gdp-MG2+ To Be Published.