Magnesium in PDB 3con: Crystal Structure of the Human Nras Gtpase Bound with Gdp

The structure of Crystal Structure of the Human Nras Gtpase Bound with Gdp, PDB code: 3con was solved by L.Nedyalkova, Y.Tong, W.Tempel, L.Shen, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.97 / 1.65
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	83.061, 83.061, 38.907, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 21.9

The binding sites of Magnesium atom in the Crystal Structure of the Human Nras Gtpase Bound with Gdp (pdb code 3con). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Human Nras Gtpase Bound with Gdp, PDB code: 3con:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Human Nras Gtpase Bound 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 the Human Nras Gtpase Bound with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:19.9 occ:1.00 O A:HOH265 2.0 18.3 1.0 O2B A:GDP201 2.1 18.6 1.0 OG A:SER17 2.1 18.1 1.0 O A:HOH279 2.1 20.6 1.0 O A:HOH282 2.1 18.2 1.0 O A:HOH226 2.2 18.7 1.0 CB A:SER17 3.2 17.9 1.0 PB A:GDP201 3.3 18.9 1.0 O1B A:GDP201 3.6 19.1 1.0 N A:SER17 3.9 17.0 1.0 O1A A:GDP201 4.0 20.5 1.0 OD2 A:ASP57 4.0 22.3 1.0 CA A:SER17 4.1 16.1 1.0 OD1 A:ASP57 4.2 22.0 1.0 O3A A:GDP201 4.3 19.0 1.0 O3B A:GDP201 4.4 17.8 1.0 O A:ASP33 4.4 20.1 1.0 CA A:PRO34 4.4 21.5 1.0 O A:THR58 4.5 22.2 1.0 PA A:GDP201 4.5 19.0 1.0 O A:ILE36 4.5 20.7 1.0 CG A:ASP57 4.5 22.9 1.0 O A:PRO34 4.6 26.0 1.0 CD1 A:TYR32 4.6 22.1 1.0 O2A A:GDP201 4.7 19.8 1.0 O A:TYR32 4.8 20.3 1.0 C A:PRO34 4.8 24.4 1.0 CB A:LYS16 4.8 19.5 1.0 C A:LYS16 5.0 15.1 1.0 CE A:LYS16 5.0 19.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Human Nras Gtpase Bound 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 the Human Nras Gtpase Bound with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:26.4 occ:1.00 O A:HOH249 2.1 23.3 1.0 O A:HOH252 2.1 26.4 1.0 O A:GLY48 2.1 22.6 1.0 O A:HOH247 2.1 23.7 1.0 O A:HOH250 2.2 28.2 1.0 O A:HOH278 2.2 28.8 1.0 C A:GLY48 3.1 21.9 1.0 CA A:GLY48 3.6 22.1 1.0 N A:GLU49 4.3 21.8 1.0 CG1 A:VAL45 4.3 23.7 1.0 O A:HOH268 4.6 32.1 1.0 OG1 A:THR50 4.7 28.5 1.0 CA A:GLU49 4.7 24.0 1.0 N A:THR50 4.9 23.9 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Human Nras Gtpase Bound with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Human Nras Gtpase Bound with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:21.6 occ:0.50 O A:HOH294 1.8 30.8 0.5 O A:HOH284 2.0 24.7 0.5 O A:HOH283 2.0 25.6 0.5 OD1 A:ASP38 2.1 25.6 1.0 O A:HOH280 2.2 27.1 0.5 CG A:ASP38 3.1 27.9 1.0 OD2 A:ASP38 3.5 32.9 1.0 N A:SER39 4.3 24.2 1.0 O A:SER39 4.3 24.5 1.0 CB A:ASP38 4.5 25.5 1.0 CA A:ASP38 4.7 22.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of the Human Nras Gtpase Bound with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of the Human Nras Gtpase Bound with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:21.3 occ:0.33 O A:HOH231 2.1 22.4 1.0 O A:HOH245 2.1 22.1 1.0 O A:THR124 4.2 18.9 1.0 O A:HOH227 4.2 21.9 1.0 OE1 A:GLN129 4.4 23.8 1.0

L.Nedyalkova, Y.Tong, W.Tempel, L.Shen, P.Loppnau, C.H.Arrowsmith, A.M.Edwards, C.Bountra, J.Weigelt, A.Bochkarev, H.Park. Crystal Structure of the Human Nras Gtpase Bound with Gdp. To Be Published.