Magnesium in PDB 6wgh: Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region

The structure of Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region, PDB code: 6wgh was solved by S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.89 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	40.460, 45.960, 89.080, 90.00, 99.77, 90.00
R / Rfree (%)	17.8 / 20.9

The binding sites of Magnesium atom in the Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region (pdb code 6wgh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region, PDB code: 6wgh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region


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 Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:23.4 occ:1.00 OA1 A:FLC203 2.0 21.1 0.8 O A:HOH326 2.0 29.9 1.0 OB1 A:FLC203 2.0 24.2 0.8 O A:HOH357 2.1 25.7 1.0 O A:HOH345 2.1 34.0 1.0 OHB A:FLC203 2.3 25.2 0.8 CBC A:FLC203 2.8 22.8 0.8 CB A:FLC203 2.9 25.1 0.8 CAC A:FLC203 3.0 21.0 0.8 CA A:FLC203 3.4 23.1 0.8 OB2 A:FLC203 4.0 21.5 0.8 OA2 A:FLC203 4.1 20.9 0.8 N A:ASP30 4.2 23.6 1.0 O A:PHE28 4.3 23.1 1.0 CB A:ASP30 4.3 24.1 1.0 NE2 A:HIS27 4.3 24.9 1.0 CG A:FLC203 4.3 27.5 0.8 OG2 A:FLC203 4.5 59.8 0.8 O B:HOH395 4.7 53.6 1.0 CE1 A:HIS27 4.8 29.4 1.0 CGC A:FLC203 4.8 47.0 0.8 CA A:VAL29 4.8 18.1 1.0 CA A:ASP30 4.9 25.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region


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 Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:18.8 occ:1.00 O2B A:GDP202 2.0 17.9 1.0 OG A:SER17 2.1 17.6 1.0 O A:HOH311 2.1 22.1 1.0 O A:HOH306 2.2 16.8 1.0 O A:HOH323 2.2 19.7 1.0 O A:HOH321 2.2 19.0 1.0 CB A:SER17 3.1 17.2 1.0 PB A:GDP202 3.3 18.6 1.0 O1B A:GDP202 3.5 20.1 1.0 N A:SER17 3.9 17.3 1.0 O1A A:GDP202 4.1 21.2 1.0 CA A:SER17 4.1 18.5 1.0 OD2 A:ASP57 4.1 26.7 1.0 O3A A:GDP202 4.3 17.9 1.0 OD1 A:ASP57 4.3 24.2 1.0 O3B A:GDP202 4.3 19.4 1.0 O A:ILE36 4.4 19.4 1.0 O A:ASP33 4.4 20.5 1.0 CD2 A:TYR32 4.4 19.1 1.0 O A:THR58 4.5 22.8 1.0 PA A:GDP202 4.5 19.5 1.0 O A:PRO34 4.6 27.9 1.0 CA A:PRO34 4.6 20.6 1.0 CG A:ASP57 4.6 26.6 1.0 O2A A:GDP202 4.7 21.2 1.0 CE A:LYS16 4.9 20.9 1.0 C A:PRO34 4.9 20.7 1.0 O A:TYR32 4.9 21.1 1.0 CB A:LYS16 4.9 19.1 1.0 C A:LYS16 5.0 19.4 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region


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 Gdp-Bound Nras with Ten Residues Long Internal Tandem Duplication in the Switch II Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:16.5 occ:1.00 O2B B:GDP202 2.0 15.3 1.0 O B:HOH330 2.0 17.8 1.0 OG B:SER17 2.0 18.7 1.0 O B:HOH316 2.1 22.0 1.0 O B:HOH315 2.1 19.9 1.0 O B:HOH308 2.2 18.0 1.0 CB B:SER17 3.2 17.3 1.0 PB B:GDP202 3.3 16.5 1.0 O3B B:GDP202 3.5 17.9 1.0 N B:SER17 4.0 16.2 1.0 O2A B:GDP202 4.1 19.3 1.0 CA B:SER17 4.1 14.7 1.0 OD2 B:ASP57 4.2 24.7 1.0 O B:PRO34 4.2 21.4 1.0 OD1 B:ASP57 4.3 24.6 1.0 O B:ASP33 4.3 21.7 1.0 O1B B:GDP202 4.3 18.2 1.0 O B:ILE36 4.3 23.8 1.0 O3A B:GDP202 4.3 16.1 1.0 CD2 B:TYR32 4.4 19.1 1.0 O B:THR58 4.5 22.8 1.0 CA B:PRO34 4.6 18.4 1.0 PA B:GDP202 4.6 18.8 1.0 CG B:ASP57 4.6 27.4 1.0 C B:PRO34 4.7 22.5 1.0 O1A B:GDP202 4.7 19.4 1.0 CB B:LYS16 4.9 15.2 1.0 CE2 B:TYR32 4.9 21.6 1.0 CE B:LYS16 5.0 18.4 1.0 CB B:ALA59 5.0 27.8 1.0

S.Dharmaiah, D.K.Simanshu. Ras Internal Tandem Duplication Disrupts Gtpase-Activating Protein (Gap) Binding to Activate Oncogenic Signaling J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X