Magnesium in PDB 6zio: Crystal Structure of Nras (C118S) in Complex with Gdp

The structure of Crystal Structure of Nras (C118S) in Complex with Gdp, PDB code: 6zio was solved by D.Kessler, G.Fischer, J.Boettcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.19 / 1.55
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	37.174, 37.161, 66.245, 78.83, 75.24, 64.70
R / Rfree (%)	23.7 / 27.8

The binding sites of Magnesium atom in the Crystal Structure of Nras (C118S) in Complex with Gdp (pdb code 6zio). 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 Nras (C118S) in Complex with Gdp, PDB code: 6zio:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Nras (C118S) 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 Nras (C118S) in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:3.0 occ:1.00 O A:HOH369 2.1 9.6 1.0 O A:HOH305 2.1 6.8 1.0 OG A:SER17 2.2 11.7 1.0 O A:HOH309 2.2 5.1 1.0 O A:HOH302 2.2 4.6 1.0 O2B A:GDP202 2.2 6.4 1.0 CB A:SER17 3.3 5.9 1.0 PB A:GDP202 3.4 4.8 1.0 O3B A:GDP202 3.5 7.2 1.0 N A:SER17 4.0 4.0 1.0 O2A A:GDP202 4.1 6.5 1.0 O A:ASP33 4.2 7.5 1.0 CA A:SER17 4.2 3.9 1.0 OD1 A:ASP57 4.3 10.9 1.0 OD2 A:ASP57 4.3 14.0 1.0 O A:PRO34 4.3 10.0 1.0 CA A:PRO34 4.3 7.0 1.0 O3A A:GDP202 4.4 6.1 1.0 O1B A:GDP202 4.4 4.5 1.0 O A:ILE36 4.6 13.8 1.0 O A:THR58 4.6 8.2 1.0 PA A:GDP202 4.6 5.6 1.0 C A:PRO34 4.6 11.2 1.0 O1A A:GDP202 4.7 5.6 1.0 CG A:ASP57 4.7 10.8 1.0 CD2 A:TYR32 4.8 9.6 1.0 CE A:LYS16 4.9 8.4 1.0 CB A:LYS16 4.9 3.1 1.0 O A:HOH301 5.0 17.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Nras (C118S) 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 Nras (C118S) in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:3.0 occ:1.00 O B:HOH312 2.0 5.6 1.0 O B:HOH315 2.0 5.8 1.0 O B:HOH314 2.1 4.4 1.0 OG B:SER17 2.1 7.6 1.0 O B:HOH301 2.1 3.0 1.0 O1B B:GDP203 2.4 5.0 1.0 CB B:SER17 3.3 3.6 1.0 PB B:GDP203 3.5 5.8 1.0 O2B B:GDP203 3.6 9.9 1.0 O B:ASP33 4.0 9.9 1.0 O1A B:GDP203 4.1 8.0 1.0 N B:SER17 4.1 3.1 1.0 OD1 B:ASP57 4.2 9.6 1.0 OD2 B:ASP57 4.2 9.3 1.0 O B:PRO34 4.2 12.8 1.0 CA B:SER17 4.3 3.0 1.0 CA B:PRO34 4.3 8.7 1.0 O B:ILE36 4.3 9.1 1.0 O3A B:GDP203 4.5 5.1 1.0 C B:PRO34 4.5 12.6 1.0 O B:THR58 4.6 5.6 1.0 O3B B:GDP203 4.6 3.6 1.0 CG B:ASP57 4.6 8.5 1.0 CD2 B:TYR32 4.7 6.1 1.0 PA B:GDP203 4.7 4.9 1.0 O2A B:GDP203 4.9 7.1 1.0 C B:ASP33 4.9 11.3 1.0 O B:HOH320 4.9 10.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Nras (C118S) in Complex 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 Nras (C118S) in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:30.0 occ:1.00 O B:ALA18 2.6 5.5 1.0 O B:HIS27 2.8 6.7 1.0 N B:VAL29 3.0 6.3 1.0 CA B:ALA18 3.1 3.6 1.0 CA B:PHE28 3.2 5.9 1.0 C B:ALA18 3.2 4.7 1.0 N B:GLN22 3.5 3.0 1.0 CG2 B:VAL29 3.6 8.6 1.0 C B:PHE28 3.6 8.4 1.0 CB B:ALA18 3.6 3.9 1.0 C B:HIS27 3.7 8.8 1.0 CB B:ILE21 3.8 5.0 1.0 N B:PHE28 3.9 6.3 1.0 CG2 B:ILE21 4.0 6.7 1.0 CD1 B:PHE28 4.0 7.5 1.0 CB B:GLN22 4.1 3.5 1.0 C B:ILE21 4.1 4.0 1.0 CA B:VAL29 4.1 6.7 1.0 CA B:GLN22 4.1 3.2 1.0 CB B:VAL29 4.1 9.2 1.0 CG1 B:VAL29 4.2 9.1 1.0 CB B:PHE28 4.3 7.0 1.0 CA B:ILE21 4.3 3.6 1.0 N B:ALA18 4.4 3.2 1.0 O B:SER17 4.4 3.5 1.0 N B:LEU19 4.6 3.3 1.0 CG B:PHE28 4.6 7.1 1.0 N B:ILE21 4.7 3.1 1.0 NE2 B:GLN22 4.7 8.2 1.0 O B:PHE28 4.8 7.8 1.0 C B:SER17 4.8 4.0 1.0 O B:VAL29 4.8 9.4 1.0 CB B:ALA146 4.9 3.7 1.0 O B:ILE21 4.9 4.0 1.0 CG1 B:ILE21 4.9 5.8 1.0 CE1 B:PHE28 5.0 7.9 1.0

D.Kessler, A.Bergner, J.Bottcher, G.Fischer, S.Dobel, M.Hinkel, B.Mullauer, A.Weiss-Puxbaum, D.B.Mcconnell. Drugging All Ras Isoforms with One Pocket. Future Med Chem V. 12 1911 2020.
ISSN: ISSN 1756-8927
PubMed: 32779487
DOI: 10.4155/FMC-2020-0221