Magnesium in PDB 5w22: Crystal Structure of Human Wt-Kras in Complex with Gdp

The structure of Crystal Structure of Human Wt-Kras in Complex with Gdp, PDB code: 5w22 was solved by S.Xu, B.Long, G.Boris, S.Ni, M.A.Kennedy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 1.76
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	93.177, 93.177, 118.431, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.5

The binding sites of Magnesium atom in the Crystal Structure of Human Wt-Kras in Complex with Gdp (pdb code 5w22). 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 Human Wt-Kras in Complex with Gdp, PDB code: 5w22:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Wt-Kras 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 Human Wt-Kras in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.2 occ:1.00 O A:HOH320 2.0 15.1 1.0 O A:HOH331 2.1 12.9 1.0 OG A:SER17 2.1 15.3 1.0 O3B A:GDP201 2.1 14.7 1.0 O A:HOH321 2.1 16.9 1.0 O A:HOH306 2.2 15.7 1.0 CB A:SER17 3.2 15.4 1.0 PB A:GDP201 3.3 14.2 1.0 O1B A:GDP201 3.5 13.6 1.0 N A:SER17 4.0 15.5 1.0 O1A A:GDP201 4.1 17.3 1.0 OD2 A:ASP57 4.1 22.0 1.0 CA A:SER17 4.2 15.2 1.0 O A:ASP33 4.2 26.8 1.0 O3A A:GDP201 4.3 14.7 1.0 OD1 A:ASP57 4.3 20.2 1.0 O A:PRO34 4.3 26.5 1.0 O2B A:GDP201 4.4 12.6 1.0 O A:ILE36 4.4 26.0 1.0 CA A:PRO34 4.5 30.6 1.0 O A:THR58 4.5 18.4 1.0 CD2 A:TYR32 4.6 25.7 1.0 PA A:GDP201 4.6 14.2 1.0 CG A:ASP57 4.6 19.8 1.0 C A:PRO34 4.6 28.2 1.0 O2A A:GDP201 4.7 17.0 1.0 CB A:ALA59 4.7 27.2 1.0 O A:HOH313 4.8 20.4 1.0 CE2 A:TYR32 4.9 26.4 1.0 CB A:LYS16 5.0 12.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Wt-Kras 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 Human Wt-Kras in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:16.4 occ:1.00 O B:HOH317 2.0 14.9 1.0 O B:HOH340 2.1 14.2 1.0 O2B B:GDP201 2.1 14.2 1.0 O B:HOH314 2.1 15.0 1.0 OG B:SER17 2.1 15.2 1.0 O B:HOH327 2.1 14.1 1.0 CB B:SER17 3.2 13.6 1.0 PB B:GDP201 3.3 14.2 1.0 O3B B:GDP201 3.6 13.6 1.0 N B:SER17 4.0 13.3 1.0 O2A B:GDP201 4.1 17.6 1.0 OD2 B:ASP57 4.1 20.7 1.0 CA B:SER17 4.2 13.7 1.0 O B:ASP33 4.2 25.0 1.0 OD1 B:ASP57 4.3 19.5 1.0 O B:PRO34 4.3 26.4 1.0 O3A B:GDP201 4.3 14.5 1.0 O1B B:GDP201 4.4 13.3 1.0 O B:ILE36 4.4 26.8 1.0 CA B:PRO34 4.5 31.6 1.0 CD2 B:TYR32 4.5 28.7 1.0 O B:THR58 4.6 18.8 1.0 PA B:GDP201 4.6 15.1 1.0 CG B:ASP57 4.6 18.3 1.0 C B:PRO34 4.6 28.6 1.0 O1A B:GDP201 4.7 18.0 1.0 CB B:ALA59 4.8 26.7 1.0 O B:HOH319 4.9 20.0 1.0 CE2 B:TYR32 4.9 29.4 1.0

S.Xu, B.N.Long, G.H.Boris, A.Chen, S.Ni, M.A.Kennedy. Structural Insight Into the Rearrangement of the Switch I Region in Gtp-Bound G12A K-Ras. Acta Crystallogr D Struct V. 73 970 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 29199977
DOI: 10.1107/S2059798317015418