Sodium in PDB 5vp7: Crystal Structure of Human Kras G12A Mutant in Complex with Gdp

The structure of Crystal Structure of Human Kras G12A Mutant in Complex with Gdp, PDB code: 5vp7 was solved by S.Xu, B.Long, G.Boris, A.Chen, S.Ni, M.A.Kennedy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.07 / 1.70
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	93.773, 93.773, 119.918, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 20.7

The structure of Crystal Structure of Human Kras G12A Mutant in Complex with Gdp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Kras G12A Mutant in Complex with Gdp (pdb code 5vp7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Kras G12A Mutant in Complex with Gdp, PDB code: 5vp7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Kras G12A Mutant in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Kras G12A Mutant in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:44.2 occ:1.00 O A:HIS27 2.6 35.9 1.0 O A:ALA18 2.6 19.9 1.0 N A:VAL29 3.2 40.9 1.0 N A:GLN22 3.3 24.1 1.0 CA A:PHE28 3.3 33.9 1.0 C A:ALA18 3.5 22.4 1.0 CA A:ALA18 3.6 24.1 1.0 C A:HIS27 3.6 41.5 1.0 CB A:ILE21 3.7 28.2 1.0 CB A:GLN22 3.7 25.8 1.0 C A:PHE28 3.8 38.8 1.0 CG2 A:ILE21 3.8 31.7 1.0 CA A:GLN22 3.8 21.4 1.0 C A:ILE21 3.8 28.0 1.0 N A:PHE28 3.9 34.7 1.0 CB A:ALA18 4.0 25.1 1.0 CD1 A:PHE28 4.2 31.5 1.0 CA A:ILE21 4.2 28.3 1.0 CB A:VAL29 4.3 60.6 1.0 CA A:VAL29 4.3 57.9 1.0 CB A:PHE28 4.4 31.9 1.0 CG2 A:VAL29 4.4 61.0 1.0 NE2 A:GLN22 4.5 27.6 1.0 O A:ALA146 4.6 29.1 1.0 N A:ILE21 4.6 24.9 1.0 O A:ILE21 4.6 26.3 1.0 O A:SER17 4.7 23.6 1.0 N A:LEU19 4.7 19.8 1.0 CG A:PHE28 4.7 30.3 1.0 O A:VAL29 4.8 59.5 1.0 CG A:GLN22 4.8 29.3 1.0 N A:ALA18 4.8 21.2 1.0 CD A:GLN22 4.9 32.9 1.0 CB A:ALA146 4.9 22.1 1.0 O A:PHE28 4.9 39.7 1.0 CG1 A:ILE21 5.0 34.6 1.0 CA A:HIS27 5.0 47.5 1.0 C A:VAL29 5.0 58.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Kras G12A Mutant in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Kras G12A Mutant in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ F:Na203 b:44.5 occ:1.00 O F:HIS27 2.6 36.5 1.0 O F:ALA18 2.6 20.7 1.0 N F:VAL29 3.2 43.6 1.0 N F:GLN22 3.3 23.5 1.0 CA F:PHE28 3.3 36.3 1.0 C F:ALA18 3.5 21.3 1.0 CA F:ALA18 3.6 22.6 1.0 C F:HIS27 3.6 41.8 1.0 CB F:ILE21 3.7 28.3 1.0 C F:PHE28 3.7 40.6 1.0 CB F:GLN22 3.8 27.2 1.0 CG2 F:ILE21 3.8 33.6 1.0 CA F:GLN22 3.8 22.5 1.0 C F:ILE21 3.8 27.2 1.0 N F:PHE28 3.9 35.4 1.0 CB F:ALA18 4.0 25.3 1.0 CD1 F:PHE28 4.2 35.1 1.0 CA F:ILE21 4.2 29.5 1.0 CB F:VAL29 4.2 59.8 1.0 CA F:VAL29 4.2 58.7 1.0 CG2 F:VAL29 4.4 59.1 1.0 CB F:PHE28 4.4 34.1 1.0 NE2 F:GLN22 4.6 30.1 1.0 O F:ALA146 4.6 28.1 1.0 N F:ILE21 4.6 24.9 1.0 O F:ILE21 4.6 28.0 1.0 O F:SER17 4.7 23.8 1.0 CG F:PHE28 4.7 33.8 1.0 N F:LEU19 4.7 18.3 1.0 O F:VAL29 4.8 60.4 1.0 N F:ALA18 4.9 21.4 1.0 CG F:GLN22 4.9 29.6 1.0 CB F:ALA146 4.9 20.8 1.0 O F:PHE28 4.9 41.9 1.0 CD F:GLN22 4.9 30.4 1.0 C F:VAL29 5.0 59.3 1.0 CA F:HIS27 5.0 47.3 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