Magnesium in PDB 8t73: Crystal Structure of KRAS4A-R151G with Bound Gdp and Mg Ion

All present enzymatic activity of Crystal Structure of KRAS4A-R151G with Bound Gdp and Mg Ion:
3.6.5.2;

The structure of Crystal Structure of KRAS4A-R151G with Bound Gdp and Mg Ion, PDB code: 8t73 was solved by T.H.Tran, M.J.Whitley, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.39 / 1.50
Space group	P 3
Cell size a, b, c (Å), α, β, γ (°)	84.779, 84.779, 41.735, 90, 90, 120
R / Rfree (%)	15.4 / 18.8

The binding sites of Magnesium atom in the Crystal Structure of KRAS4A-R151G with Bound Gdp and Mg Ion (pdb code 8t73). 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 KRAS4A-R151G with Bound Gdp and Mg Ion, PDB code: 8t73:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of KRAS4A-R151G with Bound Gdp and Mg Ion


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 KRAS4A-R151G with Bound Gdp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:13.7 occ:1.00 O2B A:GDP201 2.1 14.2 1.0 O A:HOH348 2.1 16.0 1.0 O A:HOH334 2.1 16.4 1.0 OG A:SER17 2.1 15.9 1.0 O A:HOH366 2.1 15.7 1.0 O A:HOH372 2.1 15.6 1.0 HB2 A:SER17 3.2 19.9 1.0 CB A:SER17 3.2 16.6 1.0 PB A:GDP201 3.3 14.5 1.0 H A:SER17 3.3 17.0 1.0 HA A:PRO34 3.4 21.9 1.0 HD1 A:TYR32 3.5 25.4 1.0 O1B A:GDP201 3.6 16.1 1.0 HB3 A:SER17 3.9 19.9 1.0 N A:SER17 3.9 14.2 1.0 HB2 A:LYS16 4.0 15.6 1.0 CA A:SER17 4.1 14.7 1.0 HE1 A:TYR32 4.2 24.9 1.0 O1A A:GDP201 4.2 16.2 1.0 OD2 A:ASP57 4.2 20.3 1.0 CD1 A:TYR32 4.3 21.1 1.0 OD1 A:ASP57 4.3 20.1 1.0 O3A A:GDP201 4.3 14.1 1.0 CA A:PRO34 4.3 18.3 1.0 O A:PRO34 4.3 18.3 1.0 O A:ASP33 4.3 17.3 1.0 HE2 A:LYS16 4.4 18.9 1.0 O3B A:GDP201 4.4 14.2 1.0 HA A:SER17 4.4 17.7 1.0 O A:ILE36 4.5 16.5 1.0 HB2 A:ALA59 4.6 27.3 1.0 PA A:GDP201 4.6 15.2 1.0 CE1 A:TYR32 4.6 20.7 1.0 C A:PRO34 4.6 17.6 1.0 O A:THR58 4.6 16.8 1.0 HZ3 A:LYS16 4.6 17.3 1.0 CG A:ASP57 4.7 18.4 1.0 HA A:ALA59 4.7 25.8 1.0 HZ1 A:LYS16 4.7 17.3 1.0 O2A A:GDP201 4.7 15.4 1.0 O A:TYR32 4.8 19.8 1.0 HB3 A:TYR32 4.8 23.2 1.0 HB1 A:ALA59 4.9 27.3 1.0 CB A:LYS16 4.9 13.0 1.0 NZ A:LYS16 5.0 14.4 1.0 C A:LYS16 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of KRAS4A-R151G with Bound Gdp and Mg Ion


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 KRAS4A-R151G with Bound Gdp and Mg Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:16.3 occ:1.00 O B:HOH330 2.1 19.3 1.0 O B:HOH364 2.1 18.9 1.0 O B:HOH362 2.1 18.1 1.0 O2B B:GDP201 2.1 14.6 1.0 OG B:SER17 2.2 17.4 1.0 O B:HOH328 2.2 18.4 1.0 HB2 B:SER17 3.2 22.1 1.0 CB B:SER17 3.2 18.4 1.0 H B:SER17 3.4 18.4 1.0 PB B:GDP201 3.4 15.4 1.0 HA B:PRO34 3.5 27.1 1.0 O1B B:GDP201 3.6 16.9 1.0 HD2 B:TYR32 3.8 32.5 1.0 HB3 B:SER17 3.9 22.1 1.0 N B:SER17 4.0 15.4 1.0 HB2 B:LYS16 4.0 17.5 1.0 CA B:SER17 4.1 15.9 1.0 OD2 B:ASP57 4.2 24.0 1.0 O1A B:GDP201 4.2 18.6 1.0 OD1 B:ASP57 4.2 24.7 1.0 HE2 B:LYS16 4.2 21.3 1.0 O B:PRO34 4.3 27.2 1.0 O3A B:GDP201 4.4 15.3 1.0 O B:ASP33 4.4 23.5 1.0 CA B:PRO34 4.4 22.6 1.0 HA B:SER17 4.4 19.1 1.0 HB2 B:ALA59 4.5 37.3 1.0 O B:ILE36 4.5 21.0 1.0 O3B B:GDP201 4.5 15.2 1.0 HB3 B:TYR32 4.5 26.8 1.0 O B:THR58 4.5 19.9 1.0 PA B:GDP201 4.6 16.7 1.0 CG B:ASP57 4.6 26.5 1.0 C B:PRO34 4.6 24.4 1.0 HA B:ALA59 4.7 24.9 1.0 CD2 B:TYR32 4.7 27.1 1.0 O2A B:GDP201 4.7 20.1 1.0 O B:TYR32 4.8 25.9 1.0 HZ1 B:LYS16 4.8 21.6 1.0 CB B:LYS16 4.9 14.6 1.0 HZ3 B:LYS16 5.0 21.6 1.0

M.J.Whitley, T.H.Tran, M.Yi, S.Dharmaiah, G.Cornilescu, D.K.Simanshu. Comparative Analysis of KRAS4A and KRAS4B Splice Variants Reveals Distinctive Structural and Functional Properties Sci Adv 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADJ4137