Magnesium in PDB 6dzh: Hras G13D Bound to Gdp (H13GDP)

The structure of Hras G13D Bound to Gdp (H13GDP), PDB code: 6dzh was solved by C.W.Johnson, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.70 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.571, 71.410, 94.861, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 21.8

The structure of Hras G13D Bound to Gdp (H13GDP) also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Magnesium atom in the Hras G13D Bound to Gdp (H13GDP) (pdb code 6dzh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Hras G13D Bound to Gdp (H13GDP), PDB code: 6dzh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Hras G13D Bound to Gdp (H13GDP)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Hras G13D Bound to Gdp (H13GDP) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:16.7 occ:1.00 O A:HOH330 2.0 29.9 1.0 O3B A:GDP201 2.1 14.3 1.0 O A:HOH355 2.1 26.1 1.0 OG A:SER17 2.2 19.5 1.0 O A:HOH325 2.2 17.4 1.0 O A:HOH321 2.4 21.0 1.0 CB A:SER17 3.3 18.1 1.0 PB A:GDP201 3.3 16.4 1.0 O1B A:GDP201 3.6 14.3 1.0 N A:SER17 3.9 16.5 1.0 O1A A:GDP201 4.0 19.2 1.0 CA A:SER17 4.2 16.6 1.0 OD2 A:ASP57 4.2 20.9 1.0 O A:HOH385 4.2 33.0 1.0 O2B A:GDP201 4.2 13.1 1.0 O3A A:GDP201 4.5 13.6 1.0 CD A:PRO34 4.5 57.2 1.0 OD1 A:ASP57 4.5 21.9 1.0 O A:HOH331 4.5 21.1 1.0 CE A:LYS16 4.6 17.2 1.0 O A:PRO34 4.6 49.8 1.0 PA A:GDP201 4.6 16.4 1.0 O A:THR58 4.7 27.6 1.0 O A:HOH313 4.7 17.4 1.0 CG A:ASP57 4.7 22.6 1.0 CB A:LYS16 4.8 14.1 1.0 O2A A:GDP201 4.8 18.4 1.0 NZ A:LYS16 4.9 18.0 1.0 C A:LYS16 4.9 12.0 1.0

Magnesium binding site 2 out of 4 in the Hras G13D Bound to Gdp (H13GDP)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Hras G13D Bound to Gdp (H13GDP) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:32.4 occ:1.00 O B:HOH360 2.0 58.4 1.0 O B:HOH319 2.1 28.6 1.0 O B:GLY138 2.2 35.0 1.0 O B:HOH321 2.6 33.3 1.0 O B:HOH346 2.7 39.3 1.0 O B:HOH322 2.8 33.6 1.0 C B:GLY138 3.3 33.8 1.0 NE2 B:HIS166 3.8 34.7 1.0 OD1 B:ASP108 3.8 50.5 1.0 CA B:GLY138 4.0 30.6 1.0 CE1 B:HIS166 4.1 34.8 1.0 OD2 B:ASP108 4.1 51.0 1.0 O B:HOH318 4.1 20.4 1.0 N B:ILE139 4.3 31.6 1.0 CG B:ASP108 4.3 49.1 1.0 OE2 B:GLU162 4.4 20.8 1.0 O B:TYR137 4.5 28.8 1.0 CG2 B:ILE139 4.5 24.1 1.0 CA B:ILE139 4.5 21.0 1.0

Magnesium binding site 3 out of 4 in the Hras G13D Bound to Gdp (H13GDP)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Hras G13D Bound to Gdp (H13GDP) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:13.9 occ:1.00 O B:HOH309 2.2 20.4 1.0 O B:HOH355 2.2 31.1 1.0 O3B B:GDP201 2.3 20.7 1.0 O B:HOH358 2.3 29.6 1.0 OG B:SER17 2.4 21.0 1.0 OD1 B:ASP33 2.5 31.4 1.0 OD2 B:ASP33 2.6 26.7 1.0 CG B:ASP33 2.9 31.3 1.0 CB B:SER17 3.4 20.2 1.0 PB B:GDP201 3.5 18.5 1.0 O1B B:GDP201 3.6 18.7 1.0 CA B:CA204 4.2 28.4 1.0 OD2 B:ASP57 4.2 26.1 1.0 O1A B:GDP201 4.2 26.3 1.0 N B:SER17 4.3 18.9 1.0 OD1 B:ASP57 4.4 30.0 1.0 CB B:ASP33 4.5 28.4 1.0 O2B B:GDP201 4.5 15.0 1.0 CA B:SER17 4.5 20.7 1.0 O B:PRO34 4.5 32.0 1.0 O A:HOH353 4.5 34.0 1.0 O B:HOH357 4.5 30.1 1.0 O3A B:GDP201 4.6 19.5 1.0 O2A B:GDP201 4.7 22.3 1.0 PA B:GDP201 4.7 20.3 1.0 CG B:ASP57 4.8 31.5 1.0 O B:THR58 4.8 35.0 1.0 O A:HOH339 4.9 32.5 1.0

Magnesium binding site 4 out of 4 in the Hras G13D Bound to Gdp (H13GDP)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Hras G13D Bound to Gdp (H13GDP) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg202 b:28.2 occ:1.00 O C:HOH314 1.8 26.7 1.0 O C:HOH348 2.0 30.7 1.0 O C:HOH366 2.2 37.7 1.0 OG C:SER17 2.3 31.1 1.0 O1B C:GDP201 2.3 25.6 1.0 O3B C:GDP201 3.1 30.3 1.0 PB C:GDP201 3.3 27.8 1.0 CB C:SER17 3.4 26.2 1.0 O C:HOH302 3.7 31.5 1.0 O C:HOH327 3.7 35.0 1.0 O2A C:GDP201 3.9 32.1 1.0 N C:SER17 4.2 21.5 1.0 O3A C:GDP201 4.3 19.3 1.0 O2B C:GDP201 4.3 25.0 1.0 OD2 C:ASP57 4.4 33.7 1.0 CA C:SER17 4.4 21.3 1.0 PA C:GDP201 4.4 22.2 1.0 O1A C:GDP201 4.5 22.8 1.0 OD1 C:ASP57 4.6 32.9 1.0 O C:THR58 4.8 39.6 1.0 CG C:ASP57 4.9 28.4 1.0

C.W.Johnson, Y.J.Lin, D.Reid, J.Parker, S.Pavlopoulos, P.Dischinger, C.Graveel, A.J.Aguirre, M.Steensma, K.M.Haigis, C.Mattos. Isoform-Specific Destabilization of the Active Site Reveals A Molecular Mechanism of Intrinsic Activation of Kras G13D. Cell Rep V. 28 1538 2019.
ISSN: ESSN 2211-1247
PubMed: 31390567
DOI: 10.1016/J.CELREP.2019.07.026