Magnesium in PDB 5vbz: Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp, PDB code: 5vbz was solved by D.R.Gentile, M.L.Jenkins, S.M.Moss, J.E.Burke, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.60 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.840, 75.440, 93.630, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.3

The structure of Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp (pdb code 5vbz). 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 Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp, PDB code: 5vbz:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp


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 Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:20.9 occ:1.00 O1G A:GNP201 1.9 22.7 1.0 OG A:SER17 2.1 28.0 1.0 OG1 A:THR35 2.1 50.6 1.0 O A:HOH303 2.1 21.2 1.0 O A:HOH304 2.1 24.6 1.0 O1B A:GNP201 2.2 19.5 1.0 HB A:THR35 2.8 62.3 1.0 CB A:THR35 3.0 51.9 1.0 HB2 A:SER17 3.1 27.0 1.0 CB A:SER17 3.1 22.5 1.0 PG A:GNP201 3.1 22.5 1.0 H A:THR35 3.2 50.2 1.0 H A:SER17 3.4 21.6 1.0 PB A:GNP201 3.4 20.5 1.0 N3B A:GNP201 3.5 25.8 1.0 N A:THR35 3.7 41.9 1.0 OD2 A:ASP57 3.7 33.3 1.0 HB3 A:SER17 3.8 27.0 1.0 O2A A:GNP201 3.9 27.5 1.0 N A:SER17 3.9 18.0 1.0 HG21 A:THR35 3.9 68.7 1.0 CA A:THR35 3.9 44.9 1.0 HB2 A:LYS16 4.0 29.2 1.0 O2G A:GNP201 4.0 22.2 1.0 CG2 A:THR35 4.1 57.3 1.0 CA A:SER17 4.1 20.0 1.0 HE2 A:LYS16 4.1 41.0 1.0 OD1 A:ASP57 4.1 34.9 1.0 O3G A:GNP201 4.2 24.2 1.0 HNB3 A:GNP201 4.3 30.9 1.0 O2B A:GNP201 4.3 17.9 1.0 CG A:ASP57 4.3 32.6 1.0 O A:ASP33 4.4 42.2 1.0 O3A A:GNP201 4.4 22.8 1.0 HA A:SER17 4.4 24.0 1.0 HA A:PRO34 4.4 49.7 1.0 O A:THR58 4.5 27.3 1.0 HA A:THR35 4.5 53.8 1.0 HG23 A:THR35 4.5 68.7 1.0 PA A:GNP201 4.6 25.2 1.0 C A:PRO34 4.7 41.5 1.0 HZ1 A:LYS16 4.8 43.2 1.0 HG22 A:THR35 4.8 68.7 1.0 O1A A:GNP201 4.9 28.9 1.0 HA A:ALA59 4.9 37.1 1.0 HZ3 A:LYS16 4.9 43.2 1.0 CB A:LYS16 4.9 24.3 1.0 HE1 A:TYR32 5.0 54.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp


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 Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:18.2 occ:1.00 O2B B:GNP201 2.1 18.4 1.0 O B:HOH302 2.1 20.4 1.0 O B:HOH311 2.1 20.7 1.0 O B:HOH316 2.1 21.2 1.0 O3G B:GNP201 2.3 21.9 1.0 OG B:SER17 2.4 27.8 1.0 HB2 B:SER17 2.9 28.2 1.0 CB B:SER17 3.2 23.5 1.0 H B:SER17 3.3 24.4 1.0 PB B:GNP201 3.4 20.4 1.0 PG B:GNP201 3.4 22.2 1.0 N3B B:GNP201 3.7 23.1 1.0 OD2 B:ASP57 3.8 47.4 1.0 HZ3 B:LYS16 3.8 36.4 1.0 HB3 B:SER17 3.9 28.2 1.0 HB2 B:LYS16 3.9 25.6 1.0 N B:SER17 4.0 20.3 1.0 HZ2 B:LYS16 4.0 36.4 1.0 O1B B:GNP201 4.1 13.0 1.0 O2A B:GNP201 4.1 24.3 1.0 CA B:SER17 4.2 21.5 1.0 OD1 B:ASP57 4.2 45.2 1.0 O2G B:GNP201 4.3 24.1 1.0 NZ B:LYS16 4.4 30.3 1.0 CG B:ASP57 4.4 46.1 1.0 O B:THR58 4.4 45.5 1.0 O3A B:GNP201 4.4 18.3 1.0 O1G B:GNP201 4.5 24.7 1.0 OG1 B:THR35 4.5 49.2 1.0 HA B:SER17 4.5 25.8 1.0 HNB3 B:GNP201 4.5 27.8 1.0 PA B:GNP201 4.7 19.4 1.0 HA B:ALA59 4.7 71.8 1.0 O1A B:GNP201 4.7 17.8 1.0 HZ1 B:LYS16 4.7 36.4 1.0 CB B:LYS16 4.9 21.3 1.0 HG1 B:THR35 4.9 59.0 1.0 HB B:THR35 4.9 61.4 1.0 HG23 B:THR35 4.9 63.0 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp


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 Small Molecule Disulfide 2C07 Bound to H-Ras M72C Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg303 b:19.3 occ:1.00 O3G C:GNP302 1.9 21.6 1.0 OG1 C:THR35 2.1 53.9 1.0 OG C:SER17 2.1 18.5 1.0 O C:HOH406 2.1 17.0 1.0 O2B C:GNP302 2.2 19.2 1.0 O C:THR35 2.2 49.6 1.0 HB2 C:SER17 3.0 18.7 1.0 CB C:SER17 3.1 15.6 1.0 PG C:GNP302 3.2 28.2 1.0 C C:THR35 3.2 57.7 1.0 H C:SER17 3.3 17.6 1.0 CB C:THR35 3.3 57.7 1.0 PB C:GNP302 3.4 18.2 1.0 HA C:THR35 3.4 69.2 1.0 N3B C:GNP302 3.5 27.1 1.0 CA C:THR35 3.5 57.6 1.0 HB3 C:SER17 3.7 18.7 1.0 HG23 C:THR35 3.9 75.5 1.0 N C:SER17 3.9 14.6 1.0 HB C:THR35 3.9 69.2 1.0 OD2 C:ASP57 3.9 27.0 1.0 HB2 C:LYS16 4.1 28.6 1.0 CA C:SER17 4.1 14.2 1.0 O1A C:GNP302 4.1 18.3 1.0 HE2 C:LYS16 4.1 28.6 1.0 CG2 C:THR35 4.1 62.9 1.0 O1G C:GNP302 4.1 28.6 1.0 HNB3 C:GNP302 4.2 32.5 1.0 O2G C:GNP302 4.2 26.9 1.0 OD1 C:ASP57 4.2 28.1 1.0 O1B C:GNP302 4.3 11.5 1.0 HG21 C:THR35 4.4 75.5 1.0 O3A C:GNP302 4.4 14.6 1.0 N C:ILE36 4.4 80.5 1.0 HA C:SER17 4.5 17.1 1.0 CG C:ASP57 4.5 24.8 1.0 PA C:GNP302 4.7 17.3 1.0 HA C:ILE36 4.7 84.8 1.0 O C:THR58 4.8 22.1 1.0 O2A C:GNP302 4.8 19.3 1.0 HG22 C:THR35 5.0 75.5 1.0 CA C:ILE36 5.0 70.7 1.0

D.R.Gentile, M.K.Rathinaswamy, M.L.Jenkins, S.M.Moss, B.D.Siempelkamp, A.R.Renslo, J.E.Burke, K.M.Shokat. Ras Binder Induces A Modified Switch-II Pocket in Gtp and Gdp States. Cell Chem Biol V. 24 1455 2017.
ISSN: ESSN 2451-9456
PubMed: 29033317
DOI: 10.1016/J.CHEMBIOL.2017.08.025