Magnesium in PDB 9c1b: Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II

All present enzymatic activity of Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II:
3.6.5.2;

The structure of Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II, PDB code: 9c1b was solved by S.M.Bester, R.Abrahamsen, L.R.Samora, W.-I.Wu, T.-C.Mou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.94 / 2.27
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.724, 55.604, 67.77, 103.74, 90.14, 93.64
R / Rfree (%)	19.9 / 24.7

The binding sites of Magnesium atom in the Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II (pdb code 9c1b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II, PDB code: 9c1b:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II


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 Gdp-Bound Human M-Ras Protein in Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:28.7 occ:1.00 O A:HOH430 2.1 32.7 1.0 O2B A:GDP302 2.1 28.6 1.0 O A:HOH416 2.1 22.6 1.0 O A:HOH404 2.1 25.4 1.0 OG A:SER27 2.2 31.9 1.0 O A:HOH415 2.6 30.9 1.0 CB A:SER27 3.0 20.8 1.0 PB A:GDP302 3.2 20.4 1.0 O3B A:GDP302 3.3 30.5 1.0 O1A A:GDP302 3.8 31.8 1.0 N A:SER27 3.8 25.0 1.0 OD2 A:ASP67 3.8 34.5 1.0 CA A:SER27 4.0 26.4 1.0 O1B A:GDP302 4.2 27.9 1.0 O A:ASP43 4.2 29.6 1.0 O3A A:GDP302 4.3 19.3 1.0 OD1 A:ASP67 4.4 31.0 1.0 PA A:GDP302 4.4 30.5 1.0 CA A:PRO44 4.4 32.8 1.0 O A:PRO44 4.5 36.6 1.0 O2A A:GDP302 4.5 25.0 1.0 CD2 A:TYR42 4.5 21.6 1.0 CG A:ASP67 4.5 35.0 1.0 O A:THR68 4.6 29.8 1.0 C A:PRO44 4.6 39.2 1.0 O A:ILE46 4.8 35.2 1.0 C A:LYS26 5.0 31.2 1.0 CB A:ALA69 5.0 29.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II


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 Gdp-Bound Human M-Ras Protein in Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:24.7 occ:1.00 O2B B:GDP302 2.0 22.9 1.0 O B:HOH404 2.1 20.3 1.0 O B:HOH426 2.1 25.1 1.0 OG B:SER27 2.1 21.8 1.0 O B:HOH411 2.3 24.1 1.0 O B:HOH412 2.3 27.5 1.0 CB B:SER27 3.0 21.8 1.0 PB B:GDP302 3.1 23.4 1.0 O3B B:GDP302 3.2 27.3 1.0 N B:SER27 3.7 20.6 1.0 CA B:SER27 3.8 23.9 1.0 O1A B:GDP302 4.0 30.6 1.0 O1B B:GDP302 4.1 24.1 1.0 OD2 B:ASP67 4.2 42.7 1.0 OD1 B:ASP67 4.2 38.3 1.0 O3A B:GDP302 4.3 23.7 1.0 O B:ASP43 4.4 24.2 1.0 O B:THR68 4.4 32.1 1.0 PA B:GDP302 4.5 22.2 1.0 O2A B:GDP302 4.5 24.2 1.0 CG B:ASP67 4.6 37.5 1.0 O B:PRO44 4.6 31.2 1.0 O B:ILE46 4.6 32.6 1.0 C B:LYS26 4.7 28.3 1.0 CB B:ALA69 4.7 34.8 1.0 CB B:LYS26 4.7 19.6 1.0 CD2 B:TYR42 4.7 22.3 1.0 CA B:PRO44 4.8 26.3 1.0 C B:PRO44 4.9 31.5 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II


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 Gdp-Bound Human M-Ras Protein in Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:31.6 occ:1.00 OG C:SER27 2.2 27.2 1.0 O C:HOH427 2.2 30.6 1.0 O2B C:GDP302 2.2 25.2 1.0 O C:HOH404 2.2 25.6 1.0 O C:HOH405 2.3 21.6 1.0 O C:HOH418 2.4 28.6 1.0 CB C:SER27 3.2 23.5 1.0 O3B C:GDP302 3.2 30.3 1.0 PB C:GDP302 3.3 24.9 1.0 O C:PRO44 4.0 30.1 1.0 O1A C:GDP302 4.0 33.1 1.0 N C:SER27 4.0 23.2 1.0 OD1 C:ASP67 4.0 41.3 1.0 CA C:SER27 4.2 25.5 1.0 O1B C:GDP302 4.2 29.6 1.0 O C:ASP43 4.2 31.2 1.0 O C:ILE46 4.4 39.0 1.0 CA C:PRO44 4.4 28.8 1.0 O3A C:GDP302 4.4 22.9 1.0 C C:PRO44 4.4 32.7 1.0 O C:THR68 4.5 26.8 1.0 O C:HOH453 4.5 36.6 1.0 CB C:ALA69 4.5 34.9 1.0 PA C:GDP302 4.6 26.7 1.0 CD2 C:TYR42 4.7 28.4 1.0 OD2 C:ASP67 4.7 37.7 1.0 CG C:ASP67 4.7 35.7 1.0 O2A C:GDP302 4.8 26.9 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Gdp-Bound Human M-Ras Protein in Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:33.6 occ:1.00 O D:HOH431 2.1 33.5 1.0 O D:HOH405 2.2 27.5 1.0 O2B D:GDP302 2.2 31.4 1.0 O D:HOH413 2.3 23.4 1.0 O D:HOH411 2.3 31.1 1.0 OG D:SER27 2.5 29.6 1.0 O3B D:GDP302 3.0 39.0 1.0 PB D:GDP302 3.2 28.7 1.0 CB D:SER27 3.2 25.7 1.0 O1A D:GDP302 3.9 34.3 1.0 OD2 D:ASP67 3.9 32.4 1.0 N D:SER27 4.0 25.9 1.0 CA D:SER27 4.1 26.3 1.0 O1B D:GDP302 4.1 28.1 1.0 O D:PRO44 4.2 34.1 1.0 O D:ASP43 4.2 33.6 1.0 CA D:PRO44 4.2 39.5 1.0 O3A D:GDP302 4.3 25.6 1.0 C D:PRO44 4.5 39.6 1.0 PA D:GDP302 4.5 27.8 1.0 OD1 D:ASP67 4.5 30.4 1.0 CD2 D:TYR42 4.6 27.1 1.0 CG D:ASP67 4.6 34.8 1.0 O D:ILE46 4.7 37.5 1.0 O D:THR68 4.7 31.9 1.0 O2A D:GDP302 4.7 28.4 1.0 CB D:ALA69 4.9 35.5 1.0 O D:HOH426 4.9 32.6 1.0 C D:ASP43 5.0 43.8 1.0

S.M.Bester, R.Abrahamsen, L.Rodrigues Samora, W.I.Wu, T.C.Mou. Crystal Structure of the Gdp-Bound Human M-Ras Protein in Two Crystal Forms. Acta Crystallogr.,Sect.F 2024.
ISSN: ESSN 2053-230X
PubMed: 39196705
DOI: 10.1107/S2053230X24007969