Magnesium in PDB 5wdq: H-Ras Mutant L120A Bound to Gmp-Pnp at 100K

All present enzymatic activity of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K:
3.6.5.2;

The structure of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K, PDB code: 5wdq was solved by P.Bandaru, C.L.Gee, J.Kuriyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.37 / 1.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	87.960, 87.960, 133.105, 90.00, 90.00, 120.00
R / Rfree (%)	14 / 15

The structure of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K (pdb code 5wdq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K, PDB code: 5wdq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:14.1 occ:0.32 CA A:CA202 0.0 14.0 0.7 O3G A:GNP201 2.0 16.1 1.0 O2B A:GNP201 2.0 13.6 1.0 O A:HOH340 2.1 15.4 1.0 O A:HOH321 2.1 14.7 1.0 OG A:SER17 2.1 14.2 1.0 OG1 A:THR35 2.1 15.0 1.0 HB A:THR35 3.0 17.4 1.0 CB A:THR35 3.1 14.5 1.0 HB2 A:SER17 3.1 17.4 1.0 CB A:SER17 3.2 14.5 1.0 PB A:GNP201 3.2 13.8 1.0 PG A:GNP201 3.2 14.7 1.0 H A:THR35 3.3 19.0 1.0 H A:SER17 3.3 15.7 1.0 N3B A:GNP201 3.4 14.9 1.0 N A:THR35 3.8 15.8 1.0 HB3 A:SER17 3.8 17.4 1.0 N A:SER17 3.9 13.1 1.0 HB2 A:LYS16 3.9 16.7 1.0 HG21 A:THR35 4.0 20.4 1.0 O1G A:GNP201 4.0 16.4 1.0 OD2 A:ASP57 4.0 16.4 1.0 CA A:THR35 4.1 16.3 1.0 CA A:SER17 4.1 12.9 1.0 O2A A:GNP201 4.1 14.7 1.0 O A:HOH366 4.1 20.4 1.0 OD1 A:ASP57 4.1 16.2 1.0 CG2 A:THR35 4.1 17.0 1.0 HE2 A:LYS16 4.2 18.0 1.0 HNB3 A:GNP201 4.2 17.9 1.0 O3A A:GNP201 4.3 13.7 1.0 O1B A:GNP201 4.3 13.9 1.0 HA A:PRO34 4.3 18.7 1.0 O2G A:GNP201 4.4 15.9 1.0 HA A:SER17 4.4 15.4 1.0 O A:ASP33 4.4 15.1 1.0 CG A:ASP57 4.5 15.4 1.0 O A:THR58 4.5 16.2 1.0 PA A:GNP201 4.5 14.0 1.0 HA A:THR35 4.5 19.6 1.0 HG23 A:THR35 4.6 20.4 1.0 HE1 A:TYR32 4.6 24.4 1.0 O1A A:GNP201 4.7 14.4 1.0 HZ1 A:LYS16 4.7 16.9 1.0 C A:PRO34 4.7 16.5 1.0 HZ3 A:LYS16 4.8 16.9 1.0 CB A:LYS16 4.8 13.9 1.0 HG22 A:THR35 4.9 20.4 1.0 C A:LYS16 4.9 13.2 1.0 CA A:PRO34 5.0 15.6 1.0

Magnesium binding site 2 out of 4 in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:16.4 occ:0.58 O A:HOH458 2.2 27.2 0.5 OE1 A:GLN165 2.3 23.1 1.0 O A:HOH441 2.3 36.6 1.0 O A:HOH420 2.4 36.2 1.0 O A:HOH393 2.4 29.6 1.0 CD A:GLN165 3.3 22.8 1.0 HE22 A:GLN165 3.6 23.8 1.0 NE2 A:GLN165 3.9 19.9 1.0 O A:HOH334 4.1 25.7 1.0 HB3 A:GLN165 4.2 19.6 1.0 CG A:GLN165 4.5 17.8 1.0 HB2 A:GLN165 4.6 19.6 1.0 CB A:GLN165 4.7 16.4 1.0 HE21 A:GLN165 4.7 23.8 1.0 OE2 A:GLU162 4.7 20.8 1.0 HG2 A:GLN165 4.7 21.4 1.0 OE1 A:GLU162 4.8 20.8 1.0

Magnesium binding site 3 out of 4 in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:20.2 occ:0.50 O A:ARG102 2.0 20.5 0.5 O A:HOH431 2.2 30.4 0.5 OD1 A:ASP105 2.3 22.9 0.6 O A:ARG102 2.3 21.8 0.5 OD2 A:ASP105 2.6 24.3 0.6 CG A:ASP105 2.7 19.1 0.6 C A:ARG102 3.3 22.6 0.5 HB2 A:ASP105 3.3 29.8 0.4 C A:ARG102 3.3 20.8 0.5 HA A:VAL103 3.7 24.8 1.0 HA A:ARG102 3.8 25.6 0.5 HA A:ARG102 3.8 25.5 0.5 H A:ASP105 3.9 25.3 0.4 H A:ASP105 4.0 25.3 0.6 HB3 A:ARG102 4.1 29.0 0.5 CA A:ARG102 4.1 21.3 0.5 CB A:ASP105 4.1 24.9 0.6 CA A:ARG102 4.1 21.3 0.5 CB A:ASP105 4.1 24.8 0.4 HH22 A:ARG73 4.2 42.3 1.0 N A:VAL103 4.2 19.8 1.0 HB3 A:ARG102 4.2 30.9 0.5 HA A:ASP105 4.2 25.0 0.4 HA A:ASP105 4.3 25.3 0.6 CA A:VAL103 4.3 20.7 1.0 O A:HOH451 4.3 39.4 1.0 N A:ASP105 4.3 21.1 0.4 N A:ASP105 4.4 21.1 0.6 O A:HOH313 4.4 38.9 1.0 OD1 A:ASP105 4.4 29.7 0.4 HH21 A:ARG73 4.5 42.3 1.0 C A:VAL103 4.5 21.5 1.0 CA A:ASP105 4.5 20.8 0.4 CA A:ASP105 4.5 21.1 0.6 CG A:ASP105 4.6 30.0 0.4 O A:VAL103 4.6 22.0 1.0 HB3 A:ASP105 4.6 29.9 0.6 CB A:ARG102 4.6 24.1 0.5 HB2 A:ASP105 4.7 29.9 0.6 HG2 A:ARG102 4.7 36.1 0.5 CB A:ARG102 4.7 25.8 0.5 NH2 A:ARG73 4.7 35.2 1.0 HB3 A:ASP105 4.9 29.8 0.4

Magnesium binding site 4 out of 4 in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of H-Ras Mutant L120A Bound to Gmp-Pnp at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:16.1 occ:0.33 O A:HOH332 2.0 18.9 1.0 O A:HOH335 2.2 16.9 1.0 HE22 A:GLN129 3.2 22.5 0.6 NE2 A:GLN129 4.0 18.7 0.6 O A:THR124 4.0 15.2 1.0 OE1 A:GLN129 4.2 17.7 0.4 O A:HOH350 4.3 18.5 1.0 OE1 A:GLN129 4.3 19.3 0.6 HE22 A:GLN129 4.5 19.0 0.4 HE21 A:GLN129 4.6 22.5 0.6 CD A:GLN129 4.6 18.9 0.6 HG2 A:GLU126 4.7 26.9 1.0 CD A:GLN129 4.8 24.1 0.4 NE2 A:GLN129 4.9 15.8 0.4

P.Bandaru, N.H.Shah, M.Bhattacharyya, J.P.Barton, Y.Kondo, J.C.Cofsky, C.L.Gee, A.K.Chakraborty, T.Kortemme, R.Ranganathan, J.Kuriyan. Deconstruction of the Ras Switching Cycle Through Saturation Mutagenesis. Elife V. 6 2017.
ISSN: ESSN 2050-084X
PubMed: 28686159
DOI: 10.7554/ELIFE.27810