Calcium 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:

Magnesium	(Mg)	4 atoms
Sodium	(Na)	1 atom

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K, PDB code: 5wdq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the H-Ras Mutant L120A Bound to Gmp-Pnp at 100K


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca202 b:14.0 occ:0.68 MG A:MG203 0.0 14.1 0.3 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 OG1 A:THR35 2.1 15.0 1.0 OG A:SER17 2.1 14.2 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 PG A:GNP201 3.2 14.7 1.0 PB A:GNP201 3.2 13.8 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 C A:PRO34 4.7 16.5 1.0 HZ1 A:LYS16 4.7 16.9 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 5.0 13.2 1.0 CA A:PRO34 5.0 15.6 1.0

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca204 b:16.2 occ:1.00 O A:PHE28 2.3 16.6 1.0 OD1 A:ASP30 2.3 18.9 1.0 H A:ASP30 3.3 17.8 1.0 C A:PHE28 3.5 15.2 1.0 CG A:ASP30 3.6 18.5 1.0 HA A:VAL29 3.7 17.7 1.0 N A:ASP30 4.0 14.8 1.0 HB3 A:PHE28 4.1 19.5 1.0 HB2 A:ASP30 4.1 20.3 1.0 H A:PHE28 4.3 18.1 1.0 O A:HOH354 4.3 32.5 1.0 O A:HOH407 4.3 23.7 1.0 CA A:VAL29 4.4 14.8 1.0 CB A:ASP30 4.4 16.9 1.0 N A:VAL29 4.4 14.6 1.0 HD2 A:PHE28 4.5 19.3 1.0 OD2 A:ASP30 4.5 21.2 1.0 CA A:PHE28 4.5 14.8 1.0 O A:HOH450 4.6 34.4 1.0 HB2 A:HIS27 4.6 20.6 1.0 C A:VAL29 4.6 15.2 1.0 N A:PHE28 4.6 15.1 1.0 CB A:PHE28 4.7 16.2 1.0 CA A:ASP30 4.8 15.2 1.0 CD2 A:PHE28 5.0 16.1 1.0

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