Calcium in PDB 8fji: Crystal Structure of Rala in A Covalent Complex with Sof-367

The structure of Crystal Structure of Rala in A Covalent Complex with Sof-367, PDB code: 8fji was solved by A.D.Landgraf, I.-J.Yeh, K.Bum-Erdene, G.Gonzalez-Gutierrez, S.Meroueh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.07 / 1.48
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.767, 104.63, 55.823, 90, 90, 90
R / Rfree (%)	18.3 / 20.9

The binding sites of Calcium atom in the Crystal Structure of Rala in A Covalent Complex with Sof-367 (pdb code 8fji). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Rala in A Covalent Complex with Sof-367, PDB code: 8fji:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Rala in A Covalent Complex with Sof-367


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rala in A Covalent Complex with Sof-367 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:14.4 occ:1.00 O B:HOH323 2.2 16.2 1.0 O1B B:GDP201 2.2 11.6 1.0 OG B:SER28 2.2 16.0 1.0 O B:HOH324 2.3 13.8 1.0 O B:HOH337 2.3 14.3 1.0 O B:HOH321 2.4 14.6 1.0 HB2 B:SER28 3.1 12.4 1.0 CB B:SER28 3.3 10.3 1.0 HD2 B:TYR43 3.3 19.1 1.0 H B:SER28 3.4 15.1 1.0 PB B:GDP201 3.4 11.3 1.0 O3B B:GDP201 3.6 10.7 1.0 HA B:PRO45 3.9 25.0 1.0 HB3 B:SER28 3.9 12.4 1.0 HB2 B:LYS27 4.0 13.0 1.0 N B:SER28 4.0 12.6 1.0 HB2 B:ALA70 4.1 21.3 1.0 HE2 B:LYS27 4.1 14.4 1.0 HA B:ALA70 4.1 24.6 1.0 CD2 B:TYR43 4.2 15.9 1.0 OD2 B:ASP68 4.2 16.4 1.0 CA B:SER28 4.2 12.2 1.0 HE2 B:TYR43 4.3 28.2 1.0 O B:PRO45 4.3 18.2 1.0 O2A B:GDP201 4.3 13.6 1.0 O B:GLU44 4.4 29.3 1.0 O B:LYS47 4.4 18.5 1.0 OD1 B:ASP68 4.4 14.5 1.0 HB1 B:ALA70 4.4 21.3 1.0 HA B:SER28 4.5 14.6 1.0 O2B B:GDP201 4.5 10.6 1.0 O3A B:GDP201 4.5 12.0 1.0 HB3 B:TYR43 4.6 26.9 1.0 O B:THR69 4.6 14.4 1.0 CE2 B:TYR43 4.6 23.6 1.0 CB B:ALA70 4.6 17.8 1.0 CA B:PRO45 4.7 20.8 1.0 CG B:ASP68 4.7 16.2 1.0 PA B:GDP201 4.7 12.8 1.0 C B:PRO45 4.8 16.2 1.0 HZ3 B:LYS27 4.8 13.8 1.0 CB B:LYS27 4.9 10.9 1.0 CA B:ALA70 4.9 20.6 1.0 HZ1 B:LYS27 4.9 13.8 1.0 O1A B:GDP201 5.0 13.6 1.0 CE B:LYS27 5.0 12.1 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Rala in A Covalent Complex with Sof-367


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rala in A Covalent Complex with Sof-367 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:20.9 occ:1.00 O B:HOH452 2.3 26.5 1.0 O B:LEU14 2.3 17.2 1.0 O B:HOH390 2.3 19.9 1.0 OE2 B:GLU87 2.4 24.3 1.0 O B:HOH406 2.4 28.1 1.0 O B:HOH430 2.5 22.8 1.0 OE1 B:GLU87 2.5 15.6 1.0 CD B:GLU87 2.8 19.8 1.0 C B:LEU14 3.4 13.8 1.0 H B:LEU14 3.6 22.0 1.0 HA B:HIS15 3.7 14.5 1.0 HB3 B:LEU14 3.9 18.8 1.0 H B:LYS16 4.2 15.2 1.0 N B:LEU14 4.3 18.4 1.0 CG B:GLU87 4.3 13.6 1.0 CA B:LEU14 4.3 15.0 1.0 N B:HIS15 4.3 12.7 1.0 HD2 B:LYS16 4.4 22.8 1.0 CA B:HIS15 4.4 12.1 1.0 CB B:LEU14 4.5 15.7 1.0 HG3 B:LYS16 4.6 21.0 1.0 HG B:LEU14 4.6 29.5 1.0 HG2 B:GLU87 4.6 16.2 1.0 ND1 B:HIS15 4.6 16.6 1.0 HG21 B:ILE175 4.6 15.6 1.0 HD12 B:LEU179 4.7 59.9 1.0 HG3 B:GLU87 4.7 16.2 1.0 N B:LYS16 4.8 12.8 1.0 HG22 B:ILE175 4.9 15.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Rala in A Covalent Complex with Sof-367


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rala in A Covalent Complex with Sof-367 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:43.2 occ:1.00 O B:HOH485 2.1 36.7 1.0 OD1 B:ASP37 2.1 25.9 0.4 O B:HOH393 2.4 26.1 1.0 O B:HOH311 2.6 27.5 1.0 OD2 B:ASP37 2.7 24.8 0.4 CG B:ASP37 2.8 16.0 0.4 HH22 B:ARG161 3.3 33.5 1.0 HB2 B:ASP37 3.5 19.2 0.6 HH12 B:ARG161 3.7 38.2 1.0 NH2 B:ARG161 3.8 28.0 1.0 HZ1 B:LYS53 4.0 37.8 1.0 NH1 B:ARG161 4.1 31.9 1.0 O B:PHE34 4.2 12.2 1.0 CZ B:ARG161 4.2 46.4 1.0 HH21 B:ARG161 4.2 33.5 1.0 O B:HOH309 4.3 26.3 1.0 CB B:ASP37 4.3 17.6 0.4 CB B:ASP37 4.3 16.1 0.6 CG B:ASP37 4.5 15.6 0.6 HA B:ASP37 4.5 18.1 0.4 OD1 B:ASP37 4.5 15.8 0.6 HA B:ASP37 4.5 18.4 0.6 NZ B:LYS53 4.6 31.5 1.0 OD1 B:ASP165 4.7 24.7 1.0 HH11 B:ARG161 4.7 38.2 1.0 O B:GLN33 4.7 11.9 1.0 HB3 B:ASP37 4.7 21.1 0.4 OD2 B:ASP165 4.7 18.8 1.0 H B:ASP37 4.7 18.5 0.4 H B:ASP37 4.7 18.5 0.6 HB2 B:ASP37 4.7 21.1 0.4 HA B:PHE34 4.8 13.1 1.0 CA B:ASP37 4.8 15.1 0.4 CA B:ASP37 4.9 15.4 0.6 HZ2 B:LYS53 4.9 37.8 1.0

A.D.Landgraf, I.J.Yeh, M.K.Ghozayel, K.Bum-Erdene, G.Gonzalez-Gutierrez, S.O.Meroueh. Exploring Covalent Bond Formation at Tyr-82 For Inhibition of Ral Gtpase Activation. Chemmedchem V. 18 00272 2023.
ISSN: ESSN 1860-7187
PubMed: 37269475
DOI: 10.1002/CMDC.202300272