Calcium in PDB 8fjh: Crystal Structure of Rala in A Covalent Complex with Sof-531

The structure of Crystal Structure of Rala in A Covalent Complex with Sof-531, PDB code: 8fjh 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)	55.09 / 1.54
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	64.754, 104.813, 55.347, 90, 90, 90
R / Rfree (%)	14.9 / 18.4

The structure of Crystal Structure of Rala in A Covalent Complex with Sof-531 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Rala in A Covalent Complex with Sof-531 (pdb code 8fjh). 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-531, PDB code: 8fjh:
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-531


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-531 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:19.2 occ:1.00 O B:HOH330 2.1 11.9 1.0 O1B B:GDP201 2.1 10.3 1.0 O B:HOH346 2.1 16.9 1.0 OG B:SER28 2.1 12.3 1.0 O B:HOH361 2.2 14.7 1.0 O B:HOH344 2.2 15.4 1.0 HB2 B:SER28 3.2 13.3 1.0 CB B:SER28 3.2 11.0 1.0 PB B:GDP201 3.3 11.1 1.0 HD2 B:TYR43 3.3 20.5 1.0 H B:SER28 3.4 11.7 1.0 O3B B:GDP201 3.6 12.2 1.0 HA B:PRO45 3.8 24.6 1.0 HB2 B:LYS27 3.9 11.9 1.0 HB3 B:SER28 3.9 13.3 1.0 N B:SER28 3.9 9.7 1.0 HE2 B:LYS27 4.0 17.2 1.0 OD2 B:ASP68 4.1 14.1 1.0 HE2 B:TYR43 4.1 19.9 1.0 CA B:SER28 4.1 8.9 1.0 CD2 B:TYR43 4.2 17.0 1.0 O B:PRO45 4.2 20.8 1.0 O2A B:GDP201 4.2 13.6 1.0 OD1 B:ASP68 4.3 14.2 1.0 O B:GLU44 4.3 21.3 1.0 HB2 B:ALA70 4.3 36.0 1.0 O3A B:GDP201 4.4 11.5 1.0 O2B B:GDP201 4.4 9.8 1.0 HA B:SER28 4.4 10.5 1.0 O B:THR69 4.5 17.8 1.0 O B:LYS47 4.5 26.0 1.0 CE2 B:TYR43 4.6 16.6 1.0 HA B:ALA70 4.6 32.0 1.0 CG B:ASP68 4.6 15.9 1.0 CA B:PRO45 4.6 20.4 1.0 PA B:GDP201 4.7 12.2 1.0 HZ1 B:LYS27 4.7 14.1 1.0 C B:PRO45 4.7 18.9 1.0 HB3 B:TYR43 4.7 24.3 1.0 HB1 B:ALA70 4.8 36.0 1.0 CB B:LYS27 4.8 9.8 1.0 HZ3 B:LYS27 4.8 14.1 1.0 O1A B:GDP201 4.9 12.4 1.0 O B:HOH356 4.9 18.2 1.0 CE B:LYS27 4.9 14.2 1.0 CB B:ALA70 4.9 29.9 1.0 O B:TYR43 4.9 20.1 1.0 HB3 B:LYS27 4.9 11.9 1.0 O B:HOH410 5.0 19.3 1.0 C B:LYS27 5.0 9.3 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Rala in A Covalent Complex with Sof-531


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-531 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca204 b:20.0 occ:1.00 O B:LEU14 2.2 19.6 1.0 O B:HOH465 2.3 27.8 1.0 O B:HOH432 2.3 32.3 1.0 OE2 B:GLU87 2.4 20.4 1.0 O B:HOH408 2.4 19.7 1.0 O B:HOH419 2.5 26.3 1.0 OE1 B:GLU87 2.6 13.2 1.0 CD B:GLU87 2.8 16.5 1.0 C B:LEU14 3.4 13.3 1.0 HA B:HIS15 3.6 15.1 1.0 H B:LEU14 3.7 17.5 1.0 HB3 B:LEU14 3.9 20.7 1.0 HD1 B:HIS15 4.0 18.9 1.0 HG3 B:LYS16 4.2 20.2 1.0 H B:LYS16 4.2 13.4 1.0 HD12 B:LEU179 4.3 76.2 1.0 O B:HOH532 4.3 39.3 1.0 N B:LEU14 4.3 14.6 1.0 CG B:GLU87 4.3 11.6 1.0 CA B:LEU14 4.3 14.3 1.0 N B:HIS15 4.3 13.2 1.0 CA B:HIS15 4.4 12.5 1.0 HE3 B:LYS16 4.5 80.4 1.0 CB B:LEU14 4.5 17.2 1.0 HG2 B:GLU87 4.6 13.9 1.0 O B:HOH534 4.7 37.4 1.0 HG21 B:ILE175 4.7 13.3 1.0 HG B:LEU14 4.7 23.9 1.0 ND1 B:HIS15 4.7 15.7 1.0 HG3 B:GLU87 4.7 13.9 1.0 N B:LYS16 4.8 11.1 1.0 HD2 B:LYS16 4.8 21.5 1.0 HG22 B:ILE175 4.9 13.3 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Rala in A Covalent Complex with Sof-531


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-531 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca205 b:47.1 occ:1.00 OD1 B:ASP37 2.2 40.6 0.5 O B:HOH525 2.2 37.0 1.0 O B:HOH320 2.4 26.7 1.0 O B:HOH366 2.4 29.1 1.0 O B:HOH312 2.5 37.7 1.0 OD2 B:ASP37 2.7 27.6 0.5 O B:HOH456 2.7 45.0 1.0 CG B:ASP37 2.8 25.1 0.5 HH22 B:ARG161 3.3 70.4 1.0 HH12 B:ARG161 3.4 27.7 1.0 HB2 B:ASP37 3.6 17.2 0.5 NH2 B:ARG161 3.7 58.7 1.0 HZ3 B:LYS53 3.8 55.8 1.0 NH1 B:ARG161 3.8 23.1 1.0 CZ B:ARG161 4.1 78.8 1.0 HH21 B:ARG161 4.2 70.4 1.0 O B:HOH318 4.3 29.6 1.0 O B:PHE34 4.3 12.3 1.0 CB B:ASP37 4.3 29.6 0.5 OD1 B:ASP37 4.3 13.8 0.5 CB B:ASP37 4.4 14.3 0.5 HH11 B:ARG161 4.4 27.7 1.0 CG B:ASP37 4.4 16.5 0.5 NZ B:LYS53 4.6 46.4 1.0 OD2 B:ASP165 4.6 16.7 1.0 HA B:ASP37 4.6 20.6 0.5 HA B:ASP37 4.7 14.0 0.5 OD1 B:ASP165 4.7 19.3 1.0 HZ2 B:LYS53 4.7 55.8 1.0 HZ1 B:LYS53 4.7 55.8 1.0 HB3 B:ASP37 4.8 35.5 0.5 HB2 B:ASP37 4.8 35.5 0.5 O B:GLN33 4.8 10.3 1.0 H B:ASP37 4.9 18.8 0.5 HA B:PHE34 4.9 11.6 1.0 H B:ASP37 4.9 12.6 0.5 CA B:ASP37 4.9 17.2 0.5 CA B:ASP37 5.0 11.6 0.5

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