Calcium in PDB 5x9s: Crystal Structure of Fully Modified H-Ras-Gppnhp

The structure of Crystal Structure of Fully Modified H-Ras-Gppnhp, PDB code: 5x9s was solved by S.Matsumoto, H.Ke, Y.Murashima, H.Taniguchi-Tamura, R.Miyamoto, Y.Yoshikawa, T.Kumasaka, E.Mizohata, H.Edamatsu, T.Kataoka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.68 / 2.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.475, 88.475, 134.047, 90.00, 90.00, 120.00
R / Rfree (%)	18.4 / 23.6

The structure of Crystal Structure of Fully Modified H-Ras-Gppnhp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Fully Modified H-Ras-Gppnhp (pdb code 5x9s). 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 Fully Modified H-Ras-Gppnhp, PDB code: 5x9s:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Fully Modified H-Ras-Gppnhp


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 Fully Modified H-Ras-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:24.3 occ:1.00 O A:PHE28 2.3 20.1 1.0 OD1 A:ASP30 2.4 20.1 1.0 C A:PHE28 3.5 19.3 1.0 CG A:ASP30 3.7 19.8 1.0 N A:ASP30 4.0 18.9 1.0 CA A:VAL29 4.3 19.7 1.0 N A:VAL29 4.3 19.7 1.0 CB A:ASP30 4.5 19.4 1.0 CA A:PHE28 4.5 18.6 1.0 OD2 A:ASP30 4.6 20.6 1.0 N A:PHE28 4.6 18.2 1.0 C A:VAL29 4.6 18.9 1.0 CB A:PHE28 4.7 18.6 1.0 O A:HOH326 4.7 16.9 1.0 ND1 A:HIS27 4.9 16.8 1.0 CA A:ASP30 4.9 19.1 1.0 CD2 A:PHE28 5.0 18.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Fully Modified H-Ras-Gppnhp


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 Fully Modified H-Ras-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:34.6 occ:0.33 O A:HOH314 3.5 22.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Fully Modified H-Ras-Gppnhp


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 Fully Modified H-Ras-Gppnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:48.7 occ:0.33 O A:HOH316 2.6 25.1 1.0 O A:THR124 3.9 20.9 1.0 NE2 A:GLN129 4.2 27.2 1.0 OE1 A:GLN129 4.6 25.7 1.0 CD A:GLN129 4.8 25.9 1.0

H.Ke, S.Matsumoto, Y.Murashima, H.Taniguchi-Tamura, R.Miyamoto, Y.Yoshikawa, C.Tsuda, T.Kumasaka, E.Mizohata, H.Edamatsu, T.Kataoka. Structural Basis For Intramolecular Interaction of Post-Translationally Modified H-Rasgtp Prepared By Protein Ligation Febs Lett. V. 591 2470 2017.
ISSN: ISSN 1873-3468
PubMed: 28730604
DOI: 10.1002/1873-3468.12759