Calcium in PDB 4dly: Set 1 CACL2/Dtt, Ordered Off

The structure of Set 1 CACL2/Dtt, Ordered Off, PDB code: 4dly was solved by G.Holzapfel, C.Mattos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.23 / 1.57
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	88.207, 88.207, 134.142, 90.00, 90.00, 120.00
R / Rfree (%)	15.8 / 17.9

The structure of Set 1 CACL2/Dtt, Ordered Off also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Set 1 CACL2/Dtt, Ordered Off (pdb code 4dly). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Set 1 CACL2/Dtt, Ordered Off, PDB code: 4dly:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Set 1 CACL2/Dtt, Ordered Off


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Set 1 CACL2/Dtt, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:10.6 occ:1.00 O A:PHE28 2.4 11.6 1.0 OD2 A:ASP30 2.4 12.6 1.0 O A:HOH307 2.4 16.5 1.0 O A:HOH442 2.5 18.6 1.0 C A:PHE28 3.6 9.5 1.0 CG A:ASP30 3.6 13.4 1.0 N A:ASP30 4.0 10.9 1.0 O A:HOH368 4.3 25.6 1.0 CA A:VAL29 4.3 8.9 1.0 CB A:ASP30 4.4 11.6 1.0 N A:VAL29 4.4 9.4 1.0 OD1 A:ASP30 4.5 15.5 1.0 CA A:PHE28 4.6 10.4 1.0 C A:VAL29 4.6 9.8 1.0 O A:HOH310 4.7 16.0 1.0 N A:PHE28 4.7 10.6 1.0 O A:HOH399 4.8 29.2 1.0 CA A:ASP30 4.8 11.6 1.0 CB A:PHE28 4.8 10.3 1.0 CD2 A:PHE28 5.0 11.3 1.0

Calcium binding site 2 out of 3 in the Set 1 CACL2/Dtt, Ordered Off


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Set 1 CACL2/Dtt, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:23.1 occ:0.50 O A:ARG102 2.3 23.2 1.0 OD2 A:ASP105 2.6 32.2 1.0 CG A:ASP105 3.2 29.4 1.0 OD1 A:ASP105 3.3 34.5 1.0 C A:ARG102 3.4 20.9 1.0 CG A:ARG102 4.1 29.2 1.0 CA A:VAL103 4.2 17.7 1.0 N A:VAL103 4.2 18.1 1.0 CA A:ARG102 4.3 19.4 1.0 C A:VAL103 4.5 19.0 1.0 CB A:ASP105 4.6 25.5 1.0 O A:HOH456 4.6 38.2 1.0 O A:VAL103 4.6 20.7 1.0 N A:ASP105 4.7 19.3 1.0 CA A:ASP105 4.8 21.8 1.0 CB A:ARG102 4.9 22.3 1.0

Calcium binding site 3 out of 3 in the Set 1 CACL2/Dtt, Ordered Off


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Set 1 CACL2/Dtt, Ordered Off within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:22.0 occ:1.00 O A:GLY138 2.3 13.0 1.0 O A:HOH417 2.5 19.1 1.0 O A:HOH469 2.6 27.9 1.0 O A:HOH461 2.6 29.8 1.0 O A:HOH459 2.7 26.1 1.0 O A:HOH446 2.7 25.4 1.0 C A:GLY138 3.5 14.8 1.0 CA A:GLY138 4.2 15.6 1.0 OE1 A:GLU162 4.3 14.0 1.0 O A:HOH317 4.4 14.7 1.0 O A:HOH374 4.4 25.4 1.0 CE1 A:HIS166 4.5 22.7 1.0 N A:ILE139 4.5 11.9 1.0 OD2 A:ASP108 4.6 34.8 1.0 CA A:ILE139 4.7 10.4 1.0 CG2 A:ILE139 4.8 14.1 1.0 O A:HOH379 4.8 25.0 1.0 NE2 A:HIS166 4.8 25.2 1.0 O A:TYR137 4.9 17.7 1.0

G.Holzapfel, G.Buhrman, C.Mattos. Shift in the Equilibrium Between on and Off States of the Allosteric Switch in Ras-Gppnhp Affected By Small Molecules and Bulk Solvent Composition. Biochemistry V. 51 6114 2012.
ISSN: ISSN 0006-2960
PubMed: 22845804
DOI: 10.1021/BI300509J