Calcium in PDB 4pih: X-Ray Crystal Structure of the K33S Mutant of Ubiquitin

The structure of X-Ray Crystal Structure of the K33S Mutant of Ubiquitin, PDB code: 4pih was solved by P.J.Loll, P.J.Xu, J.Schmidt, S.L.Melideo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.25 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.350, 32.740, 40.340, 69.77, 72.55, 73.12
R / Rfree (%)	16.5 / 19

The structure of X-Ray Crystal Structure of the K33S Mutant of Ubiquitin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the X-Ray Crystal Structure of the K33S Mutant of Ubiquitin (pdb code 4pih). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the X-Ray Crystal Structure of the K33S Mutant of Ubiquitin, PDB code: 4pih:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the X-Ray Crystal Structure of the K33S Mutant of Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Crystal Structure of the K33S Mutant of Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca101 b:37.7 occ:1.00 O A:HOH216 2.0 32.4 1.0 O A:HOH208 2.2 28.2 1.0 OE1 A:GLU18 2.2 39.8 1.0 O A:HOH232 2.2 16.1 1.0 OD2 A:ASP21 2.6 17.0 1.0 OD1 A:ASP21 2.7 20.7 1.0 CG A:ASP21 3.0 14.8 1.0 CD A:GLU18 3.1 39.1 1.0 OE2 A:GLU18 3.8 46.5 1.0 CG A:GLU18 4.0 20.6 1.0 NZ A:LYS29 4.1 33.7 1.0 N A:GLU18 4.3 15.1 1.0 OD1 A:ASN25 4.3 34.4 1.0 CB A:GLU18 4.4 15.3 1.0 O A:HOH256 4.4 30.2 1.0 CB A:ASP21 4.5 10.1 1.0 CA A:VAL17 4.6 14.3 1.0 C A:VAL17 4.7 14.4 1.0 O A:GLU16 4.8 19.0 1.0 CA A:GLU18 5.0 14.7 1.0

Calcium binding site 2 out of 3 in the X-Ray Crystal Structure of the K33S Mutant of Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Crystal Structure of the K33S Mutant of Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca101 b:9.3 occ:1.00 OE1 B:GLN49 2.3 14.9 1.0 OE2 B:GLU51 2.5 11.0 1.0 OE1 B:GLU51 2.6 9.4 1.0 CD B:GLU51 2.9 11.8 1.0 CD B:GLN49 3.2 12.6 1.0 NE2 B:GLN49 3.6 22.9 1.0 CG B:GLN49 4.3 15.2 1.0 CG B:GLU51 4.4 7.5 1.0 O B:HOH246 4.4 25.1 1.0 O B:HOH220 4.5 15.9 1.0 CB B:GLN49 4.8 10.9 1.0 O B:HOH208 5.0 20.6 1.0 NH2 B:ARG42 5.0 19.5 1.0

Calcium binding site 3 out of 3 in the X-Ray Crystal Structure of the K33S Mutant of Ubiquitin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Crystal Structure of the K33S Mutant of Ubiquitin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca102 b:34.3 occ:1.00 OD1 B:ASP32 2.4 30.0 1.0 O B:HOH262 2.4 17.8 1.0 OE1 B:GLN31 2.5 24.5 1.0 CD B:GLN31 3.6 28.1 1.0 CG B:ASP32 3.6 28.4 1.0 NE2 B:GLN31 4.1 29.2 1.0 O B:HOH250 4.3 25.9 1.0 OD2 B:ASP32 4.3 37.2 1.0 CA B:ASP32 4.5 15.8 1.0 N B:ASP32 4.6 11.0 1.0 CB B:ASP32 4.7 18.0 1.0 O B:ALA28 4.8 8.5 1.0 CG B:GLN31 4.8 14.6 1.0

P.J.Loll, P.Xu, J.T.Schmidt, S.L.Melideo. Enhancing Ubiquitin Crystallization Through Surface-Entropy Reduction. Acta Crystallogr.,Sect.F V. 70 1434 2014.
ISSN: ESSN 2053-230X
PubMed: 25286958
DOI: 10.1107/S2053230X14019244