Calcium in PDB 5x6i: Crystal Structure of B. Subtilis Adenylate Kinase Variant

All present enzymatic activity of Crystal Structure of B. Subtilis Adenylate Kinase Variant:
2.7.4.3;

The structure of Crystal Structure of B. Subtilis Adenylate Kinase Variant, PDB code: 5x6i was solved by S.Moon, E.Bae, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.739, 44.180, 100.595, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 25.9

The structure of Crystal Structure of B. Subtilis Adenylate Kinase Variant also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Crystal Structure of B. Subtilis Adenylate Kinase Variant (pdb code 5x6i). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of B. Subtilis Adenylate Kinase Variant, PDB code: 5x6i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of B. Subtilis Adenylate Kinase Variant


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 B. Subtilis Adenylate Kinase Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:43.9 occ:1.00 O A:HOH456 2.0 43.9 1.0 O A:GLU41 2.3 44.4 1.0 C A:GLU41 3.4 43.7 1.0 CA A:GLU41 4.2 43.6 1.0 CB A:GLU41 4.3 44.7 1.0 N A:GLU42 4.5 45.4 1.0 O A:GLU42 4.5 42.0 1.0 C A:GLU42 4.5 47.2 1.0 CB A:GLU42 4.7 49.4 1.0 CA A:GLU42 4.8 44.4 1.0 N A:THR43 4.9 42.3 1.0 CG2 A:THR43 4.9 41.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of B. Subtilis Adenylate Kinase Variant


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 B. Subtilis Adenylate Kinase Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:71.5 occ:1.00 OD2 A:ASP118 2.2 67.1 1.0 OD1 A:ASP116 2.3 66.6 1.0 CG A:ASP116 3.1 64.0 1.0 OD2 A:ASP116 3.2 70.2 1.0 CG A:ASP118 3.3 59.3 1.0 CB A:ASP118 4.2 55.6 1.0 OD1 A:ASP118 4.2 60.6 1.0 N A:ASP118 4.3 42.8 1.0 CB A:ASP116 4.5 55.0 1.0 N A:LYS117 4.7 39.3 1.0 O A:HOH408 4.8 46.1 1.0 CA A:ASP118 4.9 48.1 1.0 CA A:ASP116 4.9 48.3 1.0 C A:ASP116 5.0 41.6 1.0

S.Moon, J.Kim, J.Koo, E.Bae. Structural and Mutational Analyses of Psychrophilic and Mesophilic Adenylate Kinases Highlight the Role of Hydrophobic Interactions in Protein Thermal Stability. Struct Dyn. V. 6 24702 2019.
ISSN: ESSN 2329-7778
PubMed: 31111079
DOI: 10.1063/1.5089707