Calcium in PDB 3a13: Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca

All present enzymatic activity of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca:
4.1.1.39;

The structure of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca, PDB code: 3a13 was solved by Y.Nishitani, M.Fujihashi, T.Doi, S.Yoshida, H.Atomi, T.Imanaka, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.22 / 2.34
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	173.678, 247.090, 144.940, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 25

The structure of Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Calcium atom in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca (pdb code 3a13). 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 Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca, PDB code: 3a13:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


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 Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca445 b:27.1 occ:1.00 O E:HOH666 2.3 25.6 1.0 OE1 E:GLU192 2.3 20.3 1.0 OQ1 E:KCX189 2.4 24.7 1.0 OD1 E:ASP191 2.4 21.9 1.0 O6 E:CAP446 2.5 25.9 1.0 O4 E:CAP446 2.7 29.1 1.0 CD E:GLU192 3.3 21.8 1.0 CX E:KCX189 3.3 22.8 1.0 C E:CAP446 3.4 26.7 1.0 C4 E:CAP446 3.5 29.3 1.0 OQ2 E:KCX189 3.5 23.4 1.0 CG E:ASP191 3.6 21.5 1.0 OE2 E:GLU192 3.6 23.3 1.0 NZ E:LYS163 4.0 27.2 1.0 O7 E:CAP446 4.1 27.3 1.0 O2 E:CAP446 4.1 27.4 1.0 NZ E:LYS165 4.2 24.9 1.0 NE2 E:HIS281 4.2 14.3 1.0 N E:GLU192 4.2 18.4 1.0 C2 E:CAP446 4.2 26.7 1.0 OD2 E:ASP191 4.4 24.8 1.0 CA E:ASP191 4.4 19.1 1.0 CB E:ASP191 4.5 19.5 1.0 C3 E:CAP446 4.5 28.1 1.0 NZ E:KCX189 4.6 19.9 1.0 CG1 E:VAL161 4.6 23.4 1.0 C5 E:CAP446 4.6 30.0 1.0 CG E:GLU192 4.7 18.3 1.0 O E:HOH607 4.8 34.7 1.0 C E:ASP191 4.9 18.6 1.0 CB E:GLU192 5.0 18.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca


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 Type III Rubisco SP4 Mutant Complexed with 2-Cabp and Activated with Ca within 5.0Å range: probe atom residue distance (Å) B Occ J:Ca445 b:27.9 occ:1.00 O J:HOH678 2.3 26.3 1.0 OQ1 J:KCX189 2.3 26.0 1.0 OE1 J:GLU192 2.4 19.7 1.0 OD2 J:ASP191 2.4 19.9 1.0 O6 J:CAP446 2.4 26.8 1.0 O4 J:CAP446 2.8 30.6 1.0 C J:CAP446 3.4 27.8 1.0 CD J:GLU192 3.4 20.1 1.0 CX J:KCX189 3.4 24.1 1.0 CG J:ASP191 3.6 20.8 1.0 C4 J:CAP446 3.6 30.6 1.0 OE2 J:GLU192 3.7 22.8 1.0 OQ2 J:KCX189 3.7 24.8 1.0 NZ J:LYS163 3.8 24.0 1.0 O2 J:CAP446 4.0 28.3 1.0 O7 J:CAP446 4.1 28.4 1.0 NZ J:LYS165 4.1 23.1 1.0 C2 J:CAP446 4.2 27.9 1.0 N J:GLU192 4.3 17.1 1.0 NE2 J:HIS281 4.3 15.8 1.0 OD1 J:ASP191 4.4 23.4 1.0 CA J:ASP191 4.5 17.9 1.0 CB J:ASP191 4.5 18.1 1.0 NZ J:KCX189 4.5 21.2 1.0 C3 J:CAP446 4.5 29.2 1.0 CG1 J:VAL161 4.6 23.6 1.0 C5 J:CAP446 4.7 31.5 1.0 CG J:GLU192 4.7 17.3 1.0 CB J:GLU192 4.9 16.9 1.0 C J:ASP191 5.0 17.0 1.0

Y.Nishitani, M.Fujihashi, T.Doi, S.Yoshida, H.Atomi, T.Imanaka, K.Miki. Sturcture-Based Optimization of A Type III Rubisco From A Hyperthermophile To Be Published.