Calcium in PDB 3wmw: Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form)

The structure of Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form), PDB code: 3wmw was solved by S.Nakano, S.Okazaki, H.Tokiwa, Y.Asano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.80 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.012, 83.487, 106.200, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 26.4

The binding sites of Calcium atom in the Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form) (pdb code 3wmw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form), PDB code: 3wmw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:42.3 occ:1.00 OE2 A:GLU210 2.3 27.2 1.0 O A:ALA211 2.4 24.1 1.0 OD1 A:ASP282 2.4 20.7 1.0 O A:HOH553 2.8 29.5 1.0 C A:ALA211 3.5 18.1 1.0 CD A:GLU210 3.6 33.4 1.0 CG A:ASP282 3.7 27.1 1.0 O A:TRP280 3.9 23.3 1.0 N A:ALA211 3.9 20.5 1.0 O A:ALA277 4.0 31.3 1.0 O A:PRO281 4.0 16.5 1.0 CA A:ALA211 4.2 21.5 1.0 CD2 A:LEU212 4.2 28.2 1.0 CA A:ASP282 4.2 22.8 1.0 C A:PRO281 4.4 22.2 1.0 N A:ASP282 4.4 22.9 1.0 OE1 A:GLU210 4.4 31.0 1.0 C A:GLU210 4.4 24.7 1.0 CG A:GLU210 4.4 30.7 1.0 CB A:ASP282 4.5 27.4 1.0 OD2 A:ASP282 4.5 30.1 1.0 N A:LEU212 4.5 20.1 1.0 CB A:ALA211 4.6 17.8 1.0 O A:GLN278 4.6 28.1 1.0 CG A:LEU212 4.6 28.9 1.0 CA A:LEU212 4.7 23.5 1.0 C A:TRP280 4.8 21.8 1.0 C A:ALA277 4.8 26.1 1.0 CA A:GLU210 4.9 27.6 1.0 CA A:GLN278 4.9 31.8 1.0 C A:GLN278 5.0 26.2 1.0

Calcium binding site 2 out of 4 in the Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:31.1 occ:1.00 N A:ARG238 3.2 19.8 1.0 O A:HOH526 3.3 18.1 1.0 NE A:ARG156 3.3 21.2 1.0 O A:HOH556 3.4 29.2 1.0 NZ A:LYS135 3.5 25.5 1.0 O A:SER236 3.9 27.6 1.0 OE1 A:GLU237 3.9 18.8 1.0 N A:GLY239 3.9 21.7 1.0 CA A:GLU237 3.9 23.3 1.0 CD A:ARG156 4.0 21.5 1.0 CD A:GLU237 4.0 22.9 1.0 CA A:ARG238 4.0 22.9 1.0 OE2 A:GLU237 4.0 20.4 1.0 C A:GLU237 4.0 20.1 1.0 CB A:ARG238 4.1 28.4 1.0 CG A:ARG156 4.2 27.8 1.0 CZ A:ARG156 4.2 23.7 1.0 NH2 A:ARG156 4.2 23.9 1.0 C A:ARG238 4.3 25.6 1.0 OE1 B:GLU139 4.6 20.1 1.0 C A:SER236 4.8 21.4 1.0 N A:GLU237 4.8 23.4 1.0 CG A:GLU237 4.9 22.5 1.0 CB A:GLU237 4.9 22.3 1.0 CG A:ARG238 4.9 29.8 1.0 CE A:LYS135 4.9 23.1 1.0

Calcium binding site 3 out of 4 in the Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:37.2 occ:1.00 OD1 B:ASP282 2.3 24.0 1.0 OE2 B:GLU210 2.3 32.0 1.0 O B:ALA211 2.4 22.2 1.0 CG B:ASP282 3.5 26.8 1.0 C B:ALA211 3.5 18.3 1.0 CD B:GLU210 3.5 30.3 1.0 N B:ALA211 3.6 19.8 1.0 CA B:ALA211 4.0 22.8 1.0 OD2 B:ASP282 4.2 31.2 1.0 C B:GLU210 4.2 22.6 1.0 CB B:ALA211 4.2 18.9 1.0 OE1 B:GLU210 4.3 36.3 1.0 CA B:ASP282 4.4 23.2 1.0 CB B:ASP282 4.4 26.0 1.0 O B:TRP280 4.5 24.1 1.0 CG B:GLU210 4.5 28.7 1.0 CA B:GLU210 4.5 25.9 1.0 O B:ALA277 4.5 31.1 1.0 O B:PRO281 4.6 23.4 1.0 N B:LEU212 4.6 21.4 1.0 N B:ASP282 4.7 22.6 1.0 CD2 B:LEU212 4.7 26.6 1.0 C B:PRO281 4.8 25.7 1.0 O B:GLU210 5.0 25.0 1.0

Calcium binding site 4 out of 4 in the Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Gale-Like L-Threonine Dehydrogenase From Cupriavidus Necator (Apo Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:34.0 occ:1.00 O A:HOH558 3.0 29.4 1.0 NE B:ARG156 3.2 25.6 1.0 N B:ARG238 3.3 22.8 1.0 O B:HOH529 3.3 27.1 1.0 NZ B:LYS135 3.5 25.0 1.0 OE1 B:GLU237 3.9 20.3 1.0 CD B:ARG156 3.9 29.1 1.0 N B:GLY239 3.9 24.8 1.0 O B:SER236 4.0 27.5 1.0 CA B:GLU237 4.0 25.8 1.0 CD B:GLU237 4.0 24.7 1.0 OE2 B:GLU237 4.0 22.7 1.0 CA B:ARG238 4.1 22.7 1.0 C B:GLU237 4.1 24.6 1.0 CZ B:ARG156 4.1 26.0 1.0 CG B:ARG156 4.1 31.7 1.0 NH2 B:ARG156 4.2 24.1 1.0 CB B:ARG238 4.2 26.8 1.0 C B:ARG238 4.4 25.0 1.0 OE1 A:GLU139 4.5 18.8 1.0 C B:SER236 4.8 28.0 1.0 N B:GLU237 4.9 29.1 1.0 CG B:GLU237 4.9 22.9 1.0 CE B:LYS135 4.9 23.9 1.0 CB B:GLU237 5.0 23.2 1.0 CA B:GLY239 5.0 27.1 1.0

S.Nakano, S.Okazaki, H.Tokiwa, Y.Asano. Binding of Nad+ and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus Necator L-Threonine Dehydrogenase J.Biol.Chem. V. 289 10445 2014.
ISSN: ISSN 0021-9258
PubMed: 24558034
DOI: 10.1074/JBC.M113.540773