Sodium in PDB 3w0l: The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex

All present enzymatic activity of The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex:
2.7.1.2;

The structure of The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex, PDB code: 3w0l was solved by J.M.Choi, M.H.Seo, H.H.Kyeong, E.Kim, H.S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.48 / 2.92
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	109.318, 130.030, 175.117, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 27.7

The binding sites of Sodium atom in the The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex (pdb code 3w0l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex, PDB code: 3w0l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:42.1 occ:1.00 O A:VAL234 2.2 39.0 1.0 O A:VAL237 2.4 41.4 1.0 O A:GLY239 2.4 42.6 1.0 O A:MET231 2.5 37.8 1.0 C A:VAL234 3.3 35.0 1.0 C A:GLY239 3.5 41.2 1.0 C A:VAL237 3.6 36.8 1.0 C A:MET231 3.6 35.7 1.0 N A:GLY239 3.6 32.0 1.0 CA A:GLY239 4.1 33.7 1.0 CG A:MET231 4.1 42.2 1.0 CA A:VAL234 4.1 30.6 1.0 N A:VAL234 4.2 26.6 1.0 CB A:VAL234 4.3 31.4 1.0 N A:GLU235 4.3 34.4 1.0 CA A:VAL237 4.4 28.4 1.0 CA A:SER232 4.4 38.3 1.0 CB A:VAL237 4.4 31.1 1.0 N A:SER232 4.4 36.2 1.0 CA A:GLU235 4.4 32.0 1.0 N A:VAL237 4.4 25.0 1.0 C A:SER232 4.5 35.5 1.0 CA A:MET231 4.6 32.6 1.0 N A:GLU238 4.6 34.8 1.0 O A:SER232 4.6 35.4 1.0 CG1 A:VAL237 4.6 39.3 1.0 N A:GLU240 4.6 43.7 1.0 C A:GLU238 4.6 33.7 1.0 SD A:MET231 4.7 41.5 1.0 CA A:GLU238 4.7 36.6 1.0 CB A:MET231 4.9 33.7 1.0 OE1 A:GLU240 4.9 55.0 1.0 CG1 A:VAL234 4.9 24.6 1.0 C A:GLU235 4.9 25.5 1.0 CA A:GLU240 4.9 43.0 1.0

Sodium binding site 2 out of 2 in the The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Xenopus Glucokinase and Glucokinase Regulatory Protein Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:39.8 occ:1.00 O C:MET231 2.4 35.4 1.0 O C:VAL237 2.4 41.5 1.0 O C:HOH604 2.4 28.2 1.0 O C:GLY239 2.4 44.9 1.0 O C:VAL234 2.5 30.5 1.0 C C:GLY239 3.5 47.9 1.0 C C:MET231 3.5 33.7 1.0 C C:VAL237 3.6 36.7 1.0 C C:VAL234 3.6 28.4 1.0 N C:GLY239 3.8 34.2 1.0 OE2 C:GLU240 4.0 63.5 1.0 CA C:SER232 4.1 38.6 1.0 CA C:GLY239 4.2 38.4 1.0 CG C:MET231 4.2 50.1 1.0 N C:SER232 4.3 41.0 1.0 O C:SER232 4.3 34.1 1.0 C C:SER232 4.3 36.1 1.0 C C:GLU238 4.4 41.0 1.0 CG1 C:VAL234 4.4 27.0 1.0 N C:GLU240 4.4 49.0 1.0 CA C:VAL237 4.4 38.0 1.0 CA C:GLU235 4.5 32.6 1.0 N C:GLU235 4.5 35.8 1.0 CB C:VAL237 4.5 31.6 1.0 N C:GLU238 4.5 30.3 1.0 N C:VAL234 4.5 36.8 1.0 CA C:VAL234 4.6 32.5 1.0 N C:VAL237 4.6 32.7 1.0 CA C:MET231 4.6 35.7 1.0 CA C:GLU238 4.6 37.1 1.0 CA C:GLU240 4.6 50.0 1.0 CG1 C:VAL237 4.8 23.6 1.0 CB C:MET231 4.9 42.5 1.0 SD C:MET231 4.9 38.4 1.0 C C:GLU235 5.0 29.3 1.0 CD C:GLU240 5.0 67.9 1.0 CB C:VAL234 5.0 28.7 1.0

J.M.Choi, M.H.Seo, H.H.Kyeong, E.Kim, H.S.Kim. Molecular Basis For the Role of Glucokinase Regulatory Protein As the Allosteric Switch For Glucokinase Proc.Natl.Acad.Sci.Usa V. 110 10171 2013.
ISSN: ISSN 0027-8424
PubMed: 23733961
DOI: 10.1073/PNAS.1300457110