Sodium in PDB 2a2c: X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate

The structure of X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate, PDB code: 2a2c was solved by J.B.Thoden, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.65
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	123.800, 123.800, 60.100, 90.00, 90.00, 120.00
R / Rfree (%)	n/a / n/a

The structure of X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate (pdb code 2a2c). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate, PDB code: 2a2c:

Sodium binding site 1 out of 1 in the X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Human N-Acetyl Galactosamine Kinase Complexed with Mg-Adp and N-Acetyl Galactosamine 1-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na462 b:56.7 occ:1.00 O A:HOH871 2.2 37.5 1.0 O A:HOH833 2.4 53.0 1.0 O A:PHE207 2.4 24.4 1.0 O A:HOH626 2.4 39.4 1.0 NH2 A:ARG211 2.6 28.4 1.0 O A:SER208 2.9 34.4 1.0 C A:SER208 3.5 29.2 1.0 C A:PHE207 3.6 25.5 1.0 O A:HOH752 3.7 43.6 1.0 CZ A:ARG211 3.8 67.2 1.0 O A:HOH554 4.0 30.6 1.0 N A:PRO209 4.1 22.9 1.0 CD A:PRO209 4.2 25.5 1.0 NH1 A:ARG211 4.2 69.1 1.0 O A:HOH762 4.2 47.1 1.0 O A:HOH486 4.3 20.2 1.0 OG A:SER208 4.4 70.5 1.0 CA A:SER208 4.4 28.0 1.0 N A:SER208 4.4 26.1 1.0 N A:PHE207 4.5 19.2 1.0 O A:PRO209 4.6 22.5 1.0 CA A:PHE207 4.6 23.0 1.0 CB A:SER208 4.8 34.4 1.0 NE A:ARG211 4.9 99.9 1.0 O A:HOH769 5.0 61.5 1.0

J.B.Thoden, H.M.Holden. The Molecular Architecture of Human N-Acetylgalactosamine Kinase. J.Biol.Chem. V. 280 32784 2005.
ISSN: ISSN 0021-9258
PubMed: 16006554
DOI: 10.1074/JBC.M505730200