Sodium in PDB 6xk2: Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp

All present enzymatic activity of Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp:
2.7.1.15;

The structure of Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp, PDB code: 6xk2 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.05 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	77.170, 84.570, 98.270, 90.00, 95.27, 90.00
R / Rfree (%)	18.1 / 23

The binding sites of Sodium atom in the Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp (pdb code 6xk2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp, PDB code: 6xk2:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:74.5 occ:1.00 OE1 A:GLU188 3.7 61.5 1.0 O1A A:ADP401 3.7 54.1 0.8 OE2 A:GLU188 3.8 72.6 1.0 O1B A:ADP401 3.9 62.7 0.8 N A:GLY240 3.9 56.2 1.0 CD A:GLU188 4.1 69.5 1.0 O2A A:ADP401 4.1 52.0 0.8 CA A:GLY240 4.1 52.1 1.0 C A:LEU239 4.3 54.7 1.0 O A:HOH547 4.4 55.7 1.0 PA A:ADP401 4.5 54.8 0.8 O A:LEU239 4.7 57.6 1.0 CA A:LEU239 4.8 56.6 1.0 CB A:ASN187 4.8 56.4 1.0 O A:THR238 5.0 55.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:75.0 occ:1.00 OE2 B:GLU188 3.0 74.9 1.0 OE1 B:GLU188 3.5 80.1 1.0 N B:GLY240 3.5 64.1 1.0 O1B B:ADP401 3.5 65.9 0.8 CD B:GLU188 3.6 75.3 1.0 C B:LEU239 3.8 67.5 1.0 CA B:GLY240 3.9 63.5 1.0 O1A B:ADP401 4.0 63.4 0.8 O2A B:ADP401 4.1 62.9 0.8 CA B:LEU239 4.2 70.0 1.0 O B:LEU239 4.2 67.6 1.0 O B:THR238 4.4 63.6 1.0 CB B:ASN187 4.5 63.2 1.0 PA B:ADP401 4.7 53.3 0.8 N B:LEU239 4.8 65.6 1.0 C B:THR238 4.9 63.0 1.0 PB B:ADP401 5.0 62.5 0.8

Sodium binding site 3 out of 3 in the Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ D:Na402 b:77.9 occ:1.00 O2A D:ADP401 3.2 62.1 0.9 O1B D:ADP401 3.5 68.8 0.9 O1A D:ADP401 4.2 60.7 0.9 CA D:GLY240 4.2 58.5 1.0 PA D:ADP401 4.3 55.3 0.9 N D:GLY240 4.3 57.1 1.0 OE1 D:GLU188 4.4 71.3 1.0 OE2 D:GLU188 4.6 70.6 1.0 C D:LEU239 4.8 60.9 1.0 PB D:ADP401 4.9 71.0 0.9 CD D:GLU188 4.9 71.0 1.0

J.Abendroth, D.R.Davies, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of Ribokinase From Cryptococcus Neoformans Var. Grubii Serotype A in Complex with Adp To Be Published.