Sodium in PDB 5byf: Crystal Structure of Human Ribokinase in Complex with Amp

All present enzymatic activity of Crystal Structure of Human Ribokinase in Complex with Amp:
2.7.1.15;

The structure of Crystal Structure of Human Ribokinase in Complex with Amp, PDB code: 5byf was solved by J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.50 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.090, 63.870, 181.020, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.2

The structure of Crystal Structure of Human Ribokinase in Complex with Amp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in Complex with Amp (pdb code 5byf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Human Ribokinase in Complex with Amp, PDB code: 5byf:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amp


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 Human Ribokinase in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:41.6 occ:1.00 O A:HOH528 2.2 50.6 1.0 O A:SER301 2.3 40.6 1.0 O A:ASP263 2.3 46.1 1.0 O A:ALA304 2.4 44.8 1.0 O A:HOH550 2.5 44.8 1.0 OG A:SER310 3.0 42.4 1.0 C A:SER301 3.3 40.5 1.0 CB A:SER310 3.4 42.1 1.0 C A:ASP263 3.5 48.6 1.0 C A:ALA304 3.6 48.7 1.0 CA A:VAL302 3.8 43.8 1.0 N A:VAL302 4.0 41.0 1.0 O A:THR265 4.0 40.0 1.0 CB A:ASP263 4.2 53.0 1.0 C A:VAL302 4.2 46.7 1.0 CG A:ASP263 4.3 55.6 1.0 N A:ALA304 4.3 49.4 1.0 CA A:SER301 4.4 40.2 1.0 CA A:ASP263 4.4 51.3 1.0 N A:ALA305 4.4 49.7 1.0 N A:THR265 4.5 44.6 1.0 O A:VAL302 4.5 48.0 1.0 N A:THR264 4.5 48.2 1.0 CA A:ALA305 4.5 49.8 1.0 C A:ALA305 4.5 49.2 1.0 OD2 A:ASP263 4.5 60.8 1.0 CB A:SER301 4.5 38.9 1.0 CA A:ALA304 4.6 49.7 1.0 N A:GLY306 4.6 47.4 1.0 OG A:SER301 4.6 41.6 1.0 N A:THR307 4.6 42.7 1.0 N A:ASP263 4.6 51.6 1.0 CA A:THR264 4.6 47.0 1.0 C A:THR264 4.7 45.0 1.0 N A:GLN303 4.8 47.9 1.0 OD1 A:ASP263 4.8 54.9 1.0 O A:ALA305 4.9 49.8 1.0 CA A:SER310 4.9 40.2 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amp


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 Human Ribokinase in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:47.5 occ:1.00 O A:HOH558 2.2 37.9 1.0 O A:HOH593 2.4 43.4 1.0 O A:HOH539 2.4 31.2 1.0 O A:HOH517 2.4 28.7 1.0 O A:HOH613 2.9 52.8 1.0 CA A:GLY268 4.1 35.0 1.0 ND2 A:ASN199 4.1 38.2 1.0 NZ A:LYS54 4.2 32.9 1.0 OE2 A:GLU202 4.2 36.5 1.0 OD1 A:ASP269 4.2 31.6 1.0 O A:HOH580 4.2 41.9 1.0 ND2 A:ASN177 4.3 29.8 1.0 OD1 A:ASN177 4.4 28.6 1.0 C A:GLY268 4.4 33.1 1.0 OE1 A:GLU202 4.5 37.3 1.0 CB A:ALA179 4.5 29.5 1.0 O A:HOH510 4.6 33.1 1.0 N A:ASP269 4.7 31.9 1.0 CD A:GLU202 4.8 37.0 1.0 O A:HOH515 4.8 39.7 1.0 CG A:ASN177 4.8 28.2 1.0 O A:GLY268 4.9 32.5 1.0 CG A:ASN199 5.0 39.7 1.0 N A:GLY268 5.0 36.1 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amp


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 Human Ribokinase in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:51.8 occ:1.00 O B:HOH541 2.2 60.4 1.0 O B:SER301 2.4 52.7 1.0 O B:ASP263 2.4 59.0 1.0 O B:ALA304 2.4 59.2 1.0 O B:HOH567 2.5 46.4 1.0 OG B:SER310 2.9 50.3 1.0 CB B:SER310 3.3 51.9 1.0 C B:SER301 3.4 53.8 1.0 C B:ALA304 3.6 62.5 1.0 C B:ASP263 3.6 60.7 1.0 O B:THR265 3.9 52.1 1.0 CA B:VAL302 4.1 57.8 1.0 N B:VAL302 4.1 55.5 1.0 CB B:ASP263 4.2 64.3 1.0 CG B:ASP263 4.3 63.0 1.0 CA B:ASP263 4.4 64.1 1.0 C B:VAL302 4.4 60.9 1.0 N B:ALA304 4.4 64.4 1.0 CA B:SER301 4.4 52.4 1.0 OD2 B:ASP263 4.4 61.8 1.0 N B:THR307 4.5 55.7 1.0 N B:ALA305 4.5 63.7 1.0 C B:ALA305 4.5 60.0 1.0 CA B:ALA305 4.5 63.3 1.0 N B:GLY306 4.6 59.4 1.0 N B:THR265 4.6 55.9 1.0 N B:THR264 4.6 60.1 1.0 CA B:ALA304 4.6 65.0 1.0 CB B:SER301 4.6 49.5 1.0 OG B:SER301 4.6 49.5 1.0 O B:VAL302 4.7 60.7 1.0 N B:ASP263 4.7 66.6 1.0 CA B:THR264 4.7 58.0 1.0 OD1 B:ASP263 4.7 63.3 1.0 C B:THR264 4.8 55.9 1.0 O B:ALA305 4.8 59.0 1.0 CA B:SER310 4.9 50.9 1.0 N B:GLN303 4.9 62.0 1.0 CA B:THR307 4.9 51.7 1.0 C B:THR265 5.0 52.2 1.0 O B:THR307 5.0 49.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Human Ribokinase in Complex with Amp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Ribokinase in Complex with Amp within 5.0Å range: probe atom residue distance (Å) B Occ B:Na403 b:44.9 occ:1.00 O B:HOH508 2.0 40.0 1.0 O B:HOH514 2.3 35.6 1.0 O B:HOH529 2.3 35.6 1.0 O B:HOH609 2.3 44.7 1.0 O B:HOH611 2.5 51.2 1.0 NZ B:LYS54 3.9 40.0 1.0 ND2 B:ASN199 3.9 49.9 1.0 OE2 B:GLU202 4.0 47.5 1.0 CA B:GLY268 4.3 44.4 1.0 OD1 B:ASP269 4.3 41.1 1.0 OE1 B:GLU202 4.4 48.5 1.0 CB B:ALA179 4.4 42.8 1.0 ND2 B:ASN177 4.4 37.9 1.0 O B:HOH538 4.5 40.4 1.0 OD1 B:ASN177 4.5 34.6 1.0 CD B:GLU202 4.6 48.8 1.0 C B:GLY268 4.6 42.0 1.0 O3P B:AMP401 4.8 65.2 1.0 CG B:ASN199 4.9 50.4 1.0 N B:ASP269 4.9 41.9 1.0 CG B:ASN177 4.9 37.4 1.0

J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop. Crystal Structure of Human Ribokinase in Complex with Amp To Be Published.