Magnesium in PDB 2fv7: Crystal Structure of Human Ribokinase

All present enzymatic activity of Crystal Structure of Human Ribokinase:
2.7.1.15;

The structure of Crystal Structure of Human Ribokinase, PDB code: 2fv7 was solved by W.M.Rabeh, W.Tempel, L.Nedyalkova, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.530, 72.978, 90.958, 90.00, 91.08, 90.00
R / Rfree (%)	19.8 / 24.8

The structure of Crystal Structure of Human Ribokinase also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Ribokinase (pdb code 2fv7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Ribokinase, PDB code: 2fv7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Ribokinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Ribokinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:61.8 occ:1.00 O A:HOH825 2.3 27.6 1.0 O A:HOH817 2.3 17.7 1.0 O2B A:ADP401 2.3 41.4 1.0 O A:HOH819 2.4 20.9 1.0 O A:HOH856 3.2 29.1 1.0 O A:HOH838 3.3 29.3 1.0 PB A:ADP401 3.6 43.2 1.0 CA A:GLY268 3.8 27.5 1.0 O3B A:ADP401 4.0 43.3 1.0 NZ A:LYS54 4.0 31.5 1.0 C A:GLY268 4.1 26.7 1.0 OE2 A:GLU202 4.2 34.6 1.0 OD1 A:ASP269 4.2 31.3 1.0 OD1 A:ASN177 4.2 30.7 1.0 OE1 A:GLU202 4.3 32.4 1.0 ND2 A:ASN177 4.4 24.9 1.0 ND2 A:ASN199 4.4 30.5 1.0 N A:ASP269 4.4 26.7 1.0 O3A A:ADP401 4.5 39.6 1.0 CB A:ALA179 4.6 29.4 1.0 N A:GLY268 4.6 28.3 1.0 CD A:GLU202 4.7 32.1 1.0 UNK A:UNX510 4.7 2.0 0.0 O1B A:ADP401 4.7 45.2 1.0 O A:GLY268 4.7 26.1 1.0 CG A:ASN177 4.7 26.9 1.0 CG A:ASP269 5.0 28.9 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Ribokinase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Ribokinase within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg406 b:52.1 occ:1.00 O B:HOH859 2.3 23.6 1.0 O2B B:ADP402 2.3 45.9 1.0 O B:HOH842 2.5 23.5 1.0 O B:HOH864 2.7 31.5 1.0 O B:HOH871 2.7 30.3 1.0 PB B:ADP402 3.7 47.4 1.0 CA B:GLY268 3.8 26.3 1.0 C B:GLY268 4.1 25.9 1.0 O3B B:ADP402 4.2 47.5 1.0 OD1 B:ASP269 4.2 30.6 1.0 N B:ASP269 4.3 25.7 1.0 NZ B:LYS54 4.3 30.7 1.0 OE2 B:GLU202 4.4 39.6 1.0 OD1 B:ASN177 4.4 27.0 1.0 O3A B:ADP402 4.5 44.7 1.0 ND2 B:ASN177 4.5 27.3 1.0 ND2 B:ASN199 4.6 28.1 1.0 N B:GLY268 4.6 26.9 1.0 OE1 B:GLU202 4.7 39.6 1.0 O B:GLY268 4.7 25.4 1.0 O1B B:ADP402 4.7 47.6 1.0 CB B:ALA179 4.8 29.3 1.0 CG B:ASN177 4.9 27.9 1.0 CG B:ASP269 4.9 28.3 1.0

W.M.Rabeh, W.Tempel, L.Nedyalkova, C.Arrowsmith, A.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc). Crystal Structure of Human Ribokinase To Be Published.