Magnesium in PDB 4wh2: N-Acetylhexosamine 1-Kinase in Complex with Adp

All present enzymatic activity of N-Acetylhexosamine 1-Kinase in Complex with Adp:
2.7.1.162;

The structure of N-Acetylhexosamine 1-Kinase in Complex with Adp, PDB code: 4wh2 was solved by M.Sato, T.Arakawa, Y.W.Nam, M.Nishimoto, M.Kitaoka, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.40 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.079, 88.220, 105.895, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.2

The binding sites of Magnesium atom in the N-Acetylhexosamine 1-Kinase in Complex with Adp (pdb code 4wh2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the N-Acetylhexosamine 1-Kinase in Complex with Adp, PDB code: 4wh2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the N-Acetylhexosamine 1-Kinase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of N-Acetylhexosamine 1-Kinase in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:23.9 occ:1.00 O A:HOH547 2.0 26.1 1.0 O1A A:ADP401 2.0 21.9 1.0 O A:HOH548 2.1 29.0 1.0 OD2 A:ASP228 2.1 22.0 1.0 O1B A:ADP401 2.1 27.8 1.0 OD1 A:ASN213 2.2 21.0 1.0 CG A:ASP228 3.1 22.3 1.0 CG A:ASN213 3.2 21.6 1.0 PB A:ADP401 3.3 24.8 1.0 PA A:ADP401 3.3 22.1 1.0 CB A:ASP228 3.5 20.8 1.0 ND2 A:ASN213 3.5 21.1 1.0 O3A A:ADP401 3.6 26.2 1.0 O A:HOH550 3.7 25.9 1.0 MG A:MG403 3.8 23.3 1.0 O2B A:ADP401 3.8 22.2 1.0 O A:HOH571 4.0 25.0 1.0 OD1 A:ASP228 4.1 21.1 1.0 OD2 A:ASP208 4.3 22.2 1.0 O3' A:ADP401 4.3 27.6 1.0 O5' A:ADP401 4.3 27.0 1.0 O2A A:ADP401 4.4 20.6 1.0 C5' A:ADP401 4.4 27.5 1.0 O A:HOH749 4.5 38.9 1.0 CB A:ASN213 4.5 21.9 1.0 O A:HOH741 4.6 38.7 1.0 O3B A:ADP401 4.6 28.6 1.0 C3' A:ADP401 4.6 24.4 1.0 O A:HOH549 4.7 22.3 1.0 CB A:ASN212 4.9 30.2 1.0 CA A:ASP228 4.9 20.6 1.0 CA A:ASN213 5.0 21.1 1.0

Magnesium binding site 2 out of 2 in the N-Acetylhexosamine 1-Kinase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of N-Acetylhexosamine 1-Kinase in Complex with Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:23.3 occ:1.00 O A:HOH550 2.0 25.9 1.0 O2B A:ADP401 2.0 22.2 1.0 O A:HOH551 2.0 21.3 1.0 O A:HOH549 2.1 22.3 1.0 OD2 A:ASP228 2.2 22.0 1.0 OD1 A:ASP228 2.3 21.1 1.0 CG A:ASP228 2.5 22.3 1.0 PB A:ADP401 3.1 24.8 1.0 O1B A:ADP401 3.3 27.8 1.0 O2 A:GOL409 3.7 23.2 1.0 MG A:MG402 3.8 23.9 1.0 O A:HOH609 3.8 21.0 1.0 OD2 A:ASP208 3.9 22.2 1.0 CB A:ASP228 4.0 20.8 1.0 O A:HOH548 4.1 29.0 1.0 OD2 A:ASP230 4.1 23.8 1.0 O A:HOH618 4.1 23.9 1.0 O3A A:ADP401 4.2 26.2 1.0 O3B A:ADP401 4.3 28.6 1.0 CB A:ILE32 4.3 26.4 1.0 ND2 A:ASN33 4.4 24.4 1.0 CG1 A:ILE32 4.4 27.4 1.0 O A:HOH571 4.5 25.0 1.0 O1A A:ADP401 4.5 21.9 1.0 O A:HOH616 4.5 24.1 1.0 CG2 A:ILE32 4.7 25.0 1.0 CG A:ASP230 4.7 22.9 1.0 PA A:ADP401 4.8 22.1 1.0 CB A:ASP230 4.8 21.9 1.0 C2 A:GOL409 4.8 24.3 1.0 CA A:ASP228 4.9 20.6 1.0 CG A:ASP208 5.0 20.4 1.0

M.Sato, T.Arakawa, Y.W.Nam, M.Nishimoto, M.Kitaoka, S.Fushinobu. Open-Close Structural Change Upon Ligand Binding and Two ,Magnesium Ions Required For the Catalysis of N-Acetylhexosamine 1-Kinase Biochim.Biophys.Acta 2015.
ISSN: ISSN 0006-3002
PubMed: 25644306
DOI: 10.1016/J.BBAPAP.2015.01.011