Magnesium in PDB 4wh3: N-Acetylhexosamine 1-Kinase in Complex with Atp

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

The structure of N-Acetylhexosamine 1-Kinase in Complex with Atp, PDB code: 4wh3 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)	32.60 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.030, 88.471, 105.219, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.2

The binding sites of Magnesium atom in the N-Acetylhexosamine 1-Kinase in Complex with Atp (pdb code 4wh3). 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 Atp, PDB code: 4wh3:
Jump to Magnesium binding site number: 1; 2;

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


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 Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:19.4 occ:1.00 O2A A:ATP401 1.9 18.9 1.0 O3G A:ATP401 2.0 23.1 1.0 O A:HOH563 2.0 21.7 1.0 O A:HOH562 2.1 22.9 1.0 OD2 A:ASP228 2.1 18.4 1.0 OD1 A:ASN213 2.1 18.4 1.0 CG A:ASP228 3.1 17.2 1.0 CG A:ASN213 3.1 18.4 1.0 PA A:ATP401 3.3 19.7 1.0 PG A:ATP401 3.3 25.2 1.0 CB A:ASP228 3.4 15.7 1.0 ND2 A:ASN213 3.5 17.9 1.0 O3A A:ATP401 3.6 20.6 1.0 O1G A:ATP401 3.7 22.6 1.0 MG A:MG403 3.8 17.3 1.0 O2B A:ATP401 3.9 20.0 1.0 O5' A:ATP401 4.0 22.8 1.0 OD1 A:ASN212 4.0 23.7 1.0 O3B A:ATP401 4.1 23.3 1.0 PB A:ATP401 4.1 22.6 1.0 OD1 A:ASP228 4.2 16.2 1.0 O A:ASN212 4.4 18.2 1.0 O2G A:ATP401 4.4 26.0 1.0 O1A A:ATP401 4.4 18.7 1.0 CB A:ASN213 4.5 17.8 1.0 OD2 A:ASP208 4.6 20.6 1.0 CG A:ASN212 4.6 25.1 1.0 O A:HOH565 4.8 17.3 1.0 C A:ASN212 4.8 18.2 1.0 CA A:ASN213 4.8 16.1 1.0 CA A:ASP228 4.8 17.2 1.0 N A:ASN213 4.9 17.7 1.0 C5' A:ATP401 5.0 25.9 1.0 ND2 A:ASN212 5.0 29.6 1.0

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


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 Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:17.3 occ:1.00 O2B A:ATP401 2.0 20.0 1.0 O A:HOH564 2.1 17.8 1.0 O A:HOH565 2.1 17.3 1.0 O1G A:ATP401 2.1 22.6 1.0 OD2 A:ASP228 2.1 18.4 1.0 OD1 A:ASP228 2.1 16.2 1.0 CG A:ASP228 2.4 17.2 1.0 PG A:ATP401 3.2 25.2 1.0 PB A:ATP401 3.3 22.6 1.0 O3B A:ATP401 3.6 23.3 1.0 O3G A:ATP401 3.7 23.1 1.0 O A:HOH566 3.7 17.1 1.0 MG A:MG402 3.8 19.4 1.0 O A:ACY409 3.9 24.6 1.0 CB A:ASP228 3.9 15.7 1.0 OD2 A:ASP208 4.0 20.6 1.0 OD2 A:ASP230 4.1 20.2 1.0 O2A A:ATP401 4.2 18.9 1.0 O A:HOH568 4.2 19.7 1.0 O A:HOH634 4.2 31.7 1.0 O3A A:ATP401 4.3 20.6 1.0 CG1 A:ILE32 4.4 25.9 1.0 O1B A:ATP401 4.4 25.5 1.0 O A:HOH562 4.4 22.9 1.0 CB A:ILE32 4.4 25.2 1.0 O2G A:ATP401 4.6 26.0 1.0 PA A:ATP401 4.6 19.7 1.0 CA A:ASP228 4.8 17.2 1.0 CB A:ASP230 4.8 18.8 1.0 CG A:ASP230 4.8 17.9 1.0 C A:ACY409 4.9 31.7 1.0 ND2 A:ASN213 4.9 17.9 1.0 ND2 A:ASN33 5.0 23.8 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