Magnesium in PDB 5gz9: Crystal Structure of Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide

The structure of Crystal Structure of Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide, PDB code: 5gz9 was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.19 / 2.40
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.320, 81.320, 146.838, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 26.8

The binding sites of Magnesium atom in the Crystal Structure of Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide (pdb code 5gz9). 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 Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide, PDB code: 5gz9:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide


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 Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:48.4 occ:1.00 OD2 A:ASP228 1.7 57.3 1.0 O2G A:ANP1001 2.2 41.3 1.0 OD1 A:ASP226 2.2 54.2 1.0 O1B A:ANP1001 2.4 53.2 1.0 OD2 A:ASP226 2.4 37.1 1.0 CG A:ASP226 2.6 36.9 1.0 CG A:ASP228 2.7 44.1 1.0 CB A:ASP228 3.2 34.8 1.0 PG A:ANP1001 3.5 42.3 1.0 PB A:ANP1001 3.7 47.5 1.0 O1G A:ANP1001 3.8 51.2 1.0 OD1 A:ASP228 3.8 33.0 1.0 CG2 A:VAL91 4.0 37.2 1.0 OD2 A:ASP203 4.1 58.0 1.0 N3B A:ANP1001 4.1 45.3 1.0 CB A:ASP226 4.1 33.3 1.0 NZ A:LYS92 4.2 31.2 1.0 MG A:MG1003 4.3 45.5 1.0 N A:ASP228 4.4 24.2 1.0 CA A:ASP228 4.4 26.0 1.0 OE1 A:GLN213 4.4 45.2 1.0 CE A:LYS92 4.4 38.6 1.0 O2B A:ANP1001 4.4 40.1 1.0 CB A:VAL91 4.5 45.5 1.0 O1A A:ANP1001 4.7 44.2 1.0 O3G A:ANP1001 4.7 49.2 1.0 O3A A:ANP1001 4.9 50.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide


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 Catalytic Domain of Protein O-Mannosyl Kinase in Complexes with Amp-Pnp, Magnesium Ions and Glycopeptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:45.5 occ:1.00 NE2 A:GLN213 1.9 69.5 1.0 O1G A:ANP1001 2.0 51.2 1.0 O1A A:ANP1001 2.1 44.2 1.0 CD A:GLN213 2.6 37.0 1.0 OE1 A:GLN213 2.6 45.2 1.0 N3B A:ANP1001 3.0 45.3 1.0 PG A:ANP1001 3.0 42.3 1.0 OD1 A:ASP226 3.0 54.2 1.0 OG A:SER212 3.2 49.9 1.0 PA A:ANP1001 3.5 44.7 1.0 CG A:ASP226 3.5 36.9 1.0 CB A:ASP226 3.6 33.3 1.0 O2G A:ANP1001 3.8 41.3 1.0 PB A:ANP1001 3.8 47.5 1.0 O1B A:ANP1001 3.8 53.2 1.0 O5' A:ANP1001 4.0 44.6 1.0 CG A:GLN213 4.1 35.0 1.0 O3A A:ANP1001 4.1 50.2 1.0 O A:HOH1129 4.1 38.3 1.0 O3G A:ANP1001 4.3 49.2 1.0 O A:SER212 4.3 29.1 1.0 MG A:MG1002 4.3 48.4 1.0 CA A:GLN213 4.5 31.1 1.0 C A:SER212 4.5 33.6 1.0 CE A:LYS209 4.5 40.1 1.0 OD2 A:ASP226 4.6 37.1 1.0 CB A:SER212 4.6 27.7 1.0 O2A A:ANP1001 4.7 38.6 1.0 CB A:GLN213 4.7 27.7 1.0 N A:GLN213 4.7 33.5 1.0 OD2 A:ASP203 4.8 58.0 1.0

M.Nagae, S.K.Mishra, M.Neyazaki, R.Oi, A.Ikeda, N.Matsugaki, S.Akashi, H.Manya, M.Mizuno, H.Yagi, K.Kato, T.Senda, T.Endo, T.Nogi, Y.Yamaguchi. 3D Structural Analysis of Protein O-Mannosyl Kinase, Pomk, A Causative Gene Product of Dystroglycanopathy. Genes Cells V. 22 348 2017.
ISSN: ESSN 1365-2443
PubMed: 28251761
DOI: 10.1111/GTC.12480