Magnesium in PDB 7agh: Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg

All present enzymatic activity of Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg:
2.7.1.184;

The structure of Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg, PDB code: 7agh was solved by M.Sharma, G.J.Davies, Y.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.01 / 2.93
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	82.085, 82.224, 170.97, 90, 90, 90
R / Rfree (%)	21.4 / 25.6

The binding sites of Magnesium atom in the Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg (pdb code 7agh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg, PDB code: 7agh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg


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 Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:32.3 occ:1.00 O1G C:ANP401 2.0 51.9 1.0 OD2 C:ASP162 2.4 53.6 1.0 O2B C:ANP401 2.5 50.9 1.0 PG C:ANP401 3.3 50.8 1.0 CG C:ASP162 3.5 45.3 1.0 PB C:ANP401 3.6 41.9 1.0 O2G C:ANP401 3.7 49.0 1.0 N3B C:ANP401 3.9 45.6 1.0 O C:HOH507 4.0 44.3 1.0 OD1 C:ASP162 4.1 45.3 1.0 OD1 C:ASP244 4.2 31.4 1.0 CA C:GLY243 4.4 31.3 1.0 OD1 C:ASP160 4.5 45.9 1.0 O1B C:ANP401 4.5 42.9 1.0 CB C:ASP162 4.5 41.5 1.0 O3G C:ANP401 4.5 48.3 1.0 O3A C:ANP401 4.7 38.1 1.0 OD2 C:ASP160 4.8 47.3 1.0 C C:GLY243 4.8 30.0 1.0 N C:ASP244 4.9 28.9 1.0 CB C:SER181 4.9 31.7 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg


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 Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:27.8 occ:1.00 O2G D:ANP401 2.4 47.2 1.0 O2B D:ANP401 2.4 33.5 1.0 OD2 D:ASP162 2.5 62.6 1.0 PG D:ANP401 3.3 45.6 1.0 CG D:ASP162 3.5 44.8 1.0 O1G D:ANP401 3.6 50.9 1.0 PB D:ANP401 3.7 28.3 1.0 N3B D:ANP401 3.8 36.5 1.0 OD1 D:ASP244 4.1 32.3 1.0 OD1 D:ASP162 4.1 40.3 1.0 OD1 D:ASP160 4.3 47.5 1.0 CB D:ASP162 4.5 38.5 1.0 CA D:GLY243 4.5 35.3 1.0 O D:HOH503 4.5 18.2 1.0 OD2 D:ASP160 4.6 45.3 1.0 O1B D:ANP401 4.7 27.2 1.0 O3G D:ANP401 4.7 54.9 1.0 O3A D:ANP401 4.8 25.7 1.0 C D:GLY243 4.9 34.9 1.0 CG D:ASP160 4.9 37.5 1.0 N D:ASP244 4.9 32.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Sf Kinase Yihv From E. Coli in Complex with Amppnp-Mg within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:32.4 occ:1.00 O1A A:ANP401 2.2 43.2 1.0 O1B A:ANP401 3.0 38.0 1.0 N3B A:ANP401 3.2 54.7 1.0 NH2 A:ARG105 3.2 89.0 1.0 NH1 A:ARG105 3.4 86.2 1.0 PB A:ANP401 3.6 44.4 1.0 PA A:ANP401 3.6 38.4 1.0 CZ A:ARG105 3.8 78.0 1.0 O3A A:ANP401 4.0 38.3 1.0 OG1 A:THR239 4.2 41.8 1.0 CB A:THR239 4.3 38.8 1.0 N7 A:ANP401 4.5 39.5 1.0 PG A:ANP401 4.5 59.8 1.0 O5' A:ANP401 4.5 34.8 1.0 O A:THR239 4.5 47.0 1.0 CA A:GLY214 4.6 40.6 1.0 O2G A:ANP401 4.7 64.0 1.0 C8 A:ANP401 4.7 38.0 1.0 O2A A:ANP401 4.7 35.3 1.0

M.Sharma, P.Abayakoon, R.Epa, Y.Jin, J.P.Lingford, T.Shimada, M.Nakano, J.W.Mui, A.Ishihama, E.D.Goddard-Borger, G.J.Davies, S.J.Williams. Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis. Acs Cent.Sci. V. 7 476 2021.
ISSN: ESSN 2374-7951
PubMed: 33791429
DOI: 10.1021/ACSCENTSCI.0C01285