Magnesium in PDB 8e1i: ASP1 Kinase in Complex with Atp Mg 5-IP7

All present enzymatic activity of ASP1 Kinase in Complex with Atp Mg 5-IP7:
2.7.4.24;

The structure of ASP1 Kinase in Complex with Atp Mg 5-IP7, PDB code: 8e1i was solved by Y.Goldgur, S.Shuman, B.Benjamin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.67 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.777, 88.495, 86.569, 90, 94.78, 90
R / Rfree (%)	19.5 / 23.5

The binding sites of Magnesium atom in the ASP1 Kinase in Complex with Atp Mg 5-IP7 (pdb code 8e1i). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the ASP1 Kinase in Complex with Atp Mg 5-IP7, PDB code: 8e1i:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the ASP1 Kinase in Complex with Atp Mg 5-IP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of ASP1 Kinase in Complex with Atp Mg 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:42.5 occ:1.00 O1A A:ATP502 1.9 36.3 1.0 OD2 A:ASP321 2.1 32.8 1.0 O3G A:ATP502 2.2 40.4 1.0 O3B A:ATP502 2.2 44.7 1.0 OD2 A:ASP333 2.3 44.9 1.0 O A:HOH693 2.4 42.7 1.0 PG A:ATP502 2.7 62.2 1.0 PA A:ATP502 3.1 34.3 1.0 CG A:ASP333 3.2 40.8 1.0 CG A:ASP321 3.3 35.9 1.0 CB A:ASP333 3.4 30.9 1.0 PB A:ATP502 3.4 47.5 1.0 O3A A:ATP502 3.4 32.9 1.0 O2G A:ATP502 3.6 52.0 1.0 MG A:MG504 3.6 45.2 1.0 O1B A:ATP502 3.9 42.9 1.0 O1G A:ATP502 3.9 52.0 1.0 CB A:ASP321 4.1 26.5 1.0 O2A A:ATP502 4.1 34.6 1.0 O5' A:ATP502 4.2 35.6 1.0 NZ A:LYS260 4.2 46.4 1.0 OD1 A:ASP321 4.2 34.3 1.0 OD1 A:ASP333 4.3 40.0 1.0 ND2 A:ASN335 4.3 39.5 1.0 C5' A:ATP502 4.4 33.5 1.0 O3' A:ATP502 4.4 32.5 1.0 O2B A:ATP502 4.6 35.2 1.0 CE A:LYS260 4.8 45.3 1.0 C3' A:ATP502 4.8 34.8 1.0 OD1 A:ASN335 4.9 40.4 1.0 CA A:ASP333 4.9 27.3 1.0

Magnesium binding site 2 out of 2 in the ASP1 Kinase in Complex with Atp Mg 5-IP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of ASP1 Kinase in Complex with Atp Mg 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:45.2 occ:1.00 OD2 A:ASP333 1.9 44.9 1.0 O A:HOH708 2.0 43.1 1.0 O1B A:ATP502 2.2 42.9 1.0 OD1 A:ASN335 2.4 40.4 1.0 CG A:ASP333 2.6 40.8 1.0 OD1 A:ASP333 2.7 40.0 1.0 O1G A:ATP502 2.7 52.0 1.0 O3B A:ATP502 3.1 44.7 1.0 PG A:ATP502 3.2 62.2 1.0 PB A:ATP502 3.2 47.5 1.0 O3G A:ATP502 3.3 40.4 1.0 CG A:ASN335 3.4 39.9 1.0 MG A:MG503 3.6 42.5 1.0 ND2 A:ASN335 3.8 39.5 1.0 CB A:ASP333 4.1 30.9 1.0 NH2 A:ARG123 4.1 44.6 1.0 O3A A:ATP502 4.2 32.9 1.0 O A:GLY201 4.4 37.3 1.0 O2B A:ATP502 4.4 35.2 1.0 NH1 A:ARG123 4.6 35.7 1.0 O1A A:ATP502 4.7 36.3 1.0 O2G A:ATP502 4.7 52.0 1.0 CE1 A:HIS204 4.8 40.7 1.0 CZ A:ARG123 4.8 41.3 1.0 CB A:ASN335 4.8 31.6 1.0 PA A:ATP502 5.0 34.3 1.0 O A:HOH633 5.0 26.8 1.0 OD2 A:ASP321 5.0 32.8 1.0

B.Benjamin, Y.Goldgur, N.Jork, H.J.Jessen, B.Schwer, S.Shuman. Structures of Fission Yeast Inositol Pyrophosphate Kinase ASP1 in Ligand-Free, Substrate-Bound, and Product-Bound States. Mbio V. 13 08722 2022.
ISSN: ESSN 2150-7511
PubMed: 36468882
DOI: 10.1128/MBIO.03087-22