Magnesium in PDB 8e1h: ASP1 Kinase in Complex with Adp Mg 5-IP7

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

The structure of ASP1 Kinase in Complex with Adp Mg 5-IP7, PDB code: 8e1h 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)	47.44 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.6, 87.123, 86.025, 90, 94.73, 90
R / Rfree (%)	19.7 / 23.4

The binding sites of Magnesium atom in the ASP1 Kinase in Complex with Adp Mg 5-IP7 (pdb code 8e1h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the ASP1 Kinase in Complex with Adp Mg 5-IP7, PDB code: 8e1h:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the ASP1 Kinase in Complex with Adp 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 Adp Mg 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:35.9 occ:1.00 O A:HOH546 1.9 36.7 1.0 O3B A:ADP401 2.0 35.6 1.0 O2A A:ADP401 2.0 32.9 1.0 OD2 A:ASP321 2.0 36.8 1.0 O A:HOH610 2.2 32.2 1.0 OD2 A:ASP333 2.3 32.2 1.0 PB A:ADP401 3.2 38.2 1.0 PA A:ADP401 3.3 30.0 1.0 CG A:ASP333 3.3 34.8 1.0 CG A:ASP321 3.3 33.9 1.0 O3A A:ADP401 3.5 31.6 1.0 CB A:ASP333 3.6 27.8 1.0 MG A:MG404 3.6 39.1 1.0 O1B A:ADP401 3.8 45.3 1.0 ND2 A:ASN335 4.1 35.6 1.0 OD1 A:ASP321 4.1 35.9 1.0 CB A:ASP321 4.2 27.7 1.0 C5' A:ADP401 4.3 33.4 1.0 NZ A:LYS260 4.3 35.4 1.0 O5' A:ADP401 4.3 32.7 1.0 OD1 A:ASP333 4.4 30.4 1.0 O1A A:ADP401 4.4 28.4 1.0 O2B A:ADP401 4.5 39.0 1.0 O3' A:ADP401 4.5 32.9 1.0 O A:HOH665 4.5 42.2 1.0 CE A:LYS260 4.7 45.4 1.0 O A:HOH636 4.8 39.0 1.0 OD1 A:ASN335 4.8 35.4 1.0 CG A:ASN335 4.9 33.4 1.0 C3' A:ADP401 4.9 31.6 1.0

Magnesium binding site 2 out of 3 in the ASP1 Kinase in Complex with Adp 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 Adp Mg 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:39.1 occ:1.00 O A:HOH530 2.1 47.5 1.0 OD2 A:ASP333 2.3 32.2 1.0 O1B A:ADP401 2.4 45.3 1.0 OD1 A:ASN335 2.5 35.4 1.0 O A:HOH665 2.6 42.2 1.0 CG A:ASP333 3.0 34.8 1.0 OD1 A:ASP333 3.0 30.4 1.0 O3B A:ADP401 3.3 35.6 1.0 PB A:ADP401 3.4 38.2 1.0 CG A:ASN335 3.4 33.4 1.0 O A:HOH546 3.5 36.7 1.0 MG A:MG403 3.6 35.9 1.0 ND2 A:ASN335 3.8 35.6 1.0 CE1 A:HIS204 4.1 42.8 1.0 O A:GLY201 4.3 37.3 1.0 O3A A:ADP401 4.4 31.6 1.0 NH1 A:ARG123 4.4 38.1 1.0 CB A:ASP333 4.5 27.8 1.0 O2B A:ADP401 4.5 39.0 1.0 ND1 A:HIS204 4.6 39.0 1.0 CB A:ASN335 4.8 32.3 1.0 O A:HOH663 4.8 35.3 1.0 O2A A:ADP401 4.8 32.9 1.0 NH2 A:ARG123 5.0 35.5 1.0

Magnesium binding site 3 out of 3 in the ASP1 Kinase in Complex with Adp Mg 5-IP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of ASP1 Kinase in Complex with Adp Mg 5-IP7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:80.1 occ:1.00 O75 A:I7P402 2.2 76.9 1.0 O36 A:I7P402 2.8 81.4 1.0 C6 A:I7P402 3.1 74.9 1.0 O12 A:I7P402 3.2 73.3 1.0 PA6 A:I7P402 3.4 85.7 1.0 O15 A:I7P402 3.4 75.3 1.0 O46 A:I7P402 3.6 74.7 1.0 O16 A:I7P402 3.6 78.1 1.0 PB5 A:I7P402 3.7 77.5 1.0 C5 A:I7P402 3.8 76.0 1.0 O42 A:I7P402 3.9 56.9 1.0 C1 A:I7P402 4.1 71.5 1.0 PA2 A:I7P402 4.2 69.4 1.0 C2 A:I7P402 4.2 72.5 1.0 C4 A:I7P402 4.2 73.2 1.0 O55 A:I7P402 4.4 77.2 1.0 O11 A:I7P402 4.4 71.1 1.0 O65 A:I7P402 4.5 77.3 1.0 O45 A:I7P402 4.6 77.4 1.0 PA5 A:I7P402 4.7 80.9 1.0 C3 A:I7P402 4.8 71.8 1.0 O26 A:I7P402 4.9 73.7 1.0 NZ A:LYS341 4.9 63.8 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