Manganese in PDB 8e1s: ASP1 Kinase in Complex with Adpnp Mn IP6

All present enzymatic activity of ASP1 Kinase in Complex with Adpnp Mn IP6:
2.7.4.24;

The structure of ASP1 Kinase in Complex with Adpnp Mn IP6, PDB code: 8e1s 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)	47.90 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.076, 87.775, 86.048, 90, 94.85, 90
R / Rfree (%)	17.6 / 20.5

The binding sites of Manganese atom in the ASP1 Kinase in Complex with Adpnp Mn IP6 (pdb code 8e1s). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the ASP1 Kinase in Complex with Adpnp Mn IP6, PDB code: 8e1s:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the ASP1 Kinase in Complex with Adpnp Mn IP6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of ASP1 Kinase in Complex with Adpnp Mn IP6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:33.2 occ:1.00 N3B A:ANP401 1.9 19.7 1.0 O2A A:ANP401 1.9 16.1 1.0 OD2 A:ASP321 2.0 24.7 1.0 O1G A:ANP401 2.2 22.1 1.0 O A:HOH612 2.2 20.7 1.0 OD2 A:ASP333 2.2 20.0 1.0 PG A:ANP401 2.5 53.7 1.0 PA A:ANP401 3.2 19.5 1.0 CG A:ASP333 3.2 22.9 1.0 PB A:ANP401 3.2 20.3 1.0 CG A:ASP321 3.2 24.5 1.0 O3A A:ANP401 3.5 19.4 1.0 CB A:ASP333 3.6 17.7 1.0 O2G A:ANP401 3.6 39.6 1.0 MN A:MN404 3.7 40.9 1.0 O3G A:ANP401 3.7 40.1 1.0 O2B A:ANP401 3.9 23.0 1.0 OD1 A:ASP321 4.1 23.9 1.0 CB A:ASP321 4.1 16.9 1.0 ND2 A:ASN335 4.2 24.3 1.0 O5' A:ANP401 4.2 18.9 1.0 NZ A:LYS260 4.3 26.9 1.0 O1A A:ANP401 4.3 19.3 1.0 O3' A:ANP401 4.3 21.4 1.0 OD1 A:ASP333 4.3 21.7 1.0 C5' A:ANP401 4.3 18.8 1.0 O1B A:ANP401 4.4 22.3 1.0 C3' A:ANP401 4.8 19.5 1.0 CE A:LYS260 4.8 39.5 1.0 O A:HOH789 4.8 31.7 1.0 OD1 A:ASN335 4.9 19.8 1.0

Manganese binding site 2 out of 2 in the ASP1 Kinase in Complex with Adpnp Mn IP6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of ASP1 Kinase in Complex with Adpnp Mn IP6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:40.9 occ:1.00 O A:HOH523 2.2 29.8 1.0 OD2 A:ASP333 2.2 20.0 1.0 O3G A:ANP401 2.3 40.1 1.0 O2B A:ANP401 2.4 23.0 1.0 OD1 A:ASN335 2.4 19.8 1.0 OD1 A:ASP333 2.8 21.7 1.0 CG A:ASP333 2.8 22.9 1.0 O A:HOH511 3.0 22.9 1.0 PG A:ANP401 3.1 53.7 1.0 N3B A:ANP401 3.3 19.7 1.0 PB A:ANP401 3.3 20.3 1.0 CG A:ASN335 3.4 25.0 1.0 O1G A:ANP401 3.4 22.1 1.0 ND2 A:ASN335 3.7 24.3 1.0 MN A:MN403 3.7 33.2 1.0 NH1 A:ARG123 4.2 25.8 1.0 CE1 A:HIS204 4.3 24.7 1.0 O3A A:ANP401 4.3 19.4 1.0 CB A:ASP333 4.3 17.7 1.0 O A:GLY201 4.4 22.8 1.0 O1B A:ANP401 4.5 22.3 1.0 O2G A:ANP401 4.6 39.6 1.0 O A:HOH716 4.7 39.0 1.0 ND1 A:HIS204 4.7 20.0 1.0 O2A A:ANP401 4.7 16.1 1.0 CB A:ASN335 4.7 21.3 1.0 O A:HOH671 4.8 25.5 1.0 NH2 A:ARG123 4.9 20.7 1.0 OD2 A:ASP321 4.9 24.7 1.0 CZ A:ARG123 5.0 21.9 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