Magnesium in PDB 7xzr: Crystal Structure of Tnik-Amppnp-Thiopeptide TP15 Complex

All present enzymatic activity of Crystal Structure of Tnik-Amppnp-Thiopeptide TP15 Complex:
2.7.11.1;

The structure of Crystal Structure of Tnik-Amppnp-Thiopeptide TP15 Complex, PDB code: 7xzr was solved by K.Hamada, A.A.Vinogradov, Y.Zhang, J.S.Chang, H.Nishimura, Y.Goto, H.Onaka, H.Suga, K.Ogata, T.Sengoku, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.34 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.11, 167.65, 53.71, 90, 108.5, 90
R / Rfree (%)	18.2 / 22.6

The binding sites of Magnesium atom in the Crystal Structure of Tnik-Amppnp-Thiopeptide TP15 Complex (pdb code 7xzr). 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 Tnik-Amppnp-Thiopeptide TP15 Complex, PDB code: 7xzr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Tnik-Amppnp-Thiopeptide TP15 Complex


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 Tnik-Amppnp-Thiopeptide TP15 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1402 b:41.0 occ:1.00 O1B A:ANP1401 2.0 46.1 1.0 O A:HOH1561 2.1 42.5 1.0 OD2 A:ASP171 2.2 41.6 1.0 O A:HOH1560 2.2 35.3 1.0 OD1 A:ASN158 2.3 37.5 1.0 O2A A:ANP1401 2.3 36.9 1.0 CG A:ASP171 3.2 44.8 1.0 PB A:ANP1401 3.3 40.0 1.0 CG A:ASN158 3.3 39.7 1.0 PA A:ANP1401 3.4 37.4 1.0 ND2 A:ASN158 3.7 37.9 1.0 O A:HOH1502 3.7 48.4 1.0 O3A A:ANP1401 3.7 43.1 1.0 CB A:ASP171 3.9 43.4 1.0 N3B A:ANP1401 3.9 49.8 1.0 C5' A:ANP1401 4.2 42.9 1.0 OD1 A:ASP171 4.2 43.5 1.0 O5' A:ANP1401 4.3 37.8 1.0 O A:HOH1538 4.4 42.8 1.0 OG1 A:THR35 4.4 56.4 1.0 O2B A:ANP1401 4.6 52.9 1.0 O3' A:ANP1401 4.6 42.2 1.0 CA A:GLY34 4.6 61.8 1.0 O1A A:ANP1401 4.7 44.7 1.0 CB A:ASN158 4.7 40.0 1.0 N A:THR35 4.7 59.5 1.0 OD2 A:ASP153 4.8 45.9 1.0 CE A:LYS155 4.8 43.1 1.0 O3G A:ANP1401 4.8 56.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Tnik-Amppnp-Thiopeptide TP15 Complex


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 Tnik-Amppnp-Thiopeptide TP15 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1402 b:63.8 occ:1.00 O1G B:ANP1401 2.3 68.5 0.7 OD1 B:ASN158 2.6 40.3 1.0 O1B B:ANP1401 2.8 60.5 0.7 OD2 B:ASP171 2.9 58.9 1.0 CG B:ASN158 3.6 41.7 1.0 OE1 B:GLN157 3.7 61.3 1.0 PG B:ANP1401 3.8 73.3 0.7 O5' B:ANP1401 3.8 68.8 0.7 PB B:ANP1401 3.8 68.6 0.7 O3A B:ANP1401 3.9 71.6 0.7 CG B:ASP171 3.9 60.1 1.0 ND2 B:ASN158 3.9 36.6 1.0 N3B B:ANP1401 4.1 70.9 0.7 CB B:ASP171 4.4 46.4 1.0 O3G B:ANP1401 4.4 68.8 0.7 OG1 B:THR35 4.5 72.5 1.0 PA B:ANP1401 4.6 76.9 0.7 CB B:GLN157 4.7 44.2 1.0 CD B:GLN157 4.8 66.3 1.0 NZ B:LYS155 4.8 45.5 1.0 O B:GLN157 4.8 41.8 1.0 C5' B:ANP1401 4.8 64.1 0.7 CE B:LYS155 4.8 40.4 1.0 OD2 B:ASP153 4.9 51.2 1.0 OD1 B:ASP171 4.9 58.9 1.0 O2G B:ANP1401 4.9 79.2 0.7 CB B:ASN158 5.0 36.8 1.0

A.A.Vinogradov, Y.Zhang, K.Hamada, J.S.Chang, C.Okada, H.Nishimura, N.Terasaka, Y.Goto, K.Ogata, T.Sengoku, H.Onaka, H.Suga. De Novo Discovery of Thiopeptide Pseudo-Natural Products Acting As Potent and Selective Tnik Kinase Inhibitors. J.Am.Chem.Soc. V. 144 20332 2022.
ISSN: ESSN 1520-5126
PubMed: 36282922
DOI: 10.1021/JACS.2C07937