Magnesium in PDB 6fz5: Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound

All present enzymatic activity of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound:
2.3.1.97;

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 6fz5 was solved by F.C.Kersten, R.Brenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.94 / 1.89
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.390, 58.160, 154.001, 90.00, 92.36, 90.00
R / Rfree (%)	18.9 / 22.3

The structure of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium atom in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound (pdb code 6fz5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound, PDB code: 6fz5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:44.4 occ:1.00 O A:LEU254 2.4 39.2 1.0 O5A A:MYA1001 2.7 35.0 1.0 O1A A:MYA1001 3.1 35.9 1.0 N A:LYS257 3.2 43.7 1.0 N A:VAL259 3.4 33.9 1.0 CB A:VAL259 3.5 33.7 1.0 N A:SER256 3.5 43.1 1.0 C A:LEU254 3.5 41.5 1.0 C A:ARG255 3.6 44.2 1.0 CA A:ARG255 3.6 43.4 1.0 CG2 A:VAL259 3.7 35.5 1.0 N A:ARG258 3.8 41.4 1.0 CG1 A:VAL250 3.8 31.9 1.0 CA A:LYS257 3.9 44.8 1.0 C A:LYS257 3.9 42.2 1.0 CA A:VAL259 4.0 32.5 1.0 CB A:LYS257 4.0 46.2 1.0 P1A A:MYA1001 4.0 36.9 1.0 P2A A:MYA1001 4.0 36.0 1.0 N A:ARG255 4.0 43.0 1.0 C A:SER256 4.2 45.6 1.0 CA A:SER256 4.2 44.9 1.0 O2A A:MYA1001 4.4 36.9 1.0 O A:ARG255 4.4 45.5 1.0 N A:ALA260 4.4 28.8 1.0 C A:ARG258 4.4 35.1 1.0 O3A A:MYA1001 4.5 37.1 1.0 CA A:ARG258 4.6 38.8 1.0 CG A:LYS257 4.6 47.1 1.0 CB A:VAL250 4.6 30.3 1.0 O6A A:MYA1001 4.6 32.4 1.0 O A:LYS257 4.6 41.5 1.0 CG2 A:VAL250 4.6 30.0 1.0 CG1 A:VAL259 4.7 32.7 1.0 C A:VAL259 4.7 29.6 1.0 CA A:LEU254 4.8 42.6 1.0 CB A:LEU254 4.8 44.1 1.0 CB A:ARG255 5.0 43.2 1.0

Magnesium binding site 2 out of 2 in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:50.5 occ:1.00 O B:LEU254 2.5 42.8 1.0 O5A B:MYA1001 2.7 36.3 1.0 O1A B:MYA1001 3.0 36.5 1.0 N B:LYS257 3.1 45.2 1.0 N B:SER256 3.3 43.9 1.0 N B:VAL259 3.4 36.8 1.0 CB B:VAL259 3.5 36.0 1.0 C B:ARG255 3.6 44.6 1.0 C B:LEU254 3.6 43.2 1.0 CA B:ARG255 3.6 42.9 1.0 N B:ARG258 3.7 42.5 1.0 CG2 B:VAL259 3.8 38.2 1.0 CA B:LYS257 3.8 47.7 1.0 C B:LYS257 3.8 46.0 1.0 CG1 B:VAL250 3.9 33.8 1.0 P1A B:MYA1001 4.0 38.0 1.0 CA B:VAL259 4.0 35.6 1.0 CB B:LYS257 4.0 49.2 1.0 P2A B:MYA1001 4.0 38.5 1.0 C B:SER256 4.1 45.8 1.0 CA B:SER256 4.1 44.7 1.0 N B:ARG255 4.1 43.7 1.0 O2A B:MYA1001 4.1 39.8 1.0 O B:ARG255 4.3 47.0 1.0 C B:ARG258 4.4 38.4 1.0 N B:ALA260 4.4 32.4 1.0 CA B:ARG258 4.5 41.2 1.0 O3A B:MYA1001 4.5 38.5 1.0 O6A B:MYA1001 4.6 33.5 1.0 CG B:LYS257 4.6 50.5 1.0 O B:LYS257 4.6 47.8 1.0 CB B:VAL250 4.7 32.0 1.0 C B:VAL259 4.7 33.6 1.0 CG2 B:VAL250 4.8 31.1 1.0 CG1 B:VAL259 4.8 35.5 1.0 CA B:LEU254 4.9 43.7 1.0 CB B:LEU254 4.9 43.3 1.0 CB B:ARG255 5.0 42.0 1.0

C.Kersten, E.Fleischer, J.Kehrein, C.Borek, E.Jaenicke, C.Sotriffer, R.Brenk. How to Design Selective Ligands For Highly Conserved Binding Sites: A Case Study Usingn-Myristoyltransferases As A Model System. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31423787
DOI: 10.1021/ACS.JMEDCHEM.9B00586