Magnesium in PDB 6fz2: 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: 6fz2 was solved by F.C.Kersten, R.Brenk, E.Jaenicke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.80 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	92.530, 58.290, 153.900, 90.00, 92.52, 90.00
R / Rfree (%)	23.7 / 27.8

The binding sites of Magnesium atom in the Human N-Myristoyltransferase (NMT1) with Myristoyl-Coa and Inhibitor Bound (pdb code 6fz2). 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: 6fz2:
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:40.0 occ:1.00 O1A A:MYA1001 2.8 43.4 1.0 O5A A:MYA1001 2.8 37.1 1.0 O A:LEU254 2.8 35.2 1.0 N A:VAL259 3.1 36.0 1.0 N A:LYS257 3.3 41.4 1.0 CB A:VAL259 3.4 34.7 1.0 N A:ARG258 3.5 41.3 1.0 CG2 A:VAL259 3.5 36.0 1.0 N A:SER256 3.7 38.8 1.0 C A:LYS257 3.7 40.1 1.0 P1A A:MYA1001 3.7 41.4 1.0 CA A:VAL259 3.8 34.5 1.0 CA A:LYS257 3.8 40.9 1.0 CG1 A:VAL250 3.9 28.0 1.0 CB A:LYS257 3.9 41.1 1.0 C A:LEU254 4.0 36.0 1.0 P2A A:MYA1001 4.0 36.7 1.0 O2A A:MYA1001 4.0 42.1 1.0 C A:ARG258 4.1 37.9 1.0 N A:ALA260 4.1 30.1 1.0 C A:ARG255 4.1 38.4 1.0 CA A:ARG255 4.1 37.8 1.0 CA A:ARG258 4.2 41.5 1.0 O3A A:MYA1001 4.3 38.6 1.0 C A:SER256 4.3 40.3 1.0 O6A A:MYA1001 4.4 31.8 1.0 CA A:SER256 4.4 39.5 1.0 C A:VAL259 4.4 31.2 1.0 O A:LYS257 4.4 40.4 1.0 CG2 A:VAL250 4.5 26.0 1.0 N A:ARG255 4.5 36.7 1.0 CB A:VAL250 4.6 26.7 1.0 CG1 A:VAL259 4.8 34.2 1.0 CG A:LYS257 4.8 41.6 1.0 O A:ARG255 4.9 38.7 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:56.4 occ:1.00 O5A B:MYA1001 2.5 39.4 1.0 O B:LEU254 2.5 44.1 1.0 O1A B:MYA1001 2.9 38.3 1.0 N B:LYS257 3.3 45.8 1.0 N B:VAL259 3.4 38.9 1.0 N B:SER256 3.5 44.2 1.0 CB B:VAL259 3.5 37.0 1.0 CG1 B:VAL250 3.6 35.6 1.0 C B:LEU254 3.7 45.4 1.0 CG2 B:VAL259 3.7 38.2 1.0 CA B:ARG255 3.8 44.5 1.0 P1A B:MYA1001 3.8 40.1 1.0 P2A B:MYA1001 3.8 40.2 1.0 C B:ARG255 3.8 45.0 1.0 N B:ARG258 3.9 44.1 1.0 CA B:LYS257 4.0 46.5 1.0 CB B:LYS257 4.0 47.2 1.0 CA B:VAL259 4.0 36.5 1.0 C B:LYS257 4.0 45.2 1.0 O2A B:MYA1001 4.0 41.0 1.0 N B:ARG255 4.2 45.2 1.0 O6A B:MYA1001 4.3 35.2 1.0 N B:ALA260 4.3 33.1 1.0 O3A B:MYA1001 4.3 40.4 1.0 CA B:SER256 4.3 45.3 1.0 C B:SER256 4.3 46.5 1.0 CB B:VAL250 4.4 34.3 1.0 CG2 B:VAL250 4.4 33.3 1.0 C B:ARG258 4.5 40.8 1.0 CA B:ARG258 4.6 44.4 1.0 C B:VAL259 4.6 34.2 1.0 O B:ARG255 4.7 45.5 1.0 O B:LYS257 4.7 45.7 1.0 CG B:LYS257 4.8 48.8 1.0 CB B:LEU254 4.8 47.4 1.0 CG1 B:VAL259 4.8 36.1 1.0 CA B:LEU254 4.9 46.9 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