Magnesium in PDB 6fz3: 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: 6fz3 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)	50.87 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.278, 58.000, 153.309, 90.00, 92.18, 90.00
R / Rfree (%)	19.9 / 23.5

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 6fz3). 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: 6fz3:
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:39.1 occ:1.00 O A:LEU254 2.7 31.8 1.0 O1A A:MYA1001 2.8 23.5 1.0 O5A A:MYA1001 2.9 26.2 1.0 N A:LYS257 3.2 30.1 1.0 N A:VAL259 3.3 23.8 1.0 CB A:VAL259 3.5 25.1 1.0 N A:SER256 3.5 32.9 1.0 CG2 A:VAL259 3.6 26.7 1.0 N A:ARG258 3.6 26.2 1.0 C A:LYS257 3.8 26.6 1.0 CA A:LYS257 3.8 28.4 1.0 P1A A:MYA1001 3.8 23.7 1.0 C A:LEU254 3.8 32.6 1.0 C A:ARG255 3.9 33.9 1.0 CG1 A:VAL250 3.9 23.8 1.0 CA A:VAL259 3.9 24.1 1.0 CA A:ARG255 3.9 31.8 1.0 CB A:LYS257 3.9 28.7 1.0 O2A A:MYA1001 4.0 23.1 1.0 P2A A:MYA1001 4.1 24.9 1.0 C A:SER256 4.2 31.5 1.0 CA A:SER256 4.2 32.5 1.0 N A:ALA260 4.3 22.4 1.0 C A:ARG258 4.3 24.3 1.0 N A:ARG255 4.3 32.0 1.0 O3A A:MYA1001 4.3 23.1 1.0 CA A:ARG258 4.4 25.4 1.0 O A:LYS257 4.5 26.3 1.0 O6A A:MYA1001 4.5 22.1 1.0 CG2 A:VAL250 4.6 22.7 1.0 CB A:VAL250 4.6 23.1 1.0 C A:VAL259 4.6 23.1 1.0 CG A:LYS257 4.6 29.7 1.0 O A:ARG255 4.7 35.6 1.0 CG1 A:VAL259 4.8 25.7 1.0 CB A:LEU254 5.0 34.5 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:34.5 occ:1.00 O B:LEU254 2.6 34.0 1.0 O1A B:MYA1001 3.0 30.3 1.0 O5A B:MYA1001 3.0 30.5 1.0 N B:LYS257 3.2 33.9 1.0 N B:VAL259 3.2 30.5 1.0 CB B:VAL259 3.3 30.6 1.0 CG2 B:VAL259 3.5 31.4 1.0 N B:SER256 3.6 36.6 1.0 N B:ARG258 3.6 33.1 1.0 C B:LEU254 3.7 35.3 1.0 CA B:LYS257 3.7 35.0 1.0 C B:LYS257 3.7 34.6 1.0 CA B:VAL259 3.8 29.6 1.0 CB B:LYS257 3.9 35.1 1.0 C B:ARG255 3.9 36.9 1.0 CG1 B:VAL250 3.9 25.2 1.0 CA B:ARG255 3.9 36.5 1.0 P1A B:MYA1001 4.0 33.1 1.0 C B:SER256 4.2 35.4 1.0 C B:ARG258 4.2 31.6 1.0 P2A B:MYA1001 4.3 32.9 1.0 N B:ALA260 4.3 25.9 1.0 N B:ARG255 4.3 38.1 1.0 CA B:SER256 4.3 36.9 1.0 O2A B:MYA1001 4.3 37.3 1.0 CA B:ARG258 4.4 33.4 1.0 O B:LYS257 4.5 36.3 1.0 C B:VAL259 4.5 27.4 1.0 CG B:LYS257 4.6 34.9 1.0 O3A B:MYA1001 4.6 32.3 1.0 O6A B:MYA1001 4.6 29.7 1.0 O B:ARG255 4.6 35.7 1.0 CG2 B:VAL250 4.6 24.3 1.0 CB B:VAL250 4.6 24.4 1.0 CG1 B:VAL259 4.7 30.7 1.0 CB B:LEU254 4.9 37.2 1.0 CA B:LEU254 4.9 36.0 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